Author: "Yann Guiguen" - Searchworks@Jio Institute Digital Library Search Results

Your search keyword '"Yann Guiguen"' showing total 176 results

Start Over Author "Yann Guiguen"

176 results on '"Yann Guiguen"'

1. Multi-genome comparisons reveal gain-and-loss evolution of anti-Mullerian hormone receptor type 2 as a candidate master sex-determining gene in Percidae

Author: Heiner Kuhl, Peter T. Euclide, Christophe Klopp, Cédric Cabau, Margot Zahm, Céline Lopez-Roques, Carole Iampietro, Claire Kuchly, Cécile Donnadieu, Romain Feron, Hugues Parrinello, Charles Poncet, Lydia Jaffrelo, Carole Confolent, Ming Wen, Amaury Herpin, Elodie Jouanno, Anastasia Bestin, Pierrick Haffray, Romain Morvezen, Taina Rocha de Almeida, Thomas Lecocq, Bérénice Schaerlinger, Dominique Chardard, Daniel Żarski, Wesley A. Larson, John H. Postlethwait, Serik Timirkhanov, Werner Kloas, Sven Wuertz, Matthias Stöck, and Yann Guiguen
Subjects: Sex-determination, Genome, Perches, Pikeperches, Sex chromosomes, Biology (General), QH301-705.5
Abstract: Abstract Background The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, Perca schrenkii, and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems. Results We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene (amhr2bY), previously suggested to be the master sex-determining (MSD) gene in P. flavescens. Phylogenetically related and structurally similar amhr2 duplicates (amhr2b) were found in P. schrenkii and Sander lucioperca, potentially dating this duplication event to their last common ancestor around 19–27 Mya. In P. fluviatilis and S. vitreus, this amhr2b duplicate has been likely lost while it was subject to amplification in S. lucioperca. Analyses of the amhr2b locus in P. schrenkii suggest that this duplication could be also male-specific as it is in P. flavescens. In P. fluviatilis, a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome 18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variations (SNVs) and no large duplication/insertion event, suggesting that P. fluviatilis has a male heterogametic sex-determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three (c18h1orf198, hsdl1, tbc1d32) with higher expression in the testis than in the ovary. Conclusions Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three known Perca species.
Published: 2024
Full Text: View/download PDF

2. Expression pattern of the fused in sarcoma gene and its contextual influence on the density-specific response of the growth hormone/insulin-like growth factor 1 axis in zig-zag eels (Mastacembelus armatus)

Author: Lingzhan Xue, Yu Gao, Songpei Zhang, Manxin Weng, Gaoxiong Zeng, Jiajia Chen, Mengxiang Liao, Sayyed Mohammad Hadi Alavi, and Yann Guiguen
Subjects: culture density, GH/IGF-1 axis, FUS, miRNA, growth, Science, General. Including nature conservation, geographical distribution, QH1-199.5
Abstract: The fused in sarcoma (FUS) protein is a DNA/RNA binding protein from the ten-eleven translocation protein family that is associated with neurodegeneration, and it has been shown to promote cell proliferation through the growth hormone/insulin-like growth factor 1 (Gh/Igf-1) signaling pathway. The zig-zag eel (Mastacembelus armatus) is a newly discovered species exhibiting sexual dimorphism in growth, and the potential role of fus in the growth and development of this species remains largely unknown. Herein, we analyzed the homology, conserved domains, evolutionary characteristics, and conserved syntenies of fus in several teleost species. The expression of fus was predominant in the brain and exhibited sexual dimorphism in the brain, muscle, and liver of zig-zag eels. We found that microRNA (miR)-146-5p, miR-489-3p, and 24 other miRNAs were targeted to the fus 3′ untranslated region, which might affect muscle and bone development in adults. The igf1, insulin-like growth factor 1 receptor a (igf1ra), insulin-like growth factor 2 receptor (igf2r), growth hormone-releasing hormone-like receptor (ghrhrl), growth hormone secretagogue receptor type 1 (ghsr), and glucocorticoid receptor (gr) genes contained a higher abundance of GU-rich fus motifs compared to the other four genes analyzed in zig-zag eels. We also measured the expression of fus mRNA during fish culture at various stocking densities to further elucidate the relationship between fus expression and the Gh/Igf-1 axis. After 100 days of fish cultivation, the expression of fus and ghrhrl decreased and the expression of ghrh and gr increased as the culture density increased (p < 0.05). The expression of fus exhibited a remarkable positive correlation with a specific growth rate. These results indicate that fus mediates growth differences by regulating the expression of several growth-related genes including Gh/Igf-1 axis genes in zig-zag eels.
Published: 2024
Full Text: View/download PDF

3. Massive expansion of sex-specific SNPs, transposon-related elements, and neocentromere formation shape the young W-chromosome from the mosquitofish Gambusia affinis

Author: Stefan Müller, Kang Du, Yann Guiguen, Maria Pichler, Shinichi Nakagawa, Matthias Stöck, Manfred Schartl, and Dunja K. Lamatsch
Subjects: Sex chromosome evolution, ZZ/ZW sex chromosomes, Transposable element, SNP accumulation, W-specific non-coding gonadal expression, Neocentromere, Biology (General), QH301-705.5
Abstract: Abstract Background The Western mosquitofish, Gambusia affinis, is a model for sex chromosome organization and evolution of female heterogamety. We previously identified a G. affinis female-specific marker, orthologous to the aminomethyl transferase (amt) gene of the related platyfish (Xiphophorus maculatus). Here, we have analyzed the structure and differentiation of the G. affinis W-chromosome, using a cytogenomics and bioinformatics approach. Results The long arm of the G. affinis W-chromosome (Wq) is highly enriched in dispersed repetitive sequences, but neither heterochromatic nor epigenetically silenced by hypermethylation. In line with this, Wq sequences are highly transcribed, including an active nucleolus organizing region (NOR). Female-specific SNPs and evolutionary young transposable elements were highly enriched and dispersed along the W-chromosome long arm, suggesting constrained recombination. Wq copy number expanded elements also include female-specific transcribed sequences from the amt locus with homology to TE. Collectively, the G. affinis W-chromosome is actively differentiating by sex-specific copy number expansion of transcribed TE-related elements, but not (yet) by extensive sequence divergence or gene decay. Conclusions The G. affinis W-chromosome exhibits characteristic genomic properties of an evolutionary young sex chromosome. Strikingly, the observed sex-specific changes in the genomic landscape are confined to the W long arm, which is separated from the rest of the W-chromosome by a neocentromere acquired during sex chromosome evolution and may thus have become functionally insulated. In contrast, W short arm sequences were apparently shielded from repeat-driven differentiation, retained Z-chromosome like genomic features, and may have preserved pseudo-autosomal properties.
Published: 2023
Full Text: View/download PDF

4. A duplicated copy of id2b is an unusual sex-determining candidate gene on the Y chromosome of arapaima (Arapaima gigas)

Author: Mateus C. Adolfi, Kang Du, Susanne Kneitz, Cédric Cabau, Margot Zahm, Christophe Klopp, Romain Feron, Rômulo V. Paixão, Eduardo S. Varela, Fernanda L. de Almeida, Marcos A. de Oliveira, Rafael H. Nóbrega, Céline Lopez-Roques, Carole Iampietro, Jérôme Lluch, Werner Kloas, Sven Wuertz, Fabian Schaefer, Matthias Stöck, Yann Guiguen, and Manfred Schartl
Subjects: Medicine, Science
Abstract: Abstract Arapaima gigas is one of the largest freshwater fish species of high ecological and economic importance. Overfishing and habitat destruction are severe threats to the remaining wild populations. By incorporating a chromosomal Hi-C contact map, we improved the arapaima genome assembly to chromosome-level, revealing an unexpected high degree of chromosome rearrangements during evolution of the bonytongues (Osteoglossiformes). Combining this new assembly with pool-sequencing of male and female genomes, we identified id2bbY, a duplicated copy of the inhibitor of DNA binding 2b (id2b) gene on the Y chromosome as candidate male sex-determining gene. A PCR-test for id2bbY was developed, demonstrating that this gene is a reliable male-specific marker for genotyping. Expression analyses showed that this gene is expressed in juvenile male gonads. Its paralog, id2ba, exhibits a male-biased expression in immature gonads. Transcriptome analyses and protein structure predictions confirm id2bbY as a prime candidate for the master sex-determiner. Acting through the TGFβ signaling pathway, id2bbY from arapaima would provide the first evidence for a link of this family of transcriptional regulators to sex determination. Our study broadens our current understanding about the evolution of sex determination genetic networks and provide a tool for improving arapaima aquaculture for commercial and conservation purposes.
Published: 2021
Full Text: View/download PDF

5. Genetic determinism of spontaneous masculinisation in XX female rainbow trout: new insights using medium throughput genotyping and whole-genome sequencing

Author: Clémence Fraslin, Florence Phocas, Anastasia Bestin, Mathieu Charles, Maria Bernard, Francine Krieg, Nicolas Dechamp, Céline Ciobotaru, Chris Hozé, Florent Petitprez, Marine Milhes, Jérôme Lluch, Olivier Bouchez, Charles Poncet, Philippe Hocdé, Pierrick Haffray, Yann Guiguen, and Edwige Quillet
Subjects: Medicine, Science
Abstract: Abstract Rainbow trout has a male heterogametic (XY) sex determination system controlled by a major sex-determining gene, sdY. Unexpectedly, a few phenotypically masculinised fish are regularly observed in all-female farmed trout stocks. To better understand the genetic determinism underlying spontaneous maleness in XX-rainbow trout, we recorded the phenotypic sex of 20,210 XX-rainbow trout from a French farm population at 10 and 15 months post-hatching. The overall masculinisation rate was 1.45%. We performed two genome-wide association studies (GWAS) on a subsample of 1139 individuals classified as females, intersex or males using either medium-throughput genotyping (31,811 SNPs) or whole-genome sequencing (WGS, 8.7 million SNPs). The genomic heritability of maleness ranged between 0.48 and 0.62 depending on the method and the number of SNPs used for the estimation. At the 31K SNPs level, we detected four QTL on three chromosomes (Omy1, Omy12 and Omy20). Using WGS information, we narrowed down the positions of the two QTL detected on Omy1 to 96 kb and 347 kb respectively, with the second QTL explaining up to 14% of the total genetic variance of maleness. Within this QTL, we detected three putative candidate genes, fgfa8, cyp17a1 and an uncharacterised protein (LOC110527930), which might be involved in spontaneous maleness of XX-female rainbow trout.
Published: 2020
Full Text: View/download PDF

6. Sex chromosome and sex locus characterization in goldfish, Carassius auratus (Linnaeus, 1758)

Author: Ming Wen, Romain Feron, Qiaowei Pan, Justine Guguin, Elodie Jouanno, Amaury Herpin, Christophe Klopp, Cedric Cabau, Margot Zahm, Hugues Parrinello, Laurent Journot, Shawn M. Burgess, Yoshihiro Omori, John H. Postlethwait, Manfred Schartl, and Yann Guiguen
Subjects: Goldfish, RADseq, Poolseq, Sex determination, Sex markers, Male genome assembly, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract: Abstract Background Goldfish is an important model for various areas of research, including neural development and behavior and a species of significant importance in aquaculture, especially as an ornamental species. It has a male heterogametic (XX/XY) sex determination system that relies on both genetic and environmental factors, with high temperatures being able to produce female-to-male sex reversal. Little, however, is currently known on the molecular basis of genetic sex determination in this important cyprinid model. Here we used sequencing approaches to better characterize sex determination and sex-chromosomes in an experimental strain of goldfish. Results Our results confirmed that sex determination in goldfish is a mix of environmental and genetic factors and that its sex determination system is male heterogametic (XX/XY). Using reduced representation (RAD-seq) and whole genome (pool-seq) approaches, we characterized sex-linked polymorphisms and developed male specific genetic markers. These male specific markers were used to distinguish sex-reversed XX neomales from XY males and to demonstrate that XX female-to-male sex reversal could even occur at a relatively low rearing temperature (18 °C), for which sex reversal has been previously shown to be close to zero. We also characterized a relatively large non-recombining region (~ 11.7 Mb) on goldfish linkage group 22 (LG22) that contained a high-density of male-biased genetic polymorphisms. This large LG22 region harbors 373 genes, including a single candidate as a potential master sex gene, i.e., the anti-Mullerian hormone gene (amh). However, no sex-linked polymorphisms were detected in the coding DNA sequence of the goldfish amh gene. Conclusions These results show that our goldfish strain has a relatively large sex locus on LG22, which is likely the Y chromosome of this experimental population. The presence of a few XX males even at low temperature also suggests that other environmental factors in addition to temperature could trigger female-to-male sex reversal. Finally, we also developed sex-linked genetic markers, which will be important tools for future research on sex determination in our experimental goldfish population. However, additional work would be needed to explore whether this sex locus is conserved in other populations of goldfish.
Published: 2020
Full Text: View/download PDF

7. Genome Sequence of the Euryhaline Javafish Medaka, Oryzias javanicus: A Small Aquarium Fish Model for Studies on Adaptation to Salinity

Author: Yusuke Takehana, Margot Zahm, Cédric Cabau, Christophe Klopp, Céline Roques, Olivier Bouchez, Cécile Donnadieu, Celia Barrachina, Laurent Journot, Mari Kawaguchi, Shigeki Yasumasu, Satoshi Ansai, Kiyoshi Naruse, Koji Inoue, Chuya Shinzato, Manfred Schartl, Yann Guiguen, and Amaury Herpin
Subjects: medaka, evolution, whole genome sequencing, long reads, genetic map, transcriptome, adaptation, salinity, Genetics, QH426-470
Abstract: The genus Oryzias consists of 35 medaka-fish species each exhibiting various ecological, morphological and physiological peculiarities and adaptations. Beyond of being a comprehensive phylogenetic group for studying intra-genus evolution of several traits like sex determination, behavior, morphology or adaptation through comparative genomic approaches, all medaka species share many advantages of experimental model organisms including small size and short generation time, transparent embryos and genome editing tools for reverse and forward genetic studies. The Java medaka, Oryzias javanicus, is one of the two species of medaka perfectly adapted for living in brackish/sea-waters. Being an important component of the mangrove ecosystem, O. javanicus is also used as a valuable marine test-fish for ecotoxicology studies. Here, we sequenced and assembled the whole genome of O. javanicus, and anticipate this resource will be catalytic for a wide range of comparative genomic, phylogenetic and functional studies. Complementary sequencing approaches including long-read technology and data integration with a genetic map allowed the final assembly of 908 Mbp of the O. javanicus genome. Further analyses estimate that the O. javanicus genome contains 33% of repeat sequences and has a heterozygosity of 0.96%. The achieved draft assembly contains 525 scaffolds with a total length of 809.7 Mbp, a N50 of 6,3 Mbp and a L50 of 37 scaffolds. We identified 21454 predicted transcripts for a total transcriptome size of 57, 146, 583 bps. We provide here a high-quality chromosome scale draft genome assembly of the euryhaline Javafish medaka (321 scaffolds anchored on 24 chromosomes (representing 97.7% of the total bases)), and give emphasis on the evolutionary adaptation to salinity.
Published: 2020
Full Text: View/download PDF

8. RUNX1 maintains the identity of the fetal ovary through an interplay with FOXL2

Author: Barbara Nicol, Sara A. Grimm, Frédéric Chalmel, Estelle Lecluze, Maëlle Pannetier, Eric Pailhoux, Elodie Dupin-De-Beyssat, Yann Guiguen, Blanche Capel, and Humphrey H.-C. Yao
Subjects: Science
Abstract: Proper ovarian differentiation requires RUNX1. Here, the authors show that double knockout of Runx1/Foxl2 results in masculinization of fetal ovaries, and that RUNX1 and FOXL2 jointly occupy common chromatin regions to maintain pre-granulosa cell identity in the fetal ovary.
Published: 2019
Full Text: View/download PDF

9. A Y-linked anti-Müllerian hormone type-II receptor is the sex-determining gene in ayu, Plecoglossus altivelis.

Author: Masatoshi Nakamoto, Tsubasa Uchino, Eriko Koshimizu, Yudai Kuchiishi, Ryota Sekiguchi, Liu Wang, Ryusuke Sudo, Masato Endo, Yann Guiguen, Manfred Schartl, John H Postlethwait, and Takashi Sakamoto
Subjects: Genetics, QH426-470
Abstract: Whole-genome duplication and genome compaction are thought to have played important roles in teleost fish evolution. Ayu (or sweetfish), Plecoglossus altivelis, belongs to the superorder Stomiati, order Osmeriformes. Stomiati is phylogenetically classified as sister taxa of Neoteleostei. Thus, ayu holds an important position in the fish tree of life. Although ayu is economically important for the food industry and recreational fishing in Japan, few genomic resources are available for this species. To address this problem, we produced a draft genome sequence of ayu by whole-genome shotgun sequencing and constructed linkage maps using a genotyping-by-sequencing approach. Syntenic analyses of ayu and other teleost fish provided information about chromosomal rearrangements during the divergence of Stomiati, Protacanthopterygii and Neoteleostei. The size of the ayu genome indicates that genome compaction occurred after the divergence of the family Osmeridae. Ayu has an XX/XY sex-determination system for which we identified sex-associated loci by a genome-wide association study by genotyping-by-sequencing and whole-genome resequencing using wild populations. Genome-wide association mapping using wild ayu populations revealed three sex-linked scaffolds (total, 2.03 Mb). Comparison of whole-genome resequencing mapping coverage between males and females identified male-specific regions in sex-linked scaffolds. A duplicate copy of the anti-Müllerian hormone type-II receptor gene (amhr2bY) was found within these male-specific regions, distinct from the autosomal copy of amhr2. Expression of the Y-linked amhr2 gene was male-specific in sox9b-positive somatic cells surrounding germ cells in undifferentiated gonads, whereas autosomal amhr2 transcripts were detected in somatic cells in sexually undifferentiated gonads of both genetic males and females. Loss-of-function mutation for amhr2bY induced male to female sex reversal. Taken together with the known role of Amh and Amhr2 in sex differentiation, these results indicate that the paralog of amhr2 on the ayu Y chromosome determines genetic sex, and the male-specific amh-amhr2 pathway is critical for testicular differentiation in ayu.
Published: 2021
Full Text: View/download PDF

10. The Chromosome-Level Genome Assembly of European Grayling Reveals Aspects of a Unique Genome Evolution Process Within Salmonids

Author: Tiina Sävilammi, Craig R. Primmer, Srinidhi Varadharajan, René Guyomard, Yann Guiguen, Simen R. Sandve, L. Asbjørn Vøllestad, Spiros Papakostas, and Sigbjørn Lien
Subjects: chromosome evolution, chromosomal structure, genomic rearrangements, karyotype evolution, retrotransposons, Genetics, QH426-470
Abstract: Salmonids represent an intriguing taxonomical group for investigating genome evolution in vertebrates due to their relatively recent last common whole genome duplication event, which occurred between 80 and 100 million years ago. Here, we report on the chromosome-level genome assembly of European grayling (Thymallus thymallus), which represents one of the earliest diverged salmonid subfamilies. To achieve this, we first generated relatively long genomic scaffolds by using a previously published draft genome assembly along with long-read sequencing data and a linkage map. We then merged those scaffolds by applying synteny evidence from the Atlantic salmon (Salmo salar) genome. Comparisons of the European grayling genome assembly to the genomes of Atlantic salmon and Northern pike (Esox lucius), the latter used as a nonduplicated outgroup, detailed aspects of the characteristic chromosome evolution process that has taken place in European grayling. While Atlantic salmon and other salmonid genomes are portrayed by the typical occurrence of numerous chromosomal fusions, European grayling chromosomes were confirmed to be fusion-free and were characterized by a relatively large proportion of paracentric and pericentric inversions. We further reported on transposable elements specific to either the European grayling or Atlantic salmon genome, on the male-specific sdY gene in the European grayling chromosome 11A, and on regions under residual tetrasomy in the homeologous European grayling chromosome pairs 9A-9B and 25A-25B. The same chromosome pairs have been observed under residual tetrasomy in Atlantic salmon and in other salmonids, suggesting that this feature has been conserved since the subfamily split.
Published: 2019
Full Text: View/download PDF

11. Double maternal-effect: duplicated nucleoplasmin 2 genes, npm2a and npm2b, with essential but distinct functions are shared by fish and tetrapods

Author: Caroline T. Cheung, Jérémy Pasquier, Aurélien Bouleau, Thaovi Nguyen, Franck Chesnel, Yann Guiguen, and Julien Bobe
Subjects: npm2, Vertebrates, Evolution, Maternal-effect genes, CRISPR-cas9 knockout, QH359-425
Abstract: Abstract Background Nucleoplasmin 2 (npm2) is an essential maternal-effect gene that mediates early embryonic events through its function as a histone chaperone that remodels chromatin. Recently, two npm2 (npm2a and npm2b) genes have been annotated in zebrafish. Thus, we examined the evolution of npm2a and npm2b in a variety of vertebrates, their potential phylogenetic relationships, and their biological functions using knockout models via the CRISPR/cas9 system. Results We demonstrated that the two npm2 duplicates exist in a wide range of vertebrates, including sharks, ray-finned fish, amphibians, and sauropsids, while npm2a was lost in coelacanth and mammals, as well as some specific teleost lineages. Using phylogeny and synteny analyses, we traced their origins to the early stages of vertebrate evolution. Our findings suggested that npm2a and npm2b resulted from an ancient local gene duplication, and their functions diverged although key protein domains were conserved. We then investigated their functions by examining their tissue distribution in a wide variety of species and found that they shared ovarian-specific expression, a key feature of maternal-effect genes. We also demonstrated that both npm2a and npm2b are maternally-inherited transcripts in vertebrates, and that they play essential, but distinct, roles in early embryogenesis using zebrafish knockout models. Both npm2a and npm2b function early during oogenesis and may play a role in cortical granule function that impact egg activation and fertilization, while npm2b is also involved in early embryogenesis. Conclusion These novel findings will broaden our knowledge on the evolutionary history of maternal-effect genes and underlying mechanisms that contribute to vertebrate reproductive success. In addition, our results demonstrate the existence of a newly described maternal-effect gene, npm2a, that contributes to egg competence, an area that still requires further comprehension.
Published: 2018
Full Text: View/download PDF

12. The rise and fall of the ancient northern pike master sex-determining gene

Author: Qiaowei Pan, Romain Feron, Elodie Jouanno, Hugo Darras, Amaury Herpin, Ben Koop, Eric Rondeau, Frederick W Goetz, Wesley A Larson, Louis Bernatchez, Mike Tringali, Stephen S Curran, Eric Saillant, Gael PJ Denys, Frank A von Hippel, Songlin Chen, J Andrés López, Hugo Verreycken, Konrad Ocalewicz, Rene Guyomard, Camille Eche, Jerome Lluch, Celine Roques, Hongxia Hu, Roger Tabor, Patrick DeHaan, Krista M Nichols, Laurent Journot, Hugues Parrinello, Christophe Klopp, Elena A Interesova, Vladimir Trifonov, Manfred Schartl, John Postlethwait, and Yann Guiguen
Subjects: fish, pikes, mudminnows, esociforms, esocidae, umbridae, Medicine, Science, Biology (General), QH301-705.5
Abstract: The understanding of the evolution of variable sex determination mechanisms across taxa requires comparative studies among closely related species. Following the fate of a known master sex-determining gene, we traced the evolution of sex determination in an entire teleost order (Esociformes). We discovered that the northern pike (Esox lucius) master sex-determining gene originated from a 65 to 90 million-year-old gene duplication event and that it remained sex linked on undifferentiated sex chromosomes for at least 56 million years in multiple species. We identified several independent species- or population-specific sex determination transitions, including a recent loss of a Y chromosome. These findings highlight the diversity of evolutionary fates of master sex-determining genes and the importance of population demographic history in sex determination studies. We hypothesize that occasional sex reversals and genetic bottlenecks provide a non-adaptive explanation for sex determination transitions.
Published: 2021
Full Text: View/download PDF

13. Sox5 is involved in germ-cell regulation and sex determination in medaka following co-option of nested transposable elements

Author: Manfred Schartl, Susanne Schories, Yuko Wakamatsu, Yusuke Nagao, Hisashi Hashimoto, Chloé Bertin, Brigitte Mourot, Cornelia Schmidt, Dagmar Wilhelm, Lazaro Centanin, Yann Guiguen, and Amaury Herpin
Subjects: Exaptation, Master sex-determining gene, Transcriptional rewiring, Medaka, Dmrt1bY, Sox5, Biology (General), QH301-705.5
Abstract: Abstract Background Sex determination relies on a hierarchically structured network of genes, and is one of the most plastic processes in evolution. The evolution of sex-determining genes within a network, by neo- or sub-functionalization, also requires the regulatory landscape to be rewired to accommodate these novel gene functions. We previously showed that in medaka fish, the regulatory landscape of the master male-determining gene dmrt1bY underwent a profound rearrangement, concomitantly with acquiring a dominant position within the sex-determining network. This rewiring was brought about by the exaptation of a transposable element (TE) called Izanagi, which is co-opted to act as a silencer to turn off the dmrt1bY gene after it performed its function in sex determination. Results We now show that a second TE, Rex1, has been incorporated into Izanagi. The insertion of Rex1 brought in a preformed regulatory element for the transcription factor Sox5, which here functions in establishing the temporal and cell-type-specific expression pattern of dmrt1bY. Mutant analysis demonstrates the importance of Sox5 in the gonadal development of medaka, and possibly in mice, in a dmrt1bY-independent manner. Moreover, Sox5 medaka mutants have complete female-to-male sex reversal. Conclusions Our work reveals an unexpected complexity in TE-mediated transcriptional rewiring, with the exaptation of a second TE into a network already rewired by a TE. We also show a dual role for Sox5 during sex determination: first, as an evolutionarily conserved regulator of germ-cell number in medaka, and second, by de novo regulation of dmrt1 transcriptional activity during primary sex determination due to exaptation of the Rex1 transposable element.
Published: 2018
Full Text: View/download PDF

14. Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture

Author: Daniel J. Macqueen, Craig R. Primmer, Ross D. Houston, Barbara F. Nowak, Louis Bernatchez, Steinar Bergseth, William S. Davidson, Cristian Gallardo-Escárate, Tom Goldammer, Yann Guiguen, Patricia Iturra, James W. Kijas, Ben F. Koop, Sigbjørn Lien, Alejandro Maass, Samuel A. M. Martin, Philip McGinnity, Martin Montecino, Kerry A. Naish, Krista M. Nichols, Kristinn Ólafsson, Stig W. Omholt, Yniv Palti, Graham S. Plastow, Caird E. Rexroad, Matthew L. Rise, Rachael J. Ritchie, Simen R. Sandve, Patricia M. Schulte, Alfredo Tello, Rodrigo Vidal, Jon Olav Vik, Anna Wargelius, José Manuel Yáñez, and The FAASG Consortium
Subjects: Salmonid fish, Genome biology, Functional annotation, Comparative biology, Standardized data and metadata, Data sharing, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract: Abstract We describe an emerging initiative - the ‘Functional Annotation of All Salmonid Genomes’ (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic variation. The outcomes of FAASG will have diverse applications, ranging from improved understanding of genome evolution, to improving the efficiency and sustainability of aquaculture production, supporting the future of fundamental and applied research in an iconic fish lineage of major societal importance.
Published: 2017
Full Text: View/download PDF

15. Draft Genome Assembly and Annotation of the Gila Topminnow Poeciliopsis occidentalis

Author: Mariana Mateos, Du Kang, Christophe Klopp, Hugues Parrinello, Mateo García-Olazábal, Molly Schumer, Nathaniel K. Jue, Yann Guiguen, and Manfred Schartl
Subjects: genome assembly, genome annotation, transposable elements, topminnow, mitochondrial genome, Evolution, QH359-425, Ecology, QH540-549.5
Published: 2019
Full Text: View/download PDF

16. Identification of the master sex determining gene in Northern pike (Esox lucius) reveals restricted sex chromosome differentiation.

Author: Qiaowei Pan, Romain Feron, Ayaka Yano, René Guyomard, Elodie Jouanno, Estelle Vigouroux, Ming Wen, Jean-Mickaël Busnel, Julien Bobe, Jean-Paul Concordet, Hugues Parrinello, Laurent Journot, Christophe Klopp, Jérôme Lluch, Céline Roques, John Postlethwait, Manfred Schartl, Amaury Herpin, and Yann Guiguen
Subjects: Genetics, QH426-470
Abstract: Teleost fishes, thanks to their rapid evolution of sex determination mechanisms, provide remarkable opportunities to study the formation of sex chromosomes and the mechanisms driving the birth of new master sex determining (MSD) genes. However, the evolutionary interplay between the sex chromosomes and the MSD genes they harbor is rather unexplored. We characterized a male-specific duplicate of the anti-Müllerian hormone (amh) as the MSD gene in Northern Pike (Esox lucius), using genomic and expression evidence as well as by loss-of-function and gain-of-function experiments. Using RAD-Sequencing from a family panel, we identified Linkage Group (LG) 24 as the sex chromosome and positioned the sex locus in its sub-telomeric region. Furthermore, we demonstrated that this MSD originated from an ancient duplication of the autosomal amh gene, which was subsequently translocated to LG24. Using sex-specific pooled genome sequencing and a new male genome sequence assembled using Nanopore long reads, we also characterized the differentiation of the X and Y chromosomes, revealing a small male-specific insertion containing the MSD gene and a limited region with reduced recombination. Our study reveals an unexpectedly low level of differentiation between a pair of sex chromosomes harboring an old MSD gene in a wild teleost fish population, and highlights both the pivotal role of genes from the amh pathway in sex determination, as well as the importance of gene duplication as a mechanism driving the turnover of sex chromosomes in this clade.
Published: 2019
Full Text: View/download PDF

17. A novel evolutionary conserved mechanism of RNA stability regulates synexpression of primordial germ cell-specific genes prior to the sex-determination stage in medaka.

Author: Amaury Herpin, Cornelia Schmidt, Susanne Kneitz, Clara Gobé, Martina Regensburger, Aurélie Le Cam, Jérome Montfort, Mateus C Adolfi, Christina Lillesaar, Dagmar Wilhelm, Michael Kraeussling, Brigitte Mourot, Béatrice Porcon, Maëlle Pannetier, Eric Pailhoux, Laurence Ettwiller, Dirk Dolle, Yann Guiguen, and Manfred Schartl
Subjects: Biology (General), QH301-705.5
Abstract: Dmrt1 is a highly conserved transcription factor, which is critically involved in regulation of gonad development of vertebrates. In medaka, a duplicate of dmrt1-acting as master sex-determining gene-has a tightly timely and spatially controlled gonadal expression pattern. In addition to transcriptional regulation, a sequence motif in the 3' UTR (D3U-box) mediates transcript stability of dmrt1 mRNAs from medaka and other vertebrates. We show here that in medaka, two RNA-binding proteins with antagonizing properties target this D3U-box, promoting either RNA stabilization in germ cells or degradation in the soma. The D3U-box is also conserved in other germ-cell transcripts, making them responsive to the same RNA binding proteins. The evolutionary conservation of the D3U-box motif within dmrt1 genes of metazoans-together with preserved expression patterns of the targeting RNA binding proteins in subsets of germ cells-suggest that this new mechanism for controlling RNA stability is not restricted to fishes but might also apply to other vertebrates.
Published: 2019
Full Text: View/download PDF

18. foxr1 is a novel maternal-effect gene in fish that is required for early embryonic success

Author: Caroline T. Cheung, Amélie Patinote, Yann Guiguen, and Julien Bobe
Subjects: CRISPR-cas9, Maternal-effect genes, foxr1, p21, Cell growth and survival, Rictor, Medicine, Biology (General), QH301-705.5
Abstract: The family of forkhead box (Fox) transcription factors regulates gonadogenesis and embryogenesis, but the role of foxr1 in reproduction is unknown. Evolutionary history of foxr1 in vertebrates was examined and the gene was found to exist in most vertebrates, including mammals, ray-finned fish, amphibians, and sauropsids. By quantitative PCR and RNA-seq, we found that foxr1 had an ovarian-specific expression in zebrafish, a common feature of maternal-effect genes. In addition, it was demonstrated using in situ hybridization that foxr1 was a maternally-inherited transcript that was highly expressed even in early-stage oocytes and accumulated in the developing eggs during oogenesis. We also analyzed the function of foxr1 in female reproduction using a zebrafish CRISPR/cas9 knockout model. It was observed that embryos from the foxr1-deficient females had a significantly lower survival rate whereby they either failed to undergo cell division or underwent abnormal division that culminated in growth arrest at around the mid-blastula transition and early death. These mutant-derived eggs contained dramatically increased levels of p21, a cell cycle inhibitor, and reduced rictor, a component of mTOR and regulator of cell survival, which were in line with the observed growth arrest phenotype. Our study shows for the first time that foxr1 is an essential maternal-effect gene and may be required for proper cell division and survival via the p21 and mTOR pathways. These novel findings will broaden our knowledge on the functions of specific maternal factors stored in the developing egg and the underlying mechanisms that contribute to reproductive success.
Published: 2018
Full Text: View/download PDF

19. Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies

Author: Cédric Cabau, Frédéric Escudié, Anis Djari, Yann Guiguen, Julien Bobe, and Christophe Klopp
Subjects: RNA-Seq, De novo assembly, Compaction, Correction, Quality assessment, Medicine, Biology (General), QH301-705.5
Abstract: Background De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error correction. Trinity and Oases are two commonly used de novo transcriptome assemblers. The contig sets they produce are of good quality. Still, their compaction (number of contigs needed to represent the transcriptome) and their quality (chimera and nucleotide error rates) can be improved. Results We built a de novo RNA-Seq Assembly Pipeline (DRAP) which wraps these two assemblers (Trinity and Oases) in order to improve their results regarding the above-mentioned criteria. DRAP reduces from 1.3 to 15 fold the number of resulting contigs of the assemblies depending on the read set and the assembler used. This article presents seven assembly comparisons showing in some cases drastic improvements when using DRAP. DRAP does not significantly impair assembly quality metrics such are read realignment rate or protein reconstruction counts. Conclusion Transcriptome assembly is a challenging computational task even if good solutions are already available to end-users, these solutions can still be improved while conserving the overall representation and quality of the assembly. The de novo RNA-Seq Assembly Pipeline (DRAP) is an easy to use software package to produce compact and corrected transcript set. DRAP is free, open-source and available under GPL V3 license at http://www.sigenae.org/drap.
Published: 2017
Full Text: View/download PDF

20. Meta-Analysis of Microarray Data of Rainbow Trout Fry Gonad Differentiation Modulated by Ethynylestradiol.

Author: Sophie Depiereux, Florence Le Gac, Bertrand De Meulder, Michael Pierre, Raphaël Helaers, Yann Guiguen, Patrick Kestemont, and Eric Depiereux
Subjects: Medicine, Science
Abstract: Sex differentiation in fish is a highly labile process easily reversed by the use of exogenous hormonal treatment and has led to environmental concerns since low doses of estrogenic molecules can adversely impact fish reproduction. The goal of this study was to identify pathways altered by treatment with ethynylestradiol (EE2) in developing fish and to find new target genes to be tested further for their possible role in male-to-female sex transdifferentiation. To this end, we have successfully adapted a previously developed bioinformatics workflow to a meta-analysis of two datasets studying sex reversal following exposure to EE2 in juvenile rainbow trout. The meta-analysis consisted of retrieving the intersection of the top gene lists generated for both datasets, performed at different levels of stringency. The intersecting gene lists, enriched in true positive differentially expressed genes (DEGs), were subjected to over-representation analysis (ORA) which allowed identifying several statistically significant enriched pathways altered by EE2 treatment and several new candidate pathways, such as progesterone-mediated oocyte maturation and PPAR signalling. Moreover, several relevant key genes potentially implicated in the early transdifferentiation process were selected. Altogether, the results show that EE2 has a great effect on gene expression in juvenile rainbow trout. The feminization process seems to result from the altered transcription of genes implicated in normal female gonad differentiation, resulting in expression similar to that observed in normal females (i.e. the repression of key testicular markers cyp17a1, cyp11b, tbx1), as well as from other genes (including transcription factors) that respond specifically to the EE2 treatment. The results also showed that the bioinformatics workflow can be applied to different types of microarray platforms and could be generalized to (eco)toxicogenomics studies for environmental risk assessment purposes.
Published: 2015
Full Text: View/download PDF

21. No early gender effects on energetic status and life history in a salmonid

Author: Thomas Régnier, Jacques Labonne, Joëlle Chat, Ayaka Yano, Yann Guiguen, and Valérie Bolliet
Subjects: gender effects, energetic status, emergence from gravel, sdy, brown trout, Science
Abstract: Throughout an organism's early development, variations in physiology and behaviours may have long lasting consequences on individual life histories. While a large part of variation in critical life-history transitions remains unexplained, a significant proportion may be caused by early gender effects as part of gender-specific life histories shaped by sexual selection. In this study, we investigated the presence of early gender effects on the timing of emergence from gravel and the energetic status of brown trout (Salmo trutta) early stages. To investigate this question, individual measures of emergence timing, metabolic rate and energetic content were coupled for the first time with the use of a recent genetic marker for sdY (sexually dimorphic on the Y-chromosome), a master sex-determining gene. Our results show that gender does not influence the energetic content of emerging juveniles or their emergence timing. These findings suggest that gender differences may appear later throughout salmonid life history and that selective pressures associated with the critical period of emergence from gravel may shape early life-history traits similarly in both males and females.
Published: 2015
Full Text: View/download PDF

22. High temperature increases the masculinization rate of the all-female (XX) rainbow trout 'Mal' population.

Author: Karina Valdivia, Elodie Jouanno, Jean-Nicolas Volff, Delphine Galiana-Arnoux, René Guyomard, Louise Helary, Brigitte Mourot, Alexis Fostier, Edwige Quillet, and Yann Guiguen
Subjects: Medicine, Science
Abstract: Salmonids are generally considered to have a robust genetic sex determination system with a simple male heterogamety (XX/XY). However, spontaneous masculinization of XX females has been found in a rainbow trout population of gynogenetic doubled haploid individuals. The analysis of this masculinization phenotype transmission supported the hypothesis of the involvement of a recessive mutation (termed mal). As temperature effect on sex differentiation has been reported in some salmonid species, in this study we investigated in detail the potential implication of temperature on masculinization in this XX mal-carrying population. Seven families issued from XX mal-carrying parents were exposed from the time of hatching to different rearing water temperatures ((8, 12 and 18°C), and the resulting sex-ratios were confirmed by histological analysis of both gonads. Our results demonstrate that masculinization rates are strongly increased (up to nearly two fold) at the highest temperature treatment (18°C). Interestingly, we also found clear differences between temperatures on the masculinization of the left versus the right gonads with the right gonad consistently more often masculinized than the left one at lower temperatures (8 and 12°C). However, the masculinization rate is also strongly dependent on the genetic background of the XX mal-carrying families. Thus, masculinization in XX mal-carrying rainbow trout is potentially triggered by an interaction between the temperature treatment and a complex genetic background potentially involving some part of the genetic sex differentiation regulatory cascade along with some minor sex-influencing loci. These results indicate that despite its rather strict genetic sex determinism system, rainbow trout sex differentiation can be modulated by temperature, as described in many other fish species.
Published: 2014
Full Text: View/download PDF

23. An ancient truncated duplication of the anti‐Müllerian hormone receptor type 2 gene is a potential conserved master sex determinant in the Pangasiidae catfish family

Author: Ming Wen, Qiaowei Pan, Elodie Jouanno, Jerome Montfort, Margot Zahm, Cédric Cabau, Christophe Klopp, Carole Iampietro, Céline Roques, Olivier Bouchez, Adrien Castinel, Cécile Donnadieu, Hugues Parrinello, Charles Poncet, Elodie Belmonte, Véronique Gautier, Jean-Christophe Avarre, Remi Dugue, Rudhy Gustiano, Trần Thị Thúy Hà, Marc Campet, Kednapat Sriphairoj, Josiane Ribolli, Fernanda L. de Almeida, Thomas Desvignes, John H. Postlethwait, Christabel Floi Bucao, Marc Robinson-Rechavi, Julien Bobe, Amaury Herpin, Yann Guiguen, Hunan Normal University (HNU), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Lausanne = University of Lausanne (UNIL), Plateforme Bio-Informatique - Génotoul, Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-BioInfOmics, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génomique Fonctionnelle (IGF), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Research Institute of Freshwater Fisheries (CRIFI-RIFF), Research Institute for Aquaculture, Neovia Asia, Kasetsart University (KU), Universidade Federal de Santa Catarina = Federal University of Santa Catarina [Florianópolis] (UFSC), Embrapa Amazônia Ocidental, Partenaires INRAE, University of Oregon [Eugene], Swiss Institute of Bioinformatics [Lausanne] (SIB), Swiss Institute of Bioinformatics [Genève] (SIB), National Institutes of Health : R01 OD011116, National Institutes of Health: R35 GM139635, ANR-13-ISV7-0005,PhyloSex,Evolution des déterminants majeurs du sexe chez les poissons.(2013), ANR-16-CE12-0035,GenoFish,Evolution des génes et des génomes après duplication compléte(2016), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), MING WEN, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, QIAOWEI PAN, INRAE, LPGP, ELODIE JOUANNO, INRAE, LPGP, JEROME MONTFORT, INRAE, LPGP, MARGOT ZAHM, Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRAE, CÉDRIC CABAU, SIGENAE, GenPhySE, Université de Toulouse, INRAE, CHRISTOPHE KLOPP, SIGENAE, CAROLE IAMPIETRO, INRAE, CÉLINE ROQUES, INRAE, OLIVIER BOUCHEZ, INRAE, ADRIEN CASTINEL, INRAE, CÉCILE DONNADIEU, INRAE, HUGUES PARRINELLO, Montpellier GenomiX, CHARLES PONCET, GDEC Gentyane, INRAE, Université Clermont Auvergne, ELODIE BELMONTE, GDEC Gentyane, INRAE, Université Clermont Auvergne, VÉRONIQUE GAUTIER, GDEC Gentyane, INRAE, Université Clermont Auvergne, JEAN-CHRISTOPHE AVARRE, ISEM, CNRS, IRD, Univ Montpellier, REMI DUGUE, ISEM, CNRS, IRD, Univ Montpellier, RUDHY GUSTIANO, Research Institute of Freshwater Fisheries (CRIFI-RIFF), TRÂN THI THÚY HÀ, Research Institute for Aquaculture, MARC CAMPET, Neovia Asia, KEDNAPAT SRIPHAIROJ, Faculty of Natural Resources and Agro-Industry, JOSIANE RIBOLLI, Laboratório de Biologia e Cultivo de Peixes de Água Doce, Universidade Federal de Santa Catarina, FERNANDA LOUREIRO ALMEIDA OSULLIVAN, CPAA, THOMAS DESVIGNES, Institute of Neuroscience, University of Oregon, JOHN H. POSTLETHWAIT, Institute of Neuroscience, University of Oregon, CHRISTABEL FLOI BUCAO, Department of Ecology and Evolution, University of Lausanne, MARC ROBINSON-RECHAVI, Department of Ecology and Evolution, University of Lausanne, JULIEN BOBE, INRAE, LPGP, AMAURY HERPIN, INRAE, LPGP, and YANN GUIGUEN, INRAE, LPGP.
Subjects: Male, Male genome assembly, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, Receptors, Peptide, Animals, Catfishes/genetics, Phylogeny, Receptors, Peptide/genetics, Receptors, Transforming Growth Factor beta/genetics, Y Chromosome/genetics, amhr2, evolution, male genome assembly, pangasiid catfishes, sex determination, Evolution, Pangasiid catfishes, [SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, Sex determination, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Peixe-gato, Y Chromosome, Genetics, Hormônio, Receptors, Transforming Growth Factor beta, Catfishes, Ecology, Evolution, Behavior and Systematics, Biotechnology
Abstract: The evolution of sex determination (SD) mechanisms in teleost fishes is amazingly dynamic, as reflected by the variety of different master sex-determining genes identified, even sometimes among closely related species. Pangasiids are a group of economically important catfishes in many South-Asian countries, but little is known about their sex determination system. Here, we generated novel genomic resources for 12 Pangasiid species and provided a first characterization of their SD system. Based on an Oxford Nanopore long-read chromosome-scale high quality genome assembly of the striped catfish Pangasianodon hypophthalmus, we identified a duplication of the anti-Müllerian hormone receptor type II gene (amhr2), which was further characterized as being sex-linked in males and expressed only in testicular samples. These first results point to a male-specific duplication on the Y chromosome (amhr2by) of the autosomal amhr2a. Sequence annotation revealed that the P. hypophthalmus Amhr2by is truncated in its N-terminal domain, lacking the cysteine-rich extracellular part of the receptor that is crucial for ligand binding, suggesting a potential route for its neofunctionalization. Short-read genome sequencing and reference-guided assembly of 11 additional Pangasiid species, along with sex-linkage studies, revealed that this truncated amhr2by duplication is also conserved as a male-specific gene in many Pangasiids. Reconstructions of the amhr2 phylogeny suggested that amhr2by arose from an ancient duplication / insertion event at the root of the Siluroidei radiation that is dated around 100 million years ago. Altogether these results bring multiple lines of evidence supporting that amhr2by is an ancient and conserved master sex-determining gene in Pangasiid catfishes, a finding that highlights the recurrent usage of the transforming growth factor β pathway in teleost sex determination and brings another empirical case towards the understanding of the dynamics or stability of sex determination systems.
Published: 2022

24. Generation of a chromosome‐level genome assembly for Pacific halibut ( Hippoglossus stenolepis ) and characterization of its sex‐determining genomic region

Author: Andrew J. Jasonowicz, Anna Simeon, Margot Zahm, Cédric Cabau, Christophe Klopp, Céline Roques, Carole Iampietro, Jérôme Lluch, Cécile Donnadieu, Hugues Parrinello, Daniel P. Drinan, Lorenz Hauser, Yann Guiguen, and Josep V. Planas
Subjects: Male, Fishes, Genetics, Animals, Female, Flounder, Genomics, Chromosomes, Ecosystem, Ecology, Evolution, Behavior and Systematics, Genome-Wide Association Study, Biotechnology
Abstract: The Pacific halibut (Hippoglossus stenolepis) is a key species in the North Pacific Ocean and Bering Sea ecosystems, where it also supports important fisheries. However, the lack of genomic resources limits our understanding of evolutionary, environmental and anthropogenic forces affecting key life history characteristics of Pacific halibut and prevents the application of genomic tools in fisheries management and conservation efforts. In the present study, we report on the first generation of a high-quality chromosome-level assembly of the Pacific halibut genome, with an estimated size of 602 Mb, 24 chromosome-length scaffolds that contain 99.8% of the assembly and a N
Published: 2022

25. Genome structures resolve the early diversification of teleost fishes

Author: Elise Parey, Alexandra Louis, Jerome Montfort, Olivier Bouchez, Céline Roques, Carole Iampietro, Jerome Lluch, Adrien Castinel, Cécile Donnadieu, Thomas Desvignes, Christabel Floi Bucao, Elodie Jouanno, Ming Wen, Sahar Mejri, Ron Dirks, Hans Jansen, Christiaan Henkel, Wei-Jen Chen, Margot Zahm, Cédric Cabau, Christophe Klopp, Andrew W. Thompson, Marc Robinson-Rechavi, Ingo Braasch, Guillaume Lecointre, Julien Bobe, John H. Postlethwait, Camille Berthelot, Hugues Roest Crollius, Yann Guiguen, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Oregon [Eugene], Université de Lausanne = University of Lausanne (UNIL), Swiss Institute of Bioinformatics [Lausanne] (SIB), Hunan Normal University (HNU), Florida Atlantic University [Boca Raton], Future Genomics Technologies, Universiteit Leiden, Norwegian University of Life Sciences (NMBU), National Taiwan University [Taiwan] (NTU), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Western Michigan University [Kalamazoo], Michigan State University [East Lansing], Michigan State University System, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Génomique fonctionnelle comparative - Comparative functional genomics, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), This work was supported by the Agence Nationale de la Recherche, France (ANR) on the GenoFish project, 2016–2021 (grant No. ANR-16-CE12-003) to H.R.C., C.B., J.B., J.H.P., M.R.C., and Y.G., and by France Génomique National infrastructure, funded as part of 'Investissement d’avenir' program managed by ANR (grant No. ANR-10-INBS-09) to C.D. Part of the fellowship to E.P. was supported by funds from the European Union Horizon 2020 research and innovation program under Grant Agreement No 817923 (AQUA-FAANG). M.R.-R. was supported by the Swiss National Science Foundation grant 31003A_173048. J.H.P and I.B were supported by the National Institutes of Health under grant agreement No. R01OD011116. W.J.C. was supported by MOST grants No. 111-2611-M-002-025, 110-2611-M-002-013, and 108-2611-M-002-012-MY2., ANR-16-CE12-0035,GenoFish,Evolution des génes et des génomes après duplication compléte(2016), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), European Project: 817923,H2020,H2020-EU.3.2.1.1., H2020-EU.3.2.3.1.,AQUA-FAANG(2019), DYnamique et Organisation des GENomes - Equipe de l'IBENS (DYOGEN), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, Institute of Oceanography [Taipei], Plateforme Bio-Informatique - Génotoul, Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-BioInfOmics, Génétique des génomes - Genetics of Genomes (UMR 3525), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Swiss National Science Foundation grant 31003A_173048, National Institute of Health under grant agreement No R01OD011116, and Muséum national d'Histoire naturelle (MNHN)
Subjects: Animals, Zebrafish/genetics, Fishes/genetics, Eels/genetics, Biological Evolution, Phylogeny, Genome, Evolution, Molecular, Multidisciplinary, [SDV]Life Sciences [q-bio], [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, [SDV.BID]Life Sciences [q-bio]/Biodiversity
Abstract: Accurate species phylogenies are a prerequisite for evolutionary research. Teleosts are by far the largest and the most diversified group of extant vertebrates, but relationships among the three oldest lineages of extant teleosts remain unresolved. Based on seven high-quality new genome assemblies in Elopomorpha (tarpons, eels), we revisited the topology of the deepest branches of the teleost phylogeny using independent gene sequence and chromosomal rearrangement phylogenomic approaches. These analyses converged to a single scenario that unambiguously places the Elopomorpha and Osteoglossomorpha (bony-tongues) in a monophyletic group sister to all other teleosts, i.e., the Clupeocephala lineage. This finding resolves over 50 years of controversy on the evolutionary relationships of these lineages and highlights the power of combining different levels of genome-wide information to solve complex phylogenies.One-Sentence SummaryWhole-genome analyses place Elopomorpha (tarpons, eels) and Osteoglossomorpha (bony-tongues) as sister groups at the deepest branching of crown teleosts.
Published: 2023

26. Genome biology of the darkedged splitfin, Girardinichthys multiradiatus, and the evolution of sex chromosomes and placentation

Author: Kang Du, Martin Pippel, Susanne Kneitz, Romain Feron, Irene da Cruz, Sylke Winkler, Brigitta Wilde, Edgar G. Avila Luna, Gene Myers, Yann Guiguen, Constantino Macias Garcia, and Manfred Schartl
Subjects: Genetics, Genetics (clinical)
Abstract: Viviparity evolved independently about 150 times in vertebrates and more than 20 times in fish. Several lineages added to the protection of the embryo inside the body of the mother, the provisioning of nutrients, and physiological exchange. This often led to the evolution of a placenta. Among fish, one of the most complex systems serving the function of the placenta is the embryonal trophotaenia/ovarian luminal epithelium of the goodeid fishes. For a better understanding of this feature and others of this group of fishes, high-quality genomic resources are essential. We have sequenced the genome of the darkedged splitfin, Girardinichthys multiradiatus. The assembly is chromosome level and includes the X and Y Chromosomes. A large male-specific region on the Y was identified covering 80% of Chromosome 20, allowing some first inferences on the recent origin and a candidate male sex determining gene. Genome-wide transcriptomics uncovered sex-specific differences in brain gene expression with an enrichment for neurosteroidogenesis and testis genes in males. The expression signatures of the splitfin embryonal and maternal placenta showed overlap with homologous tissues including human placenta, the ovarian follicle epithelium of matrotrophic poeciliid fish species and the brood pouch epithelium of the seahorse. Our comparative analyses on the evolution of embryonal and maternal placenta indicate that the evolutionary novelty of maternal provisioning development repeatedly made use of genes that already had the same function in other tissues. In this way, preexisting modules are assembled and repurposed to provide the molecular changes for this novel trait.
Published: 2022

27. Inactivation of the Anti-Müllerian Hormone Receptor Type 2 (amhrII) Gene in Northern Pike (Esox lucius) Results in Male-To-Female Sex Reversal

Author: Qiaowei Pan, Amaury Herpin, and Yann Guiguen
Subjects: Embryology, Endocrinology, Diabetes and Metabolism, Developmental Biology
Abstract: Background: The anti-müllerian hormone (Amh) pathway is crucial for sexual development in teleosts. A male-specific duplicate of anti-müllerian hormone (amhby) was previously identified as the northern pike (Esox lucius) master sex determination gene. However, the role of its putative cognate receptor, i.e., the anti-müllerian hormone receptor type 2 (amhrII) was unclear in this species. Objective: Here, we investigated the role of amhrII during sexual development of northern pike. Method: We generated stable mutants with deletions in exon 9 of amhrII, inactivating the AmhrII protein using a CRISPR-Cas9-mediated gene knockout strategy. Result: The inactivation of amhrII in northern pike results in a high level of male-to-female sex reversal. Conclusion: This result demonstrates that amhrII is necessary for male sexual development in northern pike and supports the idea that AmhrII is a conserved regulator of the teleosts sex differentiation network.
Published: 2022

28. Development of a polymerase chain reaction (PCR)-based genetic sex identification method in the chub mackerel Scomber japonicus and blue mackerel S. australasicus

Author: Reoto Tani, Tetsuro Morita, Christophe Klopp, Yann Guiguen, Ryosuke Yazawa, Marine Milhes, Wataru Kawamura, Goro Yoshizaki, Tokyo University of Marine Science and Technology (TUMSAT), Plateforme Bio-Informatique - Génotoul, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse)
Subjects: Broodstock management, Pool-seq, [SDV]Life Sciences [q-bio], Molecular sexing, Mackerel, Zoology, Sexing, Broodstock, Aquatic Science, 03 medical and health sciences, Blue mackerel S. australasicus, Chub mackerel, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, 14. Life underwater, 030304 developmental biology, Scomber, 0303 health sciences, biology, [SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, 04 agricultural and veterinary sciences, Chub mackerel Scomber japonicus, biology.organism_classification, Sexual dimorphism, 040102 fisheries, 0401 agriculture, forestry, and fisheries, Heterogametic sex, Sex ratio
Abstract: International audience; Chub mackerel Scomber japonicus and blue mackerel S. australasicus have become important aquaculture target species in Japan. For an efficient and stable aquaculture production of mackerels, it is desirable to work with a female-biased broodstock and thus to be able to manage precisely their sex ratio. As these two mackerel species do not have any external sexual dimorphism, direct biopsy of the gonads or measurement of sex hormone plasma levels is used in research to determine their phenotypic sex. However, these methods are associated with handling stress that results in gonadal atresia. Besides, it is difficult to identify sex using these methods in immature individuals. Therefore, genetic sexing would be desirable in these species to overcome these problems. In this study, we developed molecular sex identification tools for both chub and blue mackerels using sex-specific single-nucleotide variations (SNVs) identified by pool-sequencing (pool-seq) analyses. Genomic DNA was isolated from 30 males and females, in each species, and sequenced as pooled samples. Results of these pool-seq analyses identified a clear XX/XY male heterogametic sex-determination system in blue mackerel and a ZZ/ZW female heterogametic system in chub mackerel. Using this pool-seq information, we designed primer sets for genetic sex identification in both species. Results demonstrated that these primer sets are robust and accurate in assessing the genotypic sex of both blue and chub mackerels (accuracy > 99.5% in the chub, and > 94.5% in the blue mackerel) in various geographical samples of different ages. This method can now be applied for the efficient management of sex ratios in both mackerel aquaculture populations and wild-caught animals for fisheries management.
Published: 2021

29. Characterization of the sex determining region of channel catfish (Ictalurus punctatus) and development of a sex-genotyping test

Author: Ming Wen, Qiaowei Pan, Wes Larson, Camille Eché, and Yann Guiguen
Subjects: Male, Ictaluridae, Genome, Genotype, Genetic Linkage, Y Chromosome, Genetics, Animals, Female, General Medicine
Abstract: Channel catfish is an important species for aquaculture that exhibits a sexually dimorphic growth in favor of males. Genetic sexing and development of sex markers are crucial for the early identification of sex and of particular genotypes (YY males) for the production of all-male population in channel catfish aquaculture. In this study, we sequenced genomic DNA from pools of males and pools of females to better characterize the sex determining region (SDR) of channel catfish and to develop sex-specific markers for genetic sexing. Performing comparative analyses on male and female pooled genomic reads, we identified a large SDR (∼8.3 Mb) in the middle of channel catfish linkage group 4 (LG04). This non-recombining SDR contains a high-density of male-specific (Y chromosome) fixed single nucleotide polymorphisms (SNPs) along with ∼ 185 kb male-specific insertions or deletions. This SDR contains 95 annotated protein-encoding genes, including the recently reported putative channel catfish master sex determining (MSD) gene, breast cancer anti-estrogen resistance protein 1 (bcar1), located at one edge of the SDR. No sex-specific SNPs and/or indels were found in the coding sequence of bcar1, but one male-specific SNP was identified in its first intron. Based on this genomic information, we developed a PCR-based sex-specific genetic test. Genotyping results confirmed strong linkage between phenotypic sexes and the identified SDR in channel catfish. Our results confirm, using a Pool-Seq approach, that channel catfish is male heterogametic (XX-XY) with a large SDR on the LG04 sex chromosome. Furthermore, our genotyping primers can be used to identify XX, XY, and YY fish that will facilitate future research on sex determination and aquaculture applications in channel catfish.
Published: 2022

30. Primordial Germ Cell Migration and Histological and Molecular Characterization of Gonadal Differentiation in Pachón Cavefish Astyanax mexicanus

Author: Amaury Herpin, Elodie Jouanno, Violette Thermes, Adèle Branthonne, Séverine Beille, Sylvie Rétaux, Boudjema Imarazene, Yann Guiguen, and Manon Thomas
Subjects: 0106 biological sciences, endocrine system, 0303 health sciences, Embryology, Sexual differentiation, Gonad, urogenital system, 010604 marine biology & hydrobiology, Endocrinology, Diabetes and Metabolism, Cavefish, Epiboly, Biology, 01 natural sciences, Cell biology, Gene expression profiling, 03 medical and health sciences, medicine.anatomical_structure, Neurula, medicine, Development of the gonads, Germ cell, 030304 developmental biology, Developmental Biology
Abstract: The genetic regulatory network governing vertebrate gonadal differentiation appears less conserved than previously thought. Here, we investigated the gonadal development of Astyanax mexicanus Pachón cavefish by looking at primordial germ cells (PGCs) migration and proliferation, gonad histology, and gene expression patterns. We showed that PGCs are first detected at the 80% epiboly stage and then reach the gonadal primordium at 1 day post-fertilization (dpf). However, in contrast to the generally described absence of PGCs proliferation during their migration phase, PGCs number in cavefish doubles between early neurula and 8–9 somites stages. Combining both gonadal histology and vasa (germ cell marker) expression patterns, we observed that ovarian and testicular differentiation occurs around 65 dpf in females and 90 dpf in males, respectively, with an important inter-individual variability. The expression patterns of dmrt1, gsdf, and amh revealed a conserved predominant male expression during cavefish gonadal development, but none of the ovarian differentiation genes, i. e., foxl2a, cyp19a1a, and wnt4b displayed an early sexually dimorphic expression, and surprisingly all these genes exhibited predominant expression in adult testes. Altogether, our results lay the foundation for further research on sex determination and differentiation in A. mexicanus and contribute to the emerging picture that the vertebrate sex differentiation downstream regulatory network is less conserved than previously thought, at least in teleost fishes.
Published: 2020

31. A supernumerary 'B-sex' chromosome drives male sex determination in the Pachón cavefish, Astyanax mexicanus

Author: Séverine Beille, Sylvie Rétaux, John H. Postlethwait, Claire Kuchly, Hugues Parrinello, Amaury Herpin, Tomáš Pavlica, Ahmed Al-Rikabi, Christophe Klopp, Cécile Donnadieu, Jorge Torres-Paz, Manfred Schartl, Lisa Gil, Thomas Liehr, Joerg Bohlen, Adrien Castinel, Romain Feron, Yann Guiguen, Céline Lopez-Roques, Margot Zahm, Cédric Cabau, Boudjema Imarazene, Frédéric Veyrunes, Thomas D. Mueller, Elodie Jouanno, Alexandr Sember, Kang Du, Sergey A. Simanovsky, Qiaowei Pan, Julie Perez, Laurent Journot, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des Neurosciences Paris-Saclay (NeuroPSI), Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Texas State University, Université de Lausanne = University of Lausanne (UNIL), Swiss Institute of Bioinformatics [Lausanne] (SIB), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génomique Fonctionnelle (IGF), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Institute of Animal Physiology and Genetics of the Czech Academy of Sciences (IAPG / CAS), Czech Academy of Sciences [Prague] (CAS), Charles University [Prague] (CU), Jena University Hospital [Jena], A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences [Moscow] (RAS), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), University of Würzburg = Universität Würzburg, University of Oregon [Eugene], This project was supported by funds from the 'Agence Nationale de la Recherche' (ANR/DFG, PhyloSex project, 2014-2016) to Y.G. and M.S. S.R. was supported by grants from an Equipe FRM (Fondation pour la Recherche Médicale, DEQ20150331745) and MITI CNRS (Mission pour les Initiatives Transverses et Interdisciplinaires). J.H.P. was supported by an NIH grant (R35 GM139635). Sequencing was supported by France Génomique as part of an 'Investissement d’avenir' program managed by ANR (contract ANR-10-INBS-09) and by the GET-PACBIO program (Programme opérationnel FEDER-FSE MIDI-PYRENEES ET GARONNE 2014-2020). The CytoEvol platform at ISEM was supported by the Labex CeMEB. J.B., T.P., and A.S. were supported by RVO: 67985904 of IAPG CAS, Liběchov. T.P. was supported by the projects of the Czech Ministry of Education (SVV 260571/2021). S.A.S. was supported by the Russian Foundation for Basic Research (RFBR) (18-34-00638). B.I.’s PhD fellowship was supported by the Doctoral School of Ecology, Geosciences, Agronomy, Nutrition of the University of Rennes 1 and INRAE. We are grateful to the genotoul bioinformatics platform Toulouse Occitanie (Bioinfo Genotoul, https://doi.org/10.15454/1.5572369328961167E12) for providing help, computing, and storage resources. Funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript., ANR-13-ISV7-0005,PhyloSex,Evolution des déterminants majeurs du sexe chez les poissons.(2013), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), University of Lausanne (UNIL), Université de Lausanne (UNIL), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Guiguen, Yann, Blanc – Accords bilatéraux 2013 - Evolution des déterminants majeurs du sexe chez les poissons. - - PhyloSex2013 - ANR-13-ISV7-0005 - Blanc – Accords bilatéraux 2013 - VALID, and Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID
Subjects: Male, [SDV]Life Sciences [q-bio], Male sex determination, sex determination, Cavefish, B chromosome, Biology, Genome, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0302 clinical medicine, Animals, gonads, Gene, genome, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, 0303 health sciences, Sexual differentiation, Characidae, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], sex chromosomes, Chromosome, Sex reversal, Biological Evolution, [SDV] Life Sciences [q-bio], Caves, cavefish, gdf6, sex differentiation, Female, General Agricultural and Biological Sciences, 030217 neurology & neurosurgery
Abstract: Sex chromosomes are generally derived from a pair of classical type-A chromosomes, and relatively few alternative models have been proposed up to now.(1,2) B chromosomes (Bs) are supernumerary and dispensable chromosomes with non-Mendelian inheritance found in many plant and animal species(3,4) that have often been considered as selfish genetic elements that behave as genome parasites.(5,6) The observation that in some species Bs can be either restricted or predominant in one sex(7–14) raised the interesting hypothesis that Bs could play a role in sex determination.(15) The characterization of putative B master sex-determining (MSD) genes, however, has not yet been provided to support this hypothesis. Here, in Astyanax mexicanus cavefish originating from Pachón cave, we show that Bs are strongly male predominant. Based on a high-quality genome assembly of a B-carrying male, we characterized the Pachón cavefish B sequence and found that it contains two duplicated loci of the putative MSD gene growth differentiation factor 6b (gdf6b). Supporting its role as an MSD gene, we found that the Pachón cavefish gdf6b gene is expressed specifically in differentiating male gonads, and that its knockout induces male-to-female sex reversal in B-carrying males. This demonstrates that gdf6b is necessary for triggering male sex determination in Pachón cavefish. Altogether these results bring multiple and independent lines of evidence supporting the conclusion that the Pachón cavefish B is a “B-sex” chromosome that contains duplicated copies of the gdf6b gene, which can promote male sex determination in this species.
Published: 2021

32. The bowfin genome illuminates the developmental evolution of ray-finned fishes

Author: Hugues Roest Crollius, Dustin J. Wcisel, Matthew P. Harris, Brett Racicot, Elise Parey, Jérôme Montfort, Solomon R. David, Quenton C. Fontenot, Kazuhiko Kawasaki, Allyse M. Ferrara, Yann Guiguen, Tatsuya Ota, Mauricio Losilla, Ingo Braasch, M. Brent Hawkins, Olivia E Fitch, Romain Feron, Andrew W. Thompson, Marine Milhes, Amy R. McCune, Qiaowei Pan, Emily Funk, Jeffrey A. Yoder, Camille Berthelot, Alex Dornburg, Alexandra Louis, Kevin L. Childs, Michigan State University [East Lansing], Michigan State University System, Harvard Medical School [Boston] (HMS), Boston Children's Hospital, Harvard University [Cambridge], Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC), Graduate University for Advanced Studies [Hayama] (SOKENDAI), Pennsylvania State University (Penn State), Penn State System, Cornell University [New York], University of California [Davis] (UC Davis), University of California, University of Lausanne (UNIL), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Nicholls State University, University of North Carolina [Charlotte] (UNC), We are thankful for grant support from NIH R01OD011116 (I.B.), NSF DDIG DEB-1600920 (M.B.H.), NSF IOS-1755242 (A.D.) and NSF IOS-1755330 (J.A.Y.). Parts of this work have been supported by the Agence Nationale de la Recherche, France (ANR GenoFish project, 2016-2021, ANR-16-CE12-0035) to H.R.C., C.B., E.P., A.L. and Y.G. E.P., C.B. and H.R.C. received support under the program ‘Investissements d’Avenir’ launched by the French government and implemented by ANR with references ANR–10–LABX–54 MEMOLIFE and ANR-10-IDEX-0001-02 PSL* Université Paris. We thank F. Feng for access to Oneida Lake bowfin spawning habitats, the Bauer Core at Harvard University for sequencing fin transcriptomes and M. Gundappa (FISH & LINES) for species illustrations. Species silhouettes were obtained from http://PhyloPic.org. We are exceedingly grateful to the late J.L. Gómez-Skarmeta for his guidance on establishing ATAC-seq in holosteans., ANR-16-CE12-0035,GenoFish,Evolution des génes et des génomes après duplication compléte(2016), ANR-10-LABX-0054,MEMOLIFE,Memory in living systems: an integrated approach(2010), ANR-10-IDEX-0001,PSL,Paris Sciences et Lettres(2010), Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3)
Subjects: Scale (anatomy), [SDV]Life Sciences [q-bio], Sequence assembly, Vertebrate Biology, Genome, Article, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, biology.animal, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Developmental biology, Genetics, Animals, 14. Life underwater, Skates, Fish, Bowfin, ComputingMilieux_MISCELLANEOUS, Amia calva, 030304 developmental biology, 0303 health sciences, Phylogenetic tree, biology, Whole Genome Sequencing, Fishes, Vertebrate, Genomics, biology.organism_classification, Biological Evolution, Chromatin, Body plan, [SDV.BDD.EO]Life Sciences [q-bio]/Development Biology/Embryology and Organogenesis, Amiidae, Evolutionary biology, Zoology, 030217 neurology & neurosurgery
Abstract: The bowfin (Amia calva) is a ray-finned fish that possesses a unique suite of ancestral and derived phenotypes, which are key to understanding vertebrate evolution. The phylogenetic position of bowfin as a representative of neopterygian fishes, its archetypical body plan and its unduplicated and slowly evolving genome make bowfin a central species for the genomic exploration of ray-finned fishes. Here we present a chromosome-level genome assembly for bowfin that enables gene-order analyses, settling long-debated neopterygian phylogenetic relationships. We examine chromatin accessibility and gene expression through bowfin development to investigate the evolution of immune, scale, respiratory and fin skeletal systems and identify hundreds of gene-regulatory loci conserved across vertebrates. These resources connect developmental evolution among bony fishes, further highlighting the bowfin’s importance for illuminating vertebrate biology and diversity in the genomic era., Analysis of a chromosome-level bowfin genome assembly sheds light into neopterygian fish evolution. Chromatin accessibility and gene expression profiling provides insight into bowfin embryonic development.
Published: 2021

33. A brief review of vertebrate sex evolution with a pledge for integrative research: towards ‘ sexomics ’

Author: Yann Guiguen, Blanche Capel, Nicole Valenzuela, Qi Zhou, Michail Rovatsos, Manfred Schartl, Ben J. Evans, Matthias Stöck, Frédéric Veyrunes, Lukáš Kratochvíl, Tony Gamble, Alexander Suh, Heiner Kuhl, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Hiroshima University, Charles University [Prague] (CU), Department of Computing and Software (McMaster University), McMaster University [Hamilton, Ontario], University of East Anglia [Norwich] (UEA), Uppsala University, Iowa State University (ISU), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Huzhou University [Zhejiang], University of Vienna [Vienna], Marquette University [Milwaukee], Duke University Medical Center, University of Würzburg, Texas State University, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), M.St. and M.Sc. were in part supported by COFASP/ERANET (STURGEoNOMICS) by the German Federal Ministry of Food and Agriculture through the Federal Office for Agriculture and Food (grant nos. 2816ERA04G, and 2816ERA05G), M.Sc. was also funded by the German Research Foundation (DFG), grant nos. SCHA408/14-1 und 15-1, H.K. was funded by the German Research Foundation (DFG), grant no. KU 3596/1-1 (project no. 324050651), L.K. and M.R. were supported by the Czech Science Foundation (project no. 17-22604S), B.J.E. was supported by the Natural Sciences and Engineering Research Council of Canada (RGPIN-2017-05770), A.S. was supported by the Swedish Research Council Vetenskapsrådet (grant nos. 2016-05139547 and 2020-04436), N.V. was supported by a grant from the National Science Foundation (grant no. IOS-1555999), B.C. was supported by a grant from the National Science Foundation (grant no. IOS-1256675), Q.Z. is supported by a European Research Council Starting Grant (grant no. 677696)., and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)
Subjects: Male, 0106 biological sciences, 0301 basic medicine, Sex Differentiation, media_common.quotation_subject, sex determination, Genomics, Fertility, [SDV.BID]Life Sciences [q-bio]/Biodiversity, 010603 evolutionary biology, 01 natural sciences, Genome, General Biochemistry, Genetics and Molecular Biology, [SDV.BDLR.RS]Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction, Evolution, Molecular, Evolutionsbiologi, reproduction, 03 medical and health sciences, Genome Size, biology.animal, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Testis, evolution, genomics, Animals, Sex organ, Clade, Review Articles, [SDV.BDD.GAM]Life Sciences [q-bio]/Development Biology/Gametogenesis, media_common, Evolutionary Biology, Dosage compensation, Sexual differentiation, biology, sex chromosomes, Ovary, Vertebrate, Articles, Sex Determination Processes, Biological Evolution, 030104 developmental biology, Evolutionary biology, Female, General Agricultural and Biological Sciences, vertebrates
Abstract: Triggers and biological processes controlling male or female gonadal differentiation vary in vertebrates, with sex determination (SD) governed by environmental factors or simple to complex genetic mechanisms that evolved repeatedly and independently in various groups. Here, we review sex evolution across major clades of vertebrates with information on SD, sexual development and reproductive modes. We offer an up-to-date review of divergence times, species diversity, genomic resources, genome size, occurrence and nature of polyploids, SD systems, sex chromosomes, SD genes, dosage compensation and sex-biased gene expression. Advances in sequencing technologies now enable us to study the evolution of SD at broader evolutionary scales, and we now hope to pursue asexomicsintegrative research initiative across vertebrates. The vertebratesexomecomprises interdisciplinary and integrated information on sexual differentiation, development and reproduction at all biological levels, from genomes, transcriptomes and proteomes, to the organs involved in sexual and sex-specific processes, including gonads, secondary sex organs and those with transcriptional sex-bias. Thesexomealso includes ontogenetic and behavioural aspects of sexual differentiation, including malfunction and impairment of SD, sexual differentiation and fertility. Starting from data generated by high-throughput approaches, we encourage others to contribute expertise to building understanding of thesexomesof many key vertebrate species.This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)’.
Published: 2021

34. Allelic diversification after transposable element exaptation promoted gsdf as the master sex determining gene of sablefish

Author: Giles Goetz, Amaury Herpin, Alexandra Depincé, Yann Guiguen, Manfred Schartl, J. Adam Luckenbach, Edward S. Hayman, Krista M. Nichols, Aurélie Hua-Van, Anna Octavera, Julien Bobe, Goro Yoshizaki, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan University [Changsha] (HNU), Biocenter University of Würzburg = Biozentrum der Universität Würzburg, Julius-Maximilians-Universität Würzburg [Wurtzbourg, Allemagne] (JMU), The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, Evolution, génomes, comportement et écologie (EGCE), Institut de Recherche pour le Développement (IRD)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA), Tokyo University of Marine Science and Technology (TUMSAT), University of Washington [Seattle], Center for Reproductive Biology, Washington State University (WSU), and ANR-16-COFA-0004,AquaCrispr,Optimization of the CRISPR/Cas9 knock-in technology and application in salmon and trout(2016)
Subjects: Male, Transposable element, [SDV]Life Sciences [q-bio], Locus (genetics), Biology, Y chromosome, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, Y Chromosome, Genetics, Animals, 14. Life underwater, Allele, Gene, Genetics (clinical), ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Research, Promoter, Genomics, Exaptation, Sex Determination Processes, Anoplopoma fimbria, Evolutionary biology, DNA Transposable Elements, 030217 neurology & neurosurgery, Heterogametic sex
Abstract: Concepts of evolutionary biology suggest that morphological change may occur by rare punctual but rather large changes, or by more steady and gradual transformations. It can therefore be asked whether genetic changes underlying morphological, physiological, and/or behavioral innovations during evolution occur in a punctual manner, whereby a single mutational event has prominent phenotypic consequences, or if many consecutive alterations in the DNA over longer time periods lead to phenotypic divergence. In the marine teleost, sablefish (Anoplopoma fimbria), complementary genomic and genetic studies led to the identification of a sex locus on the Y Chromosome. Further characterization of this locus resulted in identification of the transforming growth factor, beta receptor 1a (tgfbr1a) gene, gonadal somatic cell derived factor (gsdf), as the main candidate for fulfilling the master sex determining (MSD) function. The presence of different X and Y Chromosome copies of this gene indicated that the male heterogametic (XY) system of sex determination in sablefish arose by allelic diversification. The gsdfY gene has a spatio-temporal expression profile characteristic of a male MSD gene. We provide experimental evidence demonstrating a pivotal role of a transposable element (TE) for the divergent function of gsdfY. By insertion within the gsdfY promoter region, this TE generated allelic diversification by bringing cis-regulatory modules that led to transcriptional rewiring and thus creation of a new MSD gene. This points out, for the first time in the scenario of MSD gene evolution by allelic diversification, a single, punctual molecular event in the appearance of a new trigger for male development.
Published: 2021

35. A non-functional copy of the salmonid sex determining gene (sdY) is responsible for the 'apparent' XY females in Chinook salmon, Oncorhynchus tshawytscha

Author: Thomas Müller, Manfred Schartl, Kevin Williamson, R. Guyomard, Sylvain Bertho, Mariah H. Meek, Penny Swanson, Laurent Journot, Elodie Jouanno, Amaury Herpin, Yann Guiguen, Garrett J. McKinney, Julien Bobe, Hugues Parrinello, and Ayaka Yano
Subjects: Genetics, biology, Sex-determination system, Oncorhynchus, Missense mutation, Transfection, Asparagine, Isoleucine, biology.organism_classification, Gene, Heterogametic sex
Abstract: Many salmonids have a male heterogametic (XX/XY) sex determination system, and they are supposed to have a conserved master sex determining gene (sdY), that interacts at the protein level with Foxl2 leading to the blockage of the synergistic induction of Foxl2 and Nr5a1 of the cyp19a1a promoter. However, this hypothesis of a conserved master sex determining role of sdY in salmonids is still challenged by a few exceptions, one of them being the presence of some naturally occurring “apparent” XY Chinook salmon females. Here we show that XY Chinook salmon females have a sdY gene (sdY-N183), which has one missense mutation leading to a substitution of a conserved isoleucine to an asparagine (SdY I183N). In contrast, Chinook salmon males have both a non-mutated sdY-I183 gene and the missense mutation sdY-N183 gene. The 3D model of SdY-N183 predicts that the I183N hydrophobic to hydrophilic amino acid change leads to a local modification of the β-sandwich structure of SdY. Using in vitro cell transfection assays we found that SdY-N183, like SdY-I183, is preferentially localized in the cytoplasm. However, compared to SdY-I183, SdY-N183 is more prone to degradation, its nuclear translocation by Foxl2 is reduced and SdY-N183 is unable to significantly repress the synergistic Foxl2/Nr5a1 induction of the cyp19a1a promoter. Altogether our results suggest that the sdY-N183 gene of XY Chinook females is a non-functional gene and that SdY-N183 is no longer able to promote testicular differentiation by impairing the synthesis of estrogens in the early differentiating gonads of wild Chinook salmon XY females.
Published: 2021

36. A nonfunctional copy of the salmonid sex-determining gene (sdY) is responsible for the 'apparent' XY females in Chinook salmon, Oncorhynchus tshawytscha

Author: Sylvain Bertho, Amaury Herpin, Elodie Jouanno, Ayaka Yano, Julien Bobe, Hugues Parrinello, Laurent Journot, René Guyomard, Thomas Muller, Penny Swanson, Garrett McKinney, Kevin Williamson, Mariah Meek, Manfred Schartl, Yann Guiguen, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Würzburg = Universität Würzburg, Physiological Chemistry, Biocenter, Institut de Génomique Fonctionnelle (IGF), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Julius-von-Sachs-Institute, Department of Molecular Plant Physiology and Biophysics, University of Würzburg, Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Oceanic and Atmospheric Administration (NOAA), Washington Department of Fish and Wildlife, Partenaires INRAE, Atreca, Inc., Michigan State University System, Texas State University, Scha408/12-1, 10-1, Deutsche Forschungsgemeinschaft, ANR-11-BSV7-0016,SDS,Rôle et évolution d'un possible déterminant majeur du sexe chez les Salmonidés.(2011), Guerineau, Nathalie C., and BLANC - Rôle et évolution d'un possible déterminant majeur du sexe chez les Salmonidés. - - SDS2011 - ANR-11-BSV7-0016 - BLANC - VALID
Subjects: sex reversal, Male, [SDV.BA] Life Sciences [q-bio]/Animal biology, [SDV]Life Sciences [q-bio], [SDV.BA]Life Sciences [q-bio]/Animal biology, sex determination, [SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, Sex Determination Processes, [SDV] Life Sciences [q-bio], Salmon, salmonids, Testis, Genetics, Animals, Female, sdY, XY females, Gonads, Molecular Biology, [SDV.BDLR] Life Sciences [q-bio]/Reproductive Biology, Genetics (clinical), Salmonidae
Abstract: Many salmonids have a male heterogametic (XX/XY) sex determination system, and they are supposed to have a conserved master sex-determining gene (sdY) that interacts at the protein level with Foxl2 leading to the blockage of the synergistic induction of Foxl2 and Nr5a1 of the cyp19a1a promoter. However, this hypothesis of a conserved master sex-determining role of sdY in salmonids is challenged by a few exceptions, one of them being the presence of naturally occurring “apparent” XY Chinook salmon, Oncorhynchus tshawytscha, females. Here, we show that some XY Chinook salmon females have a sdY gene (sdY-N183), with 1 missense mutation leading to a substitution of a conserved isoleucine to an asparagine (I183N). In contrast, Chinook salmon males have both a nonmutated sdY-I183 gene and the missense mutation sdY-N183 gene. The 3-dimensional model of SdY-I183N predicts that the I183N hydrophobic to hydrophilic amino acid change leads to a modification in the SdY β-sandwich structure. Using in vitro cell transfection assays, we found that SdY-I183N, like the wild-type SdY, is preferentially localized in the cytoplasm. However, compared to wild-type SdY, SdY-I183N is more prone to degradation, its nuclear translocation by Foxl2 is reduced, and SdY-I183N is unable to significantly repress the synergistic Foxl2/Nr5a1 induction of the cyp19a1a promoter. Altogether, our results suggest that the sdY-N183 gene of XY Chinook females is nonfunctional and that SdY-I183N is no longer able to promote testicular differentiation by impairing the synthesis of estrogens in the early differentiating gonads of wild Chinook salmon XY females.
Published: 2021

37. Evolution of master sex determiners: TGF-β signalling pathways at regulatory crossroads

Author: Manfred Schartl, Amaury Herpin, Yann Guiguen, Qiaowei Pan, Alexandra Depincé, Tomas Kay, Mateus Contar Adolfi, Department of Ecology and Evolution [Lausanne], Université de Lausanne (UNIL), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biocenter University of Würzburg = Biozentrum der Universität Würzburg, Julius-Maximilians-Universität Würzburg [Wurtzbourg, Allemagne] (JMU), The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan University [Changsha] (HNU), This work was supported by the AquaCRISPR (ANR-16-COFA-0004-01), the TUNESAL (HAVBRUKR Research Council of Norway, project 301602), and 111 (China, grant no. D20007) projects to A.H. Q.P. and T.K. are supported by the University of Lausanne and Q.P. is supported by a grant from the Swiss NSF (310030B_176406) to Laurent Keller., and ANR-16-COFA-0004,AquaCrispr,Optimization of the CRISPR/Cas9 knock-in technology and application in salmon and trout(2016)
Subjects: 0301 basic medicine, [SDV]Life Sciences [q-bio], Gene regulatory network, sex determination, General Biochemistry, Genetics and Molecular Biology, Evolution, Molecular, 03 medical and health sciences, sex-determining genes, 0302 clinical medicine, Transforming Growth Factor beta, biology.animal, evolution, Animals, Gene Regulatory Networks, Gene, Transcription factor, Phylogeny, fish, Sex Chromosomes, biology, Vertebrate, Chromosome, Articles, Sex Determination Processes, Hedgehog signaling pathway, 030104 developmental biology, Evolutionary biology, GDF6, Vertebrates, %22">Fish , General Agricultural and Biological Sciences, 030217 neurology & neurosurgery, Signal Transduction
Abstract: To date, more than 20 different vertebrate master sex-determining genes have been identified on different sex chromosomes of mammals, birds, frogs and fish. Interestingly, six of these genes are transcription factors ( Dmrt1 - or Sox3 - related) and 13 others belong to the TGF-β signalling pathway ( Amh , Amhr2 , Bmpr1b , Gsdf and Gdf6 ). This pattern suggests that only a limited group of factors/signalling pathways are prone to become top regulators again and again. Although being clearly a subordinate member of the sex-regulatory network in mammals, the TGF-β signalling pathway made it to the top recurrently and independently. Facing this rolling wave of TGF-β signalling pathways, this review will decipher how the TGF-β signalling pathways cope with the canonical sex gene regulatory network and challenge the current evolutionary concepts accounting for the diversity of sex-determining mechanisms. This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)’.
Published: 2021

38. Lessons from an unusual vertebrate sex-determining gene

Author: Amaury Herpin, Manfred Schartl, Yann Guiguen, Sylvain Bertho, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biocenter University of Würzburg = Biozentrum der Universität Würzburg, Julius-Maximilians-Universität Würzburg [Wurtzbourg, Allemagne] (JMU), State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan University [Changsha] (HNU), The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, Part of this work was supported by Agence Nationale de la Recherche (ANR) grant no. ANR ANR-11-BSV7-0016 (SDS project) and grants to M.S. by the Deutsche Forschungsgemeinschaft (Scha408/12-1, 10-1), and ANR-11-BSV7-0016,SDS,Rôle et évolution d'un possible déterminant majeur du sexe chez les Salmonidés.(2011)
Subjects: 0106 biological sciences, Sex Differentiation, [SDV]Life Sciences [q-bio], sex determination, Locus (genetics), Y chromosome, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, biology.animal, salmonids, evolution, Animals, sdY, Gene, 030304 developmental biology, 0303 health sciences, Sexual differentiation, Autosome, biology, sex chromosomes, Chromosome, Vertebrate, Articles, Sex Determination Processes, Sexual dimorphism, Evolutionary biology, General Agricultural and Biological Sciences, Salmonidae
Abstract: So far, very few sex-determining genes have been identified in vertebrates and most of them, the so-called ‘usual suspects’, evolved from genes which fulfil essential functions during sexual development and are thus already tightly linked to the process that they now govern. The single exception to this ‘usual suspects’ rule in vertebrates so far is the conserved salmonid sex-determining gene, sdY (sexually dimorphic on the Y chromosome), that evolved from a gene known to be involved in regulation of the immune response. It is contained in a jumping sex locus that has been transposed or translocated into different ancestral autosomes during the evolution of salmonids. This special feature of sdY , i.e. being inserted in a ‘jumping sex locus’, could explain how salmonid sex chromosomes remain young and undifferentiated to escape degeneration. Recent knowledge on the mechanism of action of sdY demonstrates that it triggers its sex-determining action by deregulating oestrogen synthesis that is a conserved and crucial pathway for ovarian differentiation in vertebrates. This result suggests that sdY has evolved to cope with a pre-existing sex differentiation regulatory network. Therefore, ‘limited options’ for the emergence of new master sex-determining genes could be more constrained by their need to tightly interact with a conserved sex differentiation regulatory network rather than by being themselves ‘usual suspects’, already inside this sex regulatory network. This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)’.
Published: 2021

39. Genome biology of the darkedged splitfin

Author: Kang, Du, Martin, Pippel, Susanne, Kneitz, Romain, Feron, Irene, da Cruz, Sylke, Winkler, Brigitta, Wilde, Edgar G, Avila Luna, Gene, Myers, Yann, Guiguen, Constantino, Macias Garcia, and Manfred, Schartl
Subjects: Male, Cyprinodontiformes, Genome, Sex Chromosomes, Pregnancy, Animals, Female, Biology, Placentation
Abstract: Viviparity evolved independently about 150 times in vertebrates and more than 20 times in fish. Several lineages added to the protection of the embryo inside the body of the mother, the provisioning of nutrients, and physiological exchange. This often led to the evolution of a placenta. Among fish, one of the most complex systems serving the function of the placenta is the embryonal trophotaenia/ovarian luminal epithelium of the goodeid fishes. For a better understanding of this feature and others of this group of fishes, high-quality genomic resources are essential. We have sequenced the genome of the darkedged splitfin
Published: 2021

40. Development of a polymerase chain reaction (PCR) based genetic sex identification method in the chub mackerel Scomber japonicus and blue mackerel S. australasicus

Author: Christophe Klopp, Marine Milhes, and Yann Guiguen
Subjects: Aquatic Science
Published: 2022

41. Correction to: Development of a polymerase chain reaction (PCR)-based genetic sex identification method in the chub mackerel Scomber japonicus and blue mackerel S. australasicus

Author: Reoto Tani, Wataru Kawamura, Tetsuro Morita, Christophe Klopp, Marine Milhes, Yann Guiguen, Goro Yoshizaki, and Ryosuke Yazawa
Subjects: Aquatic Science
Abstract: The original article has been corrected.
Published: 2022

42. Primordial germ cell migration and histological and molecular characterization of gonadal differentiation in Pachón Cavefish Astyanax mexicanus

Author: Boudjema, Imarazene, Séverine, Beille, Elodie, Jouanno, Adéle, Branthonne, Violette, Thermes, Manon, Thomas, Amaury, Herpin, Sylvie, Rétaux, Yann, Guiguen, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des Neurosciences Paris-Saclay (NeuroPSI), Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and French National Research Agency (ANR)'Equipe FRM' grant from the Fondation pour la Recherche Medicale (DEQ20150331745)Doctoral School of Ecology, Geosciences, Agronomy, Nutrition of the university of Rennes 1 INRAE
Subjects: endocrine system, Histology, urogenital system, Astyanax mexicanus, [SDV]Life Sciences [q-bio], embryonic structures, Testis, Ovary, PGCs, vasa, nanos, Gene expression profiling
Abstract: International audience; The genetic regulatory network governing vertebrate gonadal differentiation appears less conserved than previously thought. Here, we investigated the gonadal development of Astyanax mexicanus Pachón cavefish by looking at primordial germ cells (PGCs) migration and proliferation, gonad histology, and gene expression patterns. We showed that PGCs are first detected at the 80% epiboly stage and then reach the gonadal primordium at 1 day post-fertilization (dpf). However, in contrast to the generally described absence of PGCs proliferation during their migration phase, PGCs number in cavefish doubles between early neurula and 8-9 somites stages. Combining both gonadal histology and vasa (germ cell marker) expression patterns, we observed that ovarian and testicular differentiation occurs around 65 dpf in females and 90 dpf in males, respectively, with an important inter-individual variability. The expression patterns of dmrt1, gsdf, and amh revealed a conserved predominant male expression during cavefish gonadal development, but none of the ovarian differentiation genes, i. e., foxl2a, cyp19a1a, and wnt4b displayed an early sexually dimorphic expression, and surprisingly all these genes exhibited predominant expression in adult testes. Altogether, our results lay the foundation for further research on sex determination and differentiation in A. mexicanus and contribute to the emerging picture that the vertebrate sex differentiation downstream regulatory network is less conserved than previously thought, at least in teleost fishes.
Published: 2021

43. RADSex: A computational workflow to study sex determination using restriction site-associated DNA sequencing data

Author: Ørjan Karlsen, Susanne Kneitz, Rafael Henrique Nóbrega, Qiaowei Pan, Masatoshi Nakamoto, Elodie Jouanno, Thomas Desvignes, John H. Postlethwait, Ato Takanashi, Braedan M. McCluskey, Amaury Herpin, Matthias Stöck, Alvaro S. Roco, Boudjema Imarazene, Manfred Schartl, Zhongwei Wang, Mateus Contar Adolfi, Romain Feron, Catherine Wilson, Hugues Parrinello, Takashi Sakamoto, Ingo Braasch, Christophe Klopp, Marcos Antonio de Oliveira, Frederick W. Goetz, Harry William Detrich, Robert M. Waterhouse, Ming Wen, Yann Guiguen, Mari Kawaguchi, Angel Amores, Laurent Journot, Anna Wargelius, Verena A. Kottler, Kang Du, Jennifer L. Anderson, IINRAE, Univ Lausanne, Swiss Inst Bioinformat, Hunan Normal Univ, Uppsala Univ, Univ Montpellier, INRAE, Univ Wurzburg, Texas State Univ, Univ Oregon, NOAA, Sophia Univ, Northeastern Univ, Universidade Estadual Paulista (Unesp), Tokyo Univ Marine Sci & Technol, Inst Marine Res, Chinese Acad Sci, IGB, Michigan State Univ, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Ecology and Evolution, University of Lausanne, Université de Lausanne (UNIL), Swiss Institute of Bioinformatics [Lausanne] (SIB), State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan University [Changsha] (HNU), Department of Systematic Biology [Uppsala], Evolutionary Biology Centre (EBC), Uppsala University-Uppsala University, Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Physiological Chemistry, Biocenter, University of Würzburg = Universität Würzburg, The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, Institute of Neuroscience, University of Oregon, Eugene, University of Oregon [Eugene], Tokyo University of Marine Science and Technology (TUMSAT), Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Oceanic and Atmospheric Administration (NOAA), Sophia University, Tokyo, Faculty of Science and Technology, Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP), Institute of Marine Research [Bergen] (IMR), University of Bergen (UiB), Institute of Hydrobiology [Wuhan], Chinese Academy of Sciences [Beijing] (CAS), Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Integrative Biology, Michigan State University, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, This project was supported by funds from the 'Agence Nationale de la Recherche', the 'Deutsche Forschungsgemeinschaft' (ANR/DFG, PhyloSex project,2014-2016, SCHA 408/10-1, MS), the National Institutes of Health (USA) grant R01GM085318, JHP), and the National Science Foundation (USA) Office of Polar Programs (grants PLR-1247510 and PLR-1444167 to HWD and grant OPP-1543383 to JHP, TD, and HWD). The MGX core sequencing facility was supported by France Genomique National infrastructure, funded as part of 'Investissement d’avenir' program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-09). RF was partially supported by Swiss National Science Foundation grant PP00P3_170664 to RMW., ANR-13-ISV7-0005,PhyloSex,Evolution des déterminants majeurs du sexe chez les poissons.(2013), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Department of Ecology and Evolution [Lausanne], Institute of Neuroscience, University of Oregon, Eugene, Oregon, Department of Materials and Life Sciences, Sophia University [Tokyo], Department of Structural and Functional Biology, Department of Aquatic Marine Biosciences, Developmental Biochemistry, Biocenter, Julius-Maximilians-Universität Würzburg [Wurtzbourg, Allemagne] (JMU), and This project was supported by funds from the 'Agence Nationale de la Recherche', the 'Deutsche Forschungsgemeinschaft' (ANR/DFG, PhyloSex project, 2014-2016, SCHA 408/10-1, MS), the National Institutes of Health (USA) grants R01GM085318 and R35GM139635, JHP), and the National Science Foundation (USA) Office of Polar Programs (grants PLR-1247510 and PLR-1444167 to HWD and grant OPP-1543383 to JHP, TD, and HWD). The MGX core sequencing facility was supported by France Genomique National infrastructure, funded as part of 'Investissement d’avenir' program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-09). RF was partially supported by Swiss National Science Foundation grant PP00P3_170664 to RMW.
Subjects: 0106 biological sciences, 0301 basic medicine, Male, Sex Determination Analysis, Computer science, [SDV]Life Sciences [q-bio], sex determination, Locus (genetics), Computational biology, Biology, Y chromosome, 010603 evolutionary biology, 01 natural sciences, Computational workflow, DNA sequencing, Article, Workflow, 03 medical and health sciences, Sex-determination system, Genetics, Animals, Sequencing, RAD&#8208, Computational Biology, DNA, Female, Fishes/genetics, Sequence Analysis, DNA, Sex Chromosomes, Software, RAD-Sequencing, computational workflow, fish, visualization, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Visualization, 0303 health sciences, Fishes, Japanese Medaka, Sex determination, Restriction site, 030104 developmental biology, Fish, Identification (biology), Biotechnology
Abstract: Made available in DSpace on 2021-06-25T11:54:14Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-03-09 National Institute of Health (USA) Deutsche Forschungsgemeinschaft National Science Foundation (USA) Office of Polar Programs Agence Nationale de la Recherche Schweizerischer Nationalfonds zur Forderung der Wissenschaftlichen Forschung The study of sex determination and sex chromosome organization in nonmodel species has long been technically challenging, but new sequencing methodologies now enable precise and high-throughput identification of sex-specific genomic sequences. In particular, restriction site-associated DNA sequencing (RAD-Seq) is being extensively applied to explore sex determination systems in many plant and animal species. However, software specifically designed to search for and visualize sex-biased markers using RAD-Seq data is lacking. Here, we present RADSex, a computational analysis workflow designed to study the genetic basis of sex determination using RAD-Seq data. RADSex is simple to use, requires few computational resources, makes no prior assumptions about the type of sex-determination system or structure of the sex locus, and offers convenient visualization through a dedicated R package. To demonstrate the functionality of RADSex, we re-analysed a published data set of Japanese medaka, Oryzias latipes, where we uncovered a previously unknown Y chromosome polymorphism. We then used RADSex to analyse new RAD-Seq data sets from 15 fish species spanning multiple taxonomic orders. We identified the sex determination system and sex-specific markers in six of these species, five of which had no known sex-markers prior to this study. We show that RADSex greatly facilitates the study of sex determination systems in nonmodel species thanks to its speed of analyses, low resource usage, ease of application and visualization options. Furthermore, our analysis of new data sets from 15 species provides new insights on sex determination in fish. IINRAE, LPGP, Rennes, France Univ Lausanne, Dept Ecol & Evolut, Lausanne, Switzerland Swiss Inst Bioinformat, Lausanne, Switzerland Hunan Normal Univ, Coll Life Sci, State Key Lab Dev Biol Freshwater Fish, Changsha, Peoples R China Uppsala Univ, Dept Organismal Biol, Systemat Biol, Uppsala, Sweden Univ Montpellier, Inst Genom Fonct, INSERM, IGF,CNRS, Montpellier, France INRAE, Math & Informat Appl Toulouse, SIGENAE, Castanet Tolosan, France Univ Wurzburg, Physiol Chem, Bioctr, Wurzburg, Germany Texas State Univ, Xiphophorus Genet Stock Ctr, Dept Chem & Biochem, San Marcos, TX USA Univ Wurzburg, Dev Biochem, Bioctr, Wurzburg, Germany Univ Oregon, Inst Neurosci, Eugene, OR USA NOAA, Environm & Fisheries Sci Div, Northwest Fisheries Sci Ctr, Natl Marine Fisheries Serv, Seattle, WA USA Sophia Univ, Fac Sci & Technol, Dept Mat & Life Sci, Tokyo, Japan Northeastern Univ, Ctr Marine Sci, Dept Marine & Environm Sci, Nahant, MA 01908 USA Sao Paulo State Univ, Inst Biosci, Dept Struct & Funct Biol, Reprod & Mol Biol Grp, Botucatu, SP, Brazil Tokyo Univ Marine Sci & Technol, Dept Aquat Marine Biosci, Tokyo, Japan Inst Marine Res, Bergen, Norway Chinese Acad Sci, Inst Hydrobiol, Beijing, Peoples R China IGB, Leibniz Inst Freshwater Ecol & Inland Fishe, Berlin, Germany Michigan State Univ, Dept Integrat Biol, Ecol Evolut & Behav Program, E Lansing, MI 48824 USA Sao Paulo State Univ, Inst Biosci, Dept Struct & Funct Biol, Reprod & Mol Biol Grp, Botucatu, SP, Brazil National Institute of Health (USA): R01GM085318 National Institute of Health (USA): R35GM139635 Deutsche Forschungsgemeinschaft: SCHA 408/10-1 National Science Foundation (USA) Office of Polar Programs: OPP-1543383 National Science Foundation (USA) Office of Polar Programs: PLR-1247510 National Science Foundation (USA) Office of Polar Programs: PLR-1444167 Agence Nationale de la Recherche: SCHA 408/10-1 Agence Nationale de la Recherche: ANR-10-INBS-09 Schweizerischer Nationalfonds zur Forderung der Wissenschaftlichen Forschung: PP00P3_170664
Published: 2021

44. A Supernumerary 'B-Sex' Chromosome Drives Male Sex Determination in the Pachón Cavefish, Astyanax mexicanus

Author: Claire Kuchly, Adrien Castinel, Séverine Beille, Romain Feron, Yann Guiguen, Kang Du, Jorge Torres-Paz, Sylvie Rétaux, Alexandr Sember, Boudjema Imarazene, Margot Zham, Sergey A. Simanovsky, Cédric Cabau, Tomáš Pavlica, Joerg Bohlen, Qiaowei Pan, Cécile Donnadieu, Céline Lopez-Roques, John H. Postlethwait, Manfred Schartl, Elodie Jouanno, Julie Perez, Thomas Liehr, Frédéric Veyrunes, Hugues Parrinello, Lisa Gil, Ahmed Al-Rikabi, Christophe Klopp, Laurent Journot, Amaury Herpin, and Thomas D. Mueller
Subjects: Genetics, B chromosome, GDF6, Male sex determination, Cavefish, Chromosome, Sex reversal, Biology, Gene, Genome
Abstract: Sex chromosomes are generally derived from a pair of classical type-A chromosomes, and relatively few alternative models have been proposed up to now. B chromosomes (Bs) are supernumerary and dispensable chromosomes with non-Mendelian inheritance found in many plant and animal species, that have often been considered as selfish genetic elements that behave as genome parasites. The observation that in some species Bs can be either restricted or predominant in one sex raised the interesting hypothesis that Bs could play a role in sex determination. The characterization of putative B master sex-determining (MSD) genes, however, has not yet been provided to support this hypothesis. Here, in Astyanax mexicanus cavefish originating from Pachon cave, we show that Bs are strongly male-predominant. Based on a high-quality genome assembly of a B-carrying male, we characterized the Pachon cavefish B sequence and found that it contains two duplicated loci of the putative MSD gene growth differentiation factor 6b gdf6b). Supporting its role as an MSD gene, we found that the Pachon cavefish gdf6b gene is expressed specifically in differentiating male gonads, and that its knockout induces male-to-female sex reversal in B-carrying males. This demonstrates that gdf6b is necessary for triggering male sex determination in Pachon cavefish. Altogether these results bring multiple and independent lines of evidence supporting the conclusion that the Pachon cavefish B is a “B-sex” chromosome containing duplicated copies of the gdf6b gene acting as an MSD gene promoting male sex determination in this species.
Published: 2021

45. Author response: The rise and fall of the ancient northern pike master sex-determining gene

Author: Christophe Klopp, E. A. Interesova, Songlin Chen, Laurent Journot, Amaury Herpin, René Guyomard, Wesley A. Larson, Manfred Schartl, Louis Bernatchez, Vladimir A. Trifonov, Eric Saillant, Eric Rondeau, Hugo Verreycken, Patrick W. DeHaan, Stephen S. Curran, Yann Guiguen, Hongxia Hu, Hugo Darras, Romain Feron, Qiaowei Pan, J. Andrés López, Jérôme Lluch, Gael Pj Denys, Céline Roques, Mike Tringali, Camille Eché, Roger A. Tabor, Frederick W. Goetz, Hugues Parrinello, Elodie Jouanno, Krista M. Nichols, John H. Postlethwait, Konrad Ocalewicz, Ben F. Koop, and Frank A. von Hippel
Subjects: Geography, Zoology, computer, Gene, Pike, computer.programming_language
Published: 2020

46. Genetic determinism of spontaneous masculinisation in XX female rainbow trout: new insights using medium throughput genotyping and whole-genome sequencing

Author: Charles Poncet, Florent Petitprez, Maria Bernard, Edwige Quillet, Chris Hoze, Nicolas Dechamp, Philippe Hocdé, Anastasia Bestin, Céline Ciobotaru, Yann Guiguen, Pierrick Haffray, Marine Milhes, Florence Phocas, Olivier Bouchez, Jérôme Lluch, Clémence Fraslin, Mathieu Charles, Francine Krieg, Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Edinburgh, Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Allice, Ligue Nationale Contre le Cancer - Paris, Ligue Nationale Contre le Cancer (LNCC), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Pisciculture Charles Murgat, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), European Maritime and Fisheries Fund and France Agrimer co-funded this work (NeoBio project, n° RFEA470016FA1000008), Ligue Nationnale Contre le Cancer, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse)
Subjects: 0106 biological sciences, 0301 basic medicine, Male, Candidate gene, QTL, animal diseases, [SDV]Life Sciences [q-bio], Masculinisation des poissons, Genome-wide association study, heritability, 01 natural sciences, Genome-wide association studies, Genetics, 0303 health sciences, education.field_of_study, Multidisciplinary, biology, Reproduction, 04 agricultural and veterinary sciences, Genomics, Poisson, Trout, Phenotype, Oncorhynchus mykiss, maleness, Medicine, Female, Sex, Maleness, Heterogametic sex, endocrine system, animal structures, Genotype, Science, Population, Quantitative trait locus, Déterminisme génétique du sexe, 010603 evolutionary biology, Article, Heritability, 03 medical and health sciences, Salmonide, Genetic variation, sex, Animals, 14. Life underwater, education, 030304 developmental biology, Genetic association, Animal breeding, fish, Whole Genome Sequencing, urogenital system, Truite arc-en-ciel, 0402 animal and dairy science, Sex Determination Processes, biology.organism_classification, 040201 dairy & animal science, 030104 developmental biology, Fish, Rainbow trout, Sequençage
Abstract: Rainbow trout has a male heterogametic (XY) sex determination system controlled by a major sex-determining gene, sdY. Unexpectedly, a few phenotypically masculinised fish are regularly observed in all-female farmed trout stocks. To better understand the genetic determinism underlying spontaneous maleness in XX-rainbow trout, we recorded the phenotypic sex of 20,210 XX-rainbow trout from a French farm population at 10 and 15 months post-hatching. The overall masculinisation rate was 1.45%. We performed two genome-wide association studies (GWAS) on a subsample of 1139 individuals classified as females, intersex or males using either medium-throughput genotyping (31,811 SNPs) or whole-genome sequencing (WGS, 8.7 million SNPs). The genomic heritability of maleness ranged between 0.48 and 0.62 depending on the method and the number of SNPs used for the estimation. At the 31K SNPs level, we detected four QTL on three chromosomes (Omy1, Omy12 and Omy20). Using WGS information, we narrowed down the positions of the two QTL detected on Omy1 to 96 kb and 347 kb respectively, with the second QTL explaining up to 14% of the total genetic variance of maleness. Within this QTL, we detected three putative candidate genes, fgfa8, cyp17a1 and an uncharacterised protein (LOC110527930), which might be involved in spontaneous maleness of XX-female rainbow trout.
Published: 2020

47. The genome of the bowfin (Amia calva) illuminates the developmental evolution of ray-finned fishes

Author: Qiaowei Pan, Mauricio Losilla, Allyse M. Ferrara, Alex Dornburg, Tatsuya Ota, Kevin L. Childs, Yann Guiguen, Marine Milhes, Amy R. McCune, Ingo Braasch, Michael Brent Hawkins, Andrew W. Thompson, Emily Funk, Olivia E Fitch, Hugues Roest Crollius, Dustin J. Wcisel, Quenton C. Fontenot, Romain Feron, Brett Racicot, Elise Parey, Solomon R. David, Matthew P. Harris, Kazuhiko Kawasaki, Camille Berthelot, and Jeffrey A. Yoder
Subjects: biology, Evolutionary biology, Bowfin, biology.organism_classification, Genome
Abstract: The bowfin fish (Amia calva) diverged before the genome duplication in teleost fishes, and its archetypical body plan and slow rate of molecular evolution make it a key species for genomic exploration as a basal representative of the neopterygian fishes. To investigate the evolution and development of ray-finned fishes, we generated a chromosome-level genome assembly for bowfin that enables gene-order analyses which settle its long-debated, phylogenetic relationship with gars. We analyze the genomic underpinnings of the bowfin’s unique combination of derived and ancestral phenotypes involving the immune system as well as scale, respiratory organ, and skeletal development. By detailing chromatin accessibility and gene expression through bowfin development, we connect developmental gene regulatory loci across vertebrates. We illustrate the utility of these genomic resources to connect developmental evolution across bony fishes, showing the importance of bowfin in understanding vertebrate biology and diversity.
Published: 2020

48. Synteny-Guided Resolution of Gene Trees Clarifies the Functional Impact of Whole-Genome Duplications

Author: Alexandra Louis, Camille Berthelot, Cédric Cabau, Yann Guiguen, Hugues Roest Crollius, Elise Parey, Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), This work is funded by ANR GenoFish (Grant No. ANR-16-CE12-0035), and was supported by grants from the French Government and implemented by ANR (ANR–10–LABX–54 MEMOLIFE and ANR–10–IDEX–0001– 02 PSL* Universite Paris), ANR-16-CE12-0035,GenoFish,Evolution des génes et des génomes après duplication compléte(2016), ANR-10-IDEX-0001,PSL,Paris Sciences et Lettres(2010), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de Biométrie et Intelligence Artificielle de Toulouse [Castanet-Tolosan] (UBIA), Plateforme bioinformatique du GIS GENOTOUL - Génopole Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Corvaisier, Maryse, Evolution des génes et des génomes après duplication compléte - - GenoFish2016 - ANR-16-CE12-0035 - AAPG2016 - VALID, Initiative d'excellence - Paris Sciences et Lettres - - PSL2010 - ANR-10-IDEX-0001 - IDEX - VALID, École normale supérieure - Paris (ENS-PSL), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL)
Subjects: [SDV]Life Sciences [q-bio], Biology, Genome, Polyploidy, 03 medical and health sciences, whole-genome duplications, 0302 clinical medicine, Molecular evolution, Chromosome Duplication, Genetics, Animals, Gene family, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Clade, Molecular Biology, Gene, Phylogeny, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Synteny, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, Phylogenetic tree, molecular evolution, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], synteny, Fishes, Biological Evolution, [SDV] Life Sciences [q-bio], Evolvability, Genetic Techniques, Evolutionary biology, Multigene Family, gene phylogeny, Algorithms, 030217 neurology & neurosurgery
Abstract: Whole-genome duplications (WGDs) have major impacts on the evolution of species, as they produce new gene copies contributing substantially to adaptation, isolation, phenotypic robustness, and evolvability. They result in large, complex gene families with recurrent gene losses in descendant species that sequence-based phylogenetic methods fail to reconstruct accurately. As a result, orthologs and paralogs are difficult to identify reliably in WGD-descended species, which hinders the exploration of functional consequences of WGDs. Here, we present Synteny-guided CORrection of Paralogies and Orthologies (SCORPiOs), a novel method to reconstruct gene phylogenies in the context of a known WGD event. WGDs generate large duplicated syntenic regions, which SCORPiOs systematically leverages as a complement to sequence evolution to infer the evolutionary history of genes. We applied SCORPiOs to the 320-My-old WGD at the origin of teleost fish. We find that almost one in four teleost gene phylogenies in the Ensembl database (3,394) are inconsistent with their syntenic contexts. For 70% of these gene families (2,387), we were able to propose an improved phylogenetic tree consistent with both the molecular substitution distances and the local syntenic information. We show that these synteny-guided phylogenies are more congruent with the species tree, with sequence evolution and with expected expression conservation patterns than those produced by state-of-the-art methods. Finally, we show that synteny-guided gene trees emphasize contributions of WGD paralogs to evolutionary innovations in the teleost clade.
Published: 2020

49. Double maternal effect: duplicated nucleoplasmin 2 genes, npm2a and npm2b, are shared by fish and tetrapods, and have distinct and essential roles in early embryogenesis

Author: Caroline Cheung, Julien Bobe, JĂŠrĂŠmy Pasquier, Thuy V. Nguyen, AurĂŠlien Bouleau, Yann Guiguen, Franck Chesnel, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Université de Rennes (UNIV-RENNES), auto-saisine, ANR-13-BSV7-0015,Maternal Legacy,Portait moléculaire d'un oeuf de poisson de bonne qualité(2013), ANR-10-GENM-0017,PhyloFish,Analyse phylogénomique des duplications géniques chez les poissons téléostéens: une approche par RNA-Seq(2010), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Université de Rennes (UR), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)
Subjects: Nucleoplasmin, [SDV]Life Sciences [q-bio], poisson zèbre, gène npm2, analyse phylogénétique, reproduction, 03 medical and health sciences, 0302 clinical medicine, poisson, Phylogenetics, biology.animal, cyprinidae, gène à effet maternel, education, Coelacanth, Gene, Zebrafish, CRISPR/Cas9, 030304 developmental biology, Synteny, Genetics, fish, 0303 health sciences, education.field_of_study, biology, Vertebrate, embryogenèse, biology.organism_classification, vertébré, danio rerio, Maternal to zygotic transition, vertebrates, danio devario, 030217 neurology & neurosurgery, expression des gènes
Abstract: Nucleoplasmin 2(npm2) is an essential maternal-effect gene that mediates early embryonic events through its function as a histone chaperone that remodels chromatin. Here we report the existence of twonpm2(npm2aandnpm2b) genes in zebrafish. We examined the evolution ofnpm2aandnpm2bin a variety of vertebrates, their potential phylogenetic relationships, and their biological functions using knockout models via the CRISPR/cas9 system. We demonstrated that the twonpm2duplicates exist in a wide range of vertebrates, including sharks, ray-finned fish, amphibians, and sauropsids, whilenpm2awas lost in Coelacanth and mammals, as well as some specific teleost lineages. Using phylogeny and synteny analyses, we traced their origins to the early stages of vertebrate evolution. Our findings suggested thatnpm2aandnpm2bresulted from an ancient local gene duplication, and their functions diverged although key protein domains were conserved. We then investigated their functions by examining their tissue distribution in a wide variety of species and found that they shared ovarian-specific expression, a key feature of maternal-effect genes. We also showed that bothnpm2aandnpm2bare maternally-inherited transcripts in vertebrates. Moreover, we used zebrafish knockouts to demonstrate thatnpm2aandnpm2bplay essential, but distinct, roles in early embryogenesis.npm2afunctions very early during embryogenesis, at or immediately after fertilization, whilenpm2bis involved in processes leading up to or during zygotic genome activation. These novel findings will broaden our knowledge on the evolutionary diversity of maternal-effect genes and underlying mechanisms that contribute to vertebrate reproductive success.Author SummaryThe protein and transcript of thenpm2gene have been previously demonstrated as maternal contributions to embryos of several vertebrates. Recently, twonpm2genes, denoted here asnpm2aandnpm2b, were discovered in zebrafish. This study was conducted to explore the evolutionary origin and changes that occurred that culminated in their current functions. We found that an ancient local duplication of the ancestralnpm2gene created the current two forms, and while most vertebrates retained both genes, notably, mammals and certain species of fish lostnpm2aand, albeit rarely, bothnpm2aandnpm2b. Our functional analyses showed thatnpm2aandnpm2bhave diverse but essential functions during embryogenesis, asnpm2amutants failed to undergo development at the earliest stage whilenpm2bmutants developed, although abnormally, until the zygotic genome activation stage after which their development was arrested followed subsequently by death. Our study is the first to clearly demonstrate the evolution, diversification, and functional analyses of thenpm2genes, which are essential maternal factors that are required for proper embryonic development and survival.
Published: 2020

50. Chaperone-Mediated Autophagy in the Light of Evolution: Insight from Fish

Author: Laury, Lescat, Vincent, Véron, Brigitte, Mourot, Sandrine, Péron, Nathalie, Chenais, Karine, Dias, Natàlia, Riera-Heredia, Florian, Beaumatin, Karine, Pinel, Muriel, Priault, Stéphane, Panserat, Bénédicte, Salin, Yann, Guiguen, Julien, Bobe, Amaury, Herpin, and Iban, Seiliez
Subjects: Oryzias, Chaperone-Mediated Autophagy, Exons, Fibroblasts, Lipid Metabolism, humanities, Autophagic Punctum, Cell Line, Evolution, Molecular, Mice, Lysosomal-Associated Membrane Protein 2, Animals, Carbohydrate Metabolism, Humans, health care economics and organizations
Abstract: Chaperone-mediated autophagy (CMA) is a major pathway of lysosomal proteolysis recognized as a key player of the control of numerous cellular functions, and whose defects have been associated with several human pathologies. To date, this cellular function is presumed to be restricted to mammals and birds, due to the absence of an identifiable lysosome-associated membrane protein 2A (LAMP2A), a limiting and essential protein for CMA, in nontetrapod species. However, the recent identification of expressed sequences displaying high homology with mammalian LAMP2A in several fish species challenges that view and suggests that CMA likely appeared earlier during evolution than initially thought. In the present study, we provide a comprehensive picture of the evolutionary history of the LAMP2 gene in vertebrates and demonstrate that LAMP2 indeed appeared at the root of the vertebrate lineage. Using a fibroblast cell line from medaka fish (Oryzias latipes), we further show that the splice variant lamp2a controls, upon long-term starvation, the lysosomal accumulation of a fluorescent reporter commonly used to track CMA in mammalian cells. Finally, to address the physiological role of Lamp2a in fish, we generated knockout medaka for that specific splice variant, and found that these deficient fish exhibit severe alterations in carbohydrate and fat metabolisms, in consistency with existing data in mice deficient for CMA in liver. Altogether, our data provide the first evidence for a CMA-like pathway in fish and bring new perspectives on the use of complementary genetic models, such as zebrafish or medaka, for studying CMA in an evolutionary perspective.
Published: 2020

Catalog

Books, media, physical & digital resources

See catalog results

Searchworks

Select search scope, currently: Articles Catalog books, media & more in Jio Institute collections Articles journal articles & other e-resources

Search

Search Constraints

Refine your results

Search Limiters

Topic

Publication Year Range

Language

Publication Type

Journal

Database

Publisher

176 results on '"Yann Guiguen"'

Search Results

Catalog

Select search scope, currently: Articles

Catalog

books, media & more in Jio Institute collections

Articles

journal articles & other e-resources