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1. Masculinization of the X-chromosome in aphid soma and gonads

Author

Jaquiéry, Julie, Simon, Jean-Christophe, Robin, Stéphanie, Richard, Gautier, Peccoud, Jean, Boulain, Hélène, Legeai, Fabrice, Tanguy, Sylvie, Prunier-Leterme, Nathalie, and Letrionnaire, Gaël

Subjects
Archaeology, CC1-960, Science
Abstract

Males and females share essentially the same genome but differ in their optimal values for many phenotypic traits, which can result in intra-locus conflict between the sexes. Aphids display XX/X0 sex chromosomes and combine unusual X chromosome inheritance with cyclical parthenogenesis. Theoretical and empirical works support the hypothesis that the large excess of male-biased genes observed on the aphid X chromosome compared to autosomes evolved in response to sexual conflicts, by restricting the products of sexually antagonistic alleles to the sex they benefits. However, whether such masculinization of the X affects all tissues (as expected if it evolved in response to sexual conflicts) or is limited to specific tissues remains an open question. Here, we measured gene expression in three different somatic and gonadic tissues of males, sexual females and parthenogenetic females of the pea aphid. We observed a masculinization of the X in each of the studied tissues, with male-biased genes being 2.5 to 3.5 more frequent on the X than expected. We also tested the hypothesis that gene duplication can facilitate the attenuation of conflicts by allowing gene copies to neo- or sub-functionalize and reach sex-specific optima. As predicted, X-linked copies of duplicated genes having their other copies on autosomes were more frequently male-biased (40.5% of the genes) than duplicated autosomal genes (6.6%) or X-linked single-copy genes (32.5%). These results highlight a peculiar pattern of expression of X-linked genes in aphids at the tissue level and provide further support for sex-biased expression as a mechanism to attenuate intra-locus sexual conflicts.

Published
2022
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3. LRez: C++ API and toolkit for analyzing and managing Linked-Reads data

Author

Morisse, Pierre, Lemaitre, Claire, and Legeai, Fabrice

Subjects
Quantitative Biology - Genomics
Abstract

Linked-Reads technologies, such as 10x Genomics, combine both the high-quality and low cost of short-reads sequencing and a long-range information, through the use of barcodes able to tag reads which originate from a common long DNA fragment. This technology has been employed in a broad range of applications including assembly or phasing of genomes, and structural variant calling. However, to date, no tool or API dedicated to the manipulation of Linked-Reads data exist. We introduce LRez, a C++ API and toolkit which allows easy management of Linked-Reads data. LRez includes various functionalities, for computing number of common barcodes between genomic regions, extracting barcodes from BAM files, as well as indexing and querying both BAM and FASTQ files to quickly fetch reads or alignments sharing one or multiple barcodes. LRez can thus be used in a broad range of applications requiring barcode processing, in order to improve their performances. LRez is implemented in C++, supported on Linux platforms, and available under AGPL-3.0 License at https://github.com/morispi/LRez., Comment: 4 pages, 1 table

Published
2021

5. Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum

Author

Dennis, Alice B, Ballesteros, Gabriel I, Robin, Stéphanie, Schrader, Lukas, Bast, Jens, Berghöfer, Jan, Beukeboom, Leo W, Belghazi, Maya, Bretaudeau, Anthony, Buellesbach, Jan, Cash, Elizabeth, Colinet, Dominique, Dumas, Zoé, Errbii, Mohammed, Falabella, Patrizia, Gatti, Jean-Luc, Geuverink, Elzemiek, Gibson, Joshua D, Hertaeg, Corinne, Hartmann, Stefanie, Jacquin-Joly, Emmanuelle, Lammers, Mark, Lavandero, Blas I, Lindenbaum, Ina, Massardier-Galata, Lauriane, Meslin, Camille, Montagné, Nicolas, Pak, Nina, Poirié, Marylène, Salvia, Rosanna, Smith, Chris R, Tagu, Denis, Tares, Sophie, Vogel, Heiko, Schwander, Tanja, Simon, Jean-Christophe, Figueroa, Christian C, Vorburger, Christoph, Legeai, Fabrice, and Gadau, Jürgen

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Animals, Aphids, DNA Methylation, GC Rich Sequence, Genomics, Insect Proteins, Sex Determination Processes, Venoms, Wasps, Parasitoid wasp, Aphid host, Aphidius ervi, Lysiphlebus fabarum, GC content, de novo genome assembly, DNA methylation loss, Chemosensory genes, Venom proteins, Toll and Imd pathways, Information and Computing Sciences, Medical and Health Sciences, Bioinformatics, Biological sciences, Biomedical and clinical sciences
Abstract

BackgroundParasitoid wasps have fascinating life cycles and play an important role in trophic networks, yet little is known about their genome content and function. Parasitoids that infect aphids are an important group with the potential for biological control. Their success depends on adapting to develop inside aphids and overcoming both host aphid defenses and their protective endosymbionts.ResultsWe present the de novo genome assemblies, detailed annotation, and comparative analysis of two closely related parasitoid wasps that target pest aphids: Aphidius ervi and Lysiphlebus fabarum (Hymenoptera: Braconidae: Aphidiinae). The genomes are small (139 and 141 Mbp) and the most AT-rich reported thus far for any arthropod (GC content: 25.8 and 23.8%). This nucleotide bias is accompanied by skewed codon usage and is stronger in genes with adult-biased expression. AT-richness may be the consequence of reduced genome size, a near absence of DNA methylation, and energy efficiency. We identify missing desaturase genes, whose absence may underlie mimicry in the cuticular hydrocarbon profile of L. fabarum. We highlight key gene groups including those underlying venom composition, chemosensory perception, and sex determination, as well as potential losses in immune pathway genes.ConclusionsThese findings are of fundamental interest for insect evolution and biological control applications. They provide a strong foundation for further functional studies into coevolution between parasitoids and their hosts. Both genomes are available at https://bipaa.genouest.org.

Published
2020

6. Correction to: The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest

Author

Rispe, Claude, Legeai, Fabrice, Nabity, Paul D, Fernández, Rosa, Arora, Arinder K, Baa-Puyoulet, Patrice, Banfill, Celeste R, Bao, Leticia, Barberà, Miquel, Bouallègue, Maryem, Bretaudeau, Anthony, Brisson, Jennifer A, Calevro, Federica, Capy, Pierre, Catrice, Olivier, Chertemps, Thomas, Couture, Carole, Delière, Laurent, Douglas, Angela E, Dufault-Thompson, Keith, Escuer, Paula, Feng, Honglin, Forneck, Astrid, Gabaldón, Toni, Guigó, Roderic, Hilliou, Frédérique, Hinojosa-Alvarez, Silvia, Hsiao, Yi-min, Hudaverdian, Sylvie, Jacquin-Joly, Emmanuelle, James, Edward B, Johnston, Spencer, Joubard, Benjamin, Le Goff, Gaëlle, Le Trionnaire, Gaël, Librado, Pablo, Liu, Shanlin, Lombaert, Eric, Lu, Hsiao-ling, Maïbèche, Martine, Makni, Mohamed, Marcet-Houben, Marina, Martínez-Torres, David, Meslin, Camille, Montagné, Nicolas, Moran, Nancy A, Papura, Daciana, Parisot, Nicolas, Rahbé, Yvan, Lopes, Mélanie Ribeiro, Ripoll-Cladellas, Aida, Robin, Stéphanie, Roques, Céline, Roux, Pascale, Rozas, Julio, Sánchez-Gracia, Alejandro, Sánchez-Herrero, Jose F, Santesmasses, Didac, Scatoni, Iris, Serre, Rémy-Félix, Tang, Ming, Tian, Wenhua, Umina, Paul A, van Munster, Manuella, Vincent-Monégat, Carole, Wemmer, Joshua, Wilson, Alex CC, Zhang, Ying, Zhao, Chaoyang, Zhao, Jing, Zhao, Serena, Zhou, Xin, Delmotte, François, and Tagu, Denis

Subjects
Developmental Biology
Abstract

An amendment to this paper has been published and can be accessed via the original article.

Published
2020

7. The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest

Author

Rispe, Claude, Legeai, Fabrice, Nabity, Paul D, Fernández, Rosa, Arora, Arinder K, Baa-Puyoulet, Patrice, Banfill, Celeste R, Bao, Leticia, Barberà, Miquel, Bouallègue, Maryem, Bretaudeau, Anthony, Brisson, Jennifer A, Calevro, Federica, Capy, Pierre, Catrice, Olivier, Chertemps, Thomas, Couture, Carole, Delière, Laurent, Douglas, Angela E, Dufault-Thompson, Keith, Escuer, Paula, Feng, Honglin, Forneck, Astrid, Gabaldón, Toni, Guigó, Roderic, Hilliou, Frédérique, Hinojosa-Alvarez, Silvia, Hsiao, Yi-min, Hudaverdian, Sylvie, Jacquin-Joly, Emmanuelle, James, Edward B, Johnston, Spencer, Joubard, Benjamin, Le Goff, Gaëlle, Le Trionnaire, Gaël, Librado, Pablo, Liu, Shanlin, Lombaert, Eric, Lu, Hsiao-ling, Maïbèche, Martine, Makni, Mohamed, Marcet-Houben, Marina, Martínez-Torres, David, Meslin, Camille, Montagné, Nicolas, Moran, Nancy A, Papura, Daciana, Parisot, Nicolas, Rahbé, Yvan, Lopes, Mélanie Ribeiro, Ripoll-Cladellas, Aida, Robin, Stéphanie, Roques, Céline, Roux, Pascale, Rozas, Julio, Sánchez-Gracia, Alejandro, Sánchez-Herrero, Jose F, Santesmasses, Didac, Scatoni, Iris, Serre, Rémy-Félix, Tang, Ming, Tian, Wenhua, Umina, Paul A, van Munster, Manuella, Vincent-Monégat, Carole, Wemmer, Joshua, Wilson, Alex CC, Zhang, Ying, Zhao, Chaoyang, Zhao, Jing, Zhao, Serena, Zhou, Xin, Delmotte, François, and Tagu, Denis

Subjects
Biological Sciences, Genetics, Human Genome, Infection, Climate Action, Adaptation, Biological, Animal Distribution, Animals, Biological Evolution, Genome, Insect, Hemiptera, Introduced Species, Vitis, Arthropod genomes, Daktulosphaira vitifoliae, Gene duplications, Host plant interactions, Effectors, Biological invasions, Developmental Biology, Biological sciences
Abstract

BackgroundAlthough native to North America, the invasion of the aphid-like grape phylloxera Daktulosphaira vitifoliae across the globe altered the course of grape cultivation. For the past 150 years, viticulture relied on grafting-resistant North American Vitis species as rootstocks, thereby limiting genetic stocks tolerant to other stressors such as pathogens and climate change. Limited understanding of the insect genetics resulted in successive outbreaks across the globe when rootstocks failed. Here we report the 294-Mb genome of D. vitifoliae as a basic tool to understand host plant manipulation, nutritional endosymbiosis, and enhance global viticulture.ResultsUsing a combination of genome, RNA, and population resequencing, we found grape phylloxera showed high duplication rates since its common ancestor with aphids, but similarity in most metabolic genes, despite lacking obligate nutritional symbioses and feeding from parenchyma. Similarly, no enrichment occurred in development genes in relation to viviparity. However, phylloxera evolved > 2700 unique genes that resemble putative effectors and are active during feeding. Population sequencing revealed the global invasion began from the upper Mississippi River in North America, spread to Europe and from there to the rest of the world.ConclusionsThe grape phylloxera genome reveals genetic architecture relative to the evolution of nutritional endosymbiosis, viviparity, and herbivory. The extraordinary expansion in effector genes also suggests novel adaptations to plant feeding and how insects induce complex plant phenotypes, for instance galls. Finally, our understanding of the origin of this invasive species and its genome provide genetics resources to alleviate rootstock bottlenecks restricting the advancement of viticulture.

Published
2020

9. The evolutionary process of invasion in the fall armyworm (Spodoptera frugiperda)

Author

Yainna, Sudeeptha, Tay, Wee Tek, Durand, Karine, Fiteni, Estelle, Hilliou, Frédérique, Legeai, Fabrice, Clamens, Anne-Laure, Gimenez, Sylvie, Asokan, R., Kalleshwaraswamy, C. M., Deshmukh, Sharanabasappa S., Meagher, Jr., Robert L., Blanco, Carlos A., Silvie, Pierre, Brévault, Thierry, Dassou, Anicet, Kergoat, Gael J., Walsh, Thomas, Gordon, Karl, Nègre, Nicolas, d’Alençon, Emmanuelle, and Nam, Kiwoong

Published
2022
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11. Multiple deletions of candidate effector genes lead to the breakdown of partial grapevine resistance to downy mildew.

Author

Paineau, Manon, Minio, Andrea, Mestre, Pere, Fabre, Frédéric, Mazet, Isabelle D., Couture, Carole, Legeai, Fabrice, Dumartinet, Thomas, Cantu, Dario, and Delmotte, François

Subjects
SIGNAL peptides, GRAPES, PROTEIN structure, GENETIC code, CELL death
Abstract

Summary: Grapevine downy mildew, caused by the oomycete Plasmopara viticola (P. viticola, Berk. & M. A. Curtis; Berl. & De Toni), is a global threat to Eurasian wine grapes Vitis vinifera. Although resistant grapevine varieties are becoming more accessible, P. viticola populations are rapidly evolving to overcome these resistances. We aimed to uncover avirulence genes related to Rpv3.1‐mediated grapevine resistance.We sequenced the genomes and characterized the development of 136 P. viticola strains on resistant and sensitive grapevine cultivars. A genome‐wide association study was conducted to identify genomic variations associated with resistant‐breaking phenotypes.We identified a genomic region associated with the breakdown of Rpv3.1 grapevine resistance (avrRpv3.1 locus). A diploid‐aware reassembly of the P. viticola INRA‐Pv221 genome revealed structural variations in this locus, including a 30 kbp deletion. Virulent P. viticola strains displayed multiple deletions on both haplotypes at the avrRpv3.1 locus. These deletions involve two paralog genes coding for proteins with 800–900 amino acids and signal peptides. These proteins exhibited a structure featuring LWY‐fold structural modules, common among oomycete effectors. When transiently expressed, these proteins induced cell death in grapevines carrying Rpv3.1 resistance, confirming their avirulence nature.This discovery sheds light on the genetic mechanisms enabling P. viticola to adapt to grapevine resistance, laying a foundation for developing strategies to manage this destructive crop pathogen. [ABSTRACT FROM AUTHOR]

Published
2024
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13. Soybean aphid biotype 1 genome: Insights into the invasive biology and adaptive evolution of a major agricultural pest

Author

Akraiko, Tatsiana, Aschwanden, Andrew, Avalos, Arian, Band, Mark, Bonning, Bryony, Bretaudeau, Anthony, Chiesa, Olga, Chirumamilla, Anitha, Coates, Brad S., Cocuzza, Giuseppe, Cullen, Eileen, Desborough, Peter, Diers, Brian, DiFonzo, Christina, Heimpel, George E., Herman, Theresa, Huanga, Yongping, Knodel, Janet, Ko, Chiun-Cheng, Labrie, Genevieve, Lagos-Kutz, Doris, Lee, Joon-Ho, Lee, Seunghwan, Legeai, Fabrice, Mandrioli, Mauro, Manicardi, Gian Carlo, Mazzoni, Emanuele, Melchiori, Giulia, Micijevic, Ana, Miller, Nick, Nasuddin, Andi, Nault, Brian A., O'Neal, Matthew E., Panini, Michela, Pessino, Massimo, Prischmann-Voldseth, Deirdre, Robertson, Hugh M., Sijun Liu, Song, Hojun, Tilmon, Kelley, Tooker, John, Wu, Kongming, Zhan, Shuai, Giordano, Rosanna, Donthu, Ravi Kiran, Zimin, Aleksey V., Julca Chavez, Irene Consuelo, Gabaldon, Toni, van Munster, Manuella, Hon, Lawrence, Hall, Richard, Badger, Jonathan H., Nguyen, Minh, Flores, Alejandra, Potter, Bruce, Giray, Tugrul, Soto-Adames, Felipe N., Weber, Everett, Marcelino, Jose A.P., Fields, Christopher J., Voegtlin, David J., Hill, Curt B., and Hartman, Glen L.

Published
2020
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15. Identification of a viral gene essential for the genome replication of a domesticated endogenous virus in ichneumonid parasitoid wasps

Author

Lorenzi, Ange, primary, Legeai, Fabrice, additional, Jouan, Véronique, additional, Girard, Pierre-Alain, additional, Strand, Mickael, additional, Ravallec, Marc, additional, Eychenne, Magali, additional, Bretaudeau, Anthony, additional, Robin, Stéphanie, additional, Rochefort, Jeanne, additional, Villegas, Mathilde, additional, Burke, Gaelen, additional, Rebollo, Rita, additional, Nègre, Nicolas, additional, and Volkoff, Anne-Nathalie, additional

Published
2024
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16. Global patterns in genomic diversity underpinning the evolution of insecticide resistance in the aphid crop pest Myzuspersicae

Author

Singh, Kumar Saurabh, Cordeiro, Erick M. G., Troczka, Bartlomiej J., Pym, Adam, Mackisack, Joanna, Mathers, Thomas C., Duarte, Ana, Legeai, Fabrice, Robin, Stéphanie, Bielza, Pablo, Burrack, Hannah J., Charaabi, Kamel, Denholm, Ian, Figueroa, Christian C., ffrench-Constant, Richard H., Jander, Georg, Margaritopoulos, John T., Mazzoni, Emanuele, Nauen, Ralf, Ramírez, Claudio C., Ren, Guangwei, Stepanyan, Ilona, Umina, Paul A., Voronova, Nina V., Vontas, John, Williamson, Martin S., Wilson, Alex C. C., Xi-Wu, Gao, Youn, Young-Nam, Zimmer, Christoph T., Simon, Jean-Christophe, Hayward, Alex, and Bass, Chris

Published
2021
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17. Author Correction: Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization

Author

Gauthier, Jérémy, Boulain, Hélène, van Vugt, Joke J. F. A., Baudry, Lyam, Persyn, Emma, Aury, Jean-Marc, Noel, Benjamin, Bretaudeau, Anthony, Legeai, Fabrice, Warris, Sven, Chebbi, Mohamed A., Dubreuil, Géraldine, Duvic, Bernard, Kremer, Natacha, Gayral, Philippe, Musset, Karine, Josse, Thibaut, Bigot, Diane, Bressac, Christophe, Moreau, Sébastien, Periquet, Georges, Harry, Myriam, Montagné, Nicolas, Boulogne, Isabelle, Sabeti-Azad, Mahnaz, Maïbèche, Martine, Chertemps, Thomas, Hilliou, Frédérique, Siaussat, David, Amselem, Joëlle, Luyten, Isabelle, Capdevielle-Dulac, Claire, Labadie, Karine, Merlin, Bruna Laís, Barbe, Valérie, de Boer, Jetske G., Marbouty, Martial, Cônsoli, Fernando Luis, Dupas, Stéphane, Hua-Van, Aurélie, Le Goff, Gaelle, Bézier, Annie, Jacquin-Joly, Emmanuelle, Whitfield, James B., Vet, Louise E. M., Smid, Hans M., Kaiser, Laure, Koszul, Romain, Huguet, Elisabeth, Herniou, Elisabeth A., and Drezen, Jean-Michel

Published
2021
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18. Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization

Author

Gauthier, Jérémy, Boulain, Hélène, van Vugt, Joke J. F. A., Baudry, Lyam, Persyn, Emma, Aury, Jean-Marc, Noel, Benjamin, Bretaudeau, Anthony, Legeai, Fabrice, Warris, Sven, Chebbi, Mohamed A., Dubreuil, Géraldine, Duvic, Bernard, Kremer, Natacha, Gayral, Philippe, Musset, Karine, Josse, Thibaut, Bigot, Diane, Bressac, Christophe, Moreau, Sébastien, Periquet, Georges, Harry, Myriam, Montagné, Nicolas, Boulogne, Isabelle, Sabeti-Azad, Mahnaz, Maïbèche, Martine, Chertemps, Thomas, Hilliou, Frédérique, Siaussat, David, Amselem, Joëlle, Luyten, Isabelle, Capdevielle-Dulac, Claire, Labadie, Karine, Merlin, Bruna Laís, Barbe, Valérie, de Boer, Jetske G., Marbouty, Martial, Cônsoli, Fernando Luis, Dupas, Stéphane, Hua-Van, Aurélie, Le Goff, Gaelle, Bézier, Annie, Jacquin-Joly, Emmanuelle, Whitfield, James B., Vet, Louise E. M., Smid, Hans M., Kaiser, Laure, Koszul, Romain, Huguet, Elisabeth, Herniou, Elisabeth A., and Drezen, Jean-Michel

Published
2021
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20. Identification of a viral gene essential for the genome replication of a domesticated endogenous virus in ichneumonid parasitoid wasps.

Author

Lorenzi, Ange, Legeai, Fabrice, Jouan, Véronique, Girard, Pierre-Alain, Strand, Michael R., Ravallec, Marc, Eychenne, Magali, Bretaudeau, Anthony, Robin, Stéphanie, Rochefort, Jeanne, Villegas, Mathilde, Burke, Gaelen R., Rebollo, Rita, Nègre, Nicolas, and Volkoff, Anne-Nathalie

Subjects
*VIRAL genes, *GLYCOCALYX, *INSECT eggs, *WASPS, *RNA interference, *GENOMES, *VIRAL genomes
Abstract

Thousands of endoparasitoid wasp species in the families Braconidae and Ichneumonidae harbor "domesticated endogenous viruses" (DEVs) in their genomes. This study focuses on ichneumonid DEVs, named ichnoviruses (IVs). Large quantities of DNA-containing IV virions are produced in ovary calyx cells during the pupal and adult stages of female wasps. Females parasitize host insects by injecting eggs and virions into the body cavity. After injection, virions rapidly infect host cells which is followed by expression of IV genes that promote the successful development of wasp offspring. IV genomes consist of two components: proviral segment loci that serve as templates for circular dsDNAs that are packaged into capsids, and genes from an ancestral virus that produce virions. In this study, we generated a chromosome-scale genome assembly for Hyposotor didymator that harbors H. didymator ichnovirus (HdIV). We identified a total of 67 HdIV loci that are amplified in calyx cells during the wasp pupal stage. We then focused on an HdIV gene, U16, which is transcribed in calyx cells during the initial stages of replication. Sequence analysis indicated that U16 contains a conserved domain in primases from select other viruses. Knockdown of U16 by RNA interference inhibited virion morphogenesis in calyx cells. Genome-wide analysis indicated U16 knockdown also inhibited amplification of HdIV loci in calyx cells. Altogether, our results identified several previously unknown HdIV loci, demonstrated that all HdIV loci are amplified in calyx cells during the pupal stage, and showed that U16 is required for amplification and virion morphogenesis. Author summary: Parasitoid "domesticated endogenous viruses" (DEVs) provide a fascinating example of eukaryotes acquiring new functions through integration of a viral genome. DEVs consist of multiple loci in the genomes of wasps. Upon activation, these elements collectively orchestrate the production of virions or virus-like particles that are crucial for successful parasitism of host insects. Despite the significance of DEVs for parasitoid biology, the mechanisms regulating key steps in virion morphogenesis are largely unknown. In this study, we focused on the ichneumonid parasitoid Hyposoter didymator, which harbors an ichnovirus consisting of 67 proviral loci. Our findings reveal that all proviral loci are simultaneously amplified in ovary calyx cells of female wasps during the pupal stage suggesting the hijacking of cellular replication complexes by viral proteins. We functionally studied the ichnovirus gene U16, which encodes a protein with a weakly conserved primase C-terminal domain. Silencing U16 inhibited viral DNA amplification and virion production, underscoring the key role of this gene for ichnovirus replication. Our study provides evidence that many genes involved in viral DNA replication have been conserved during the domestication of ichnoviruses. [ABSTRACT FROM AUTHOR]

Published
2024
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23. Contrasting Evolutionary Patterns Between Sexual and Asexual Lineages in a Genomic Region Linked to Reproductive Mode Variation in the pea aphid

Author

Rimbault, Maud, primary, Legeai, Fabrice, additional, Peccoud, Jean, additional, Mieuzet, Lucie, additional, Call, Elsa, additional, Nouhaud, Pierre, additional, Defendini, Hélène, additional, Mahéo, Frédérique, additional, Marande, William, additional, Théron, Nicolas, additional, Tagu, Denis, additional, Le Trionnaire, Gaël, additional, Simon, Jean-Christophe, additional, and Jaquiéry, Julie, additional

Published
2023
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28. Identification of transcriptional modules linked to the drought response of Brassica napus during seed development and their mitigation by early biotic stress.

Author

Bianchetti, Grégoire, Clouet, Vanessa, Legeai, Fabrice, Baron, Cécile, Gazengel, Kévin, Vu, Benoit Ly, Baud, Sébastien, To, Alexandra, Manzanares‐Dauleux, Maria J., Buitink, Julia, and Nesi, Nathalie

Subjects
PLASMODIOPHORA brassicae, SEED development, RAPESEED, DROUGHT management, HEAT shock proteins, DROUGHTS, SEED proteins
Abstract

In order to capture the drought impacts on seed quality acquisition in Brassica napus and its potential interaction with early biotic stress, seeds of the 'Express' genotype of oilseed rape were characterized from late embryogenesis to full maturity from plants submitted to reduced watering (WS) with or without pre‐occurring inoculation by the telluric pathogen Plasmodiophora brassicae (Pb + WS or Pb, respectively), and compared to control conditions (C). Drought as a single constraint led to significantly lower accumulation of lipids, higher protein content and reduced longevity of the WS‐treated seeds. In contrast, when water shortage was preceded by clubroot infection, these phenotypic differences were completely abolished despite the upregulation of the drought sensor RD20. A weighted gene co‐expression network of seed development in oilseed rape was generated using 72 transcriptomes from developing seeds from the four treatments and identified 33 modules. Module 29 was highly enriched in heat shock proteins and chaperones that showed a stronger upregulation in Pb + WS compared to the WS condition, pointing to a possible priming effect by the early P. brassicae infection on seed quality acquisition. Module 13 was enriched with genes encoding 12S and 2S seed storage proteins, with the latter being strongly upregulated under WS conditions. Cis‐element promotor enrichment identified PEI1/TZF6, FUS3 and bZIP68 as putative regulators significantly upregulated upon WS compared to Pb + WS. Our results provide a temporal co‐expression atlas of seed development in oilseed rape and will serve as a resource to characterize the plant response towards combinations of biotic and abiotic stresses. [ABSTRACT FROM AUTHOR]

Published
2024
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29. First chromosome scale genomes of ithomiine butterflies (Nymphalidae: Ithomiini): Comparative models for mimicry genetic studies

Author

Gauthier, Jérémy, Meier, Joana, Legeai, Fabrice, Mcclure, Melanie, Whibley, Annabel, Bretaudeau, Anthony, Boulain, Hélène, Parrinello, Hugues, Mugford, Sam T., Durbin, Richard, Zhou, Chenxi, Mccarthy, Shane, Wheat, Christopher W., Piron‐prunier, Florence, Monsempes, Christelle, François, Marie‐christine, Jay, Paul, Noûs, Camille, Persyn, Emma, Jacquin‐joly, Emmanuelle, Meslin, Camille, Montagné, Nicolas, Lemaitre, Claire, Elias, Marianne, Gauthier, Jérémy, Meier, Joana, Legeai, Fabrice, Mcclure, Melanie, Whibley, Annabel, Bretaudeau, Anthony, Boulain, Hélène, Parrinello, Hugues, Mugford, Sam T., Durbin, Richard, Zhou, Chenxi, Mccarthy, Shane, Wheat, Christopher W., Piron‐prunier, Florence, Monsempes, Christelle, François, Marie‐christine, Jay, Paul, Noûs, Camille, Persyn, Emma, Jacquin‐joly, Emmanuelle, Meslin, Camille, Montagné, Nicolas, Lemaitre, Claire, and Elias, Marianne

Abstract

The ithomiine butterflies (Nymphalidae: Danainae) represent the largest known radiation of Müllerian mimetic butterflies. They dominate by number the mimetic butterfly communities, which include species such as the iconic neotropical Heliconius genus. Recent studies on the ecology and genetics of speciation in Ithomiini have suggested that sexual pheromones, colour pattern and perhaps hostplant could drive reproductive isolation. However, no reference genome was available for Ithomiini, which has hindered further exploration on the genetic architecture of these candidate traits, and more generally on the genomic patterns of divergence. Here, we generated high-quality, chromosome-scale genome assemblies for two Melinaea species, M. marsaeus and M. menophilus, and a draft genome of the species Ithomia salapia. We obtained genomes with a size ranging from 396 to 503 Mb across the three species and scaffold N50 of 40.5 and 23.2 Mb for the two chromosome-scale assemblies. Using collinearity analyses we identified massive rearrangements between the two closely related Melinaea species. An annotation of transposable elements and gene content was performed, as well as a specialist annotation to target chemosensory genes, which is crucial for host plant detection and mate recognition in mimetic species. A comparative genomic approach revealed independent gene expansions in ithomiines and particularly in gustatory receptor genes. These first three genomes of ithomiine mimetic butterflies constitute a valuable addition and a welcome comparison to existing biological models such as Heliconius, and will enable further understanding of the mechanisms of adaptation in butterflies.

Published
2023
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31. First chromosome scale genomes of ithomiine butterflies (Nymphalidae: Ithomiini): Comparative models for mimicry genetic studies

Author

Gauthier, Jérémy, primary, Meier, Joana, additional, Legeai, Fabrice, additional, McClure, Melanie, additional, Whibley, Annabel, additional, Bretaudeau, Anthony, additional, Boulain, Hélène, additional, Parrinello, Hugues, additional, Mugford, Sam T., additional, Durbin, Richard, additional, Zhou, Chenxi, additional, McCarthy, Shane, additional, Wheat, Christopher W., additional, Piron‐Prunier, Florence, additional, Monsempes, Christelle, additional, François, Marie‐Christine, additional, Jay, Paul, additional, Noûs, Camille, additional, Persyn, Emma, additional, Jacquin‐Joly, Emmanuelle, additional, Meslin, Camille, additional, Montagné, Nicolas, additional, Lemaitre, Claire, additional, and Elias, Marianne, additional

Published
2023
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34. Intégration de données de phénotypiques, environnementales et de biodiversité à l'aide des technologies du Web Sémantique

Author

Dameron, Olivier, Tirlet, Yael, Boudet, Matéo, Legeai, Fabrice, Dynamics, Logics and Inference for biological Systems and Sequences (Dyliss), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Plateforme bioinformatique GenOuest [Rennes], Université de Rennes (UR)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, and Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut National des Sciences Appliquées - Rennes (INSA Rennes)

Subjects
[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

National audience; De nombreuses études reposent sur des observations phénotypiques d’espèces d’intérêt, des données sur les conditions environnementales d’observation et des données de métagénomique mesurant la biodiversité. Le problème est que chaque étude développe un modèle de données ad hoc que les experts doivent s’approprier. Ceci complique à la fois la phase d’acquisition des données et la phase d’analyse, surtout lorsque celle-ci nécessite du raisonnement automatique sur les bases de connaissances associées comme la hiérarchie des espèces du NCBI Taxon, ou des ontologies de phénotypes.

Published
2022

38. Spodoptera littoralis genome mining brings insights on the dynamic of expansion of gustatory receptors in polyphagous noctuidae

Author

Meslin, Camille, Mainet, Pauline, Montagné, Nicolas, Robin, Stéphanie, Legeai, Fabrice, Bretaudeau, Anthony, Johnston, J Spencer, Koutroumpa, Fotini, Persyn, Emma, Monsempès, Christelle, François, Marie-Christine, Jacquin-Jolyb, Emmanuelle, Meslin, Camille, Mainet, Pauline, Montagné, Nicolas, Robin, Stéphanie, Legeai, Fabrice, Bretaudeau, Anthony, Johnston, J Spencer, Koutroumpa, Fotini, Persyn, Emma, Monsempès, Christelle, François, Marie-Christine, and Jacquin-Jolyb, Emmanuelle

Abstract

The bitter taste, triggered via gustatory receptors, serves as an important natural defense against the ingestion of poisonous foods in animals, and the increased host breadth is usually linked to an increase in the number of gustatory receptor genes. This has been especially observed in polyphagous insect species, such as noctuid species from the Spodoptera genus. However, the dynamic and physical mechanisms leading to these gene expansions and the evolutionary pressures behind them remain elusive. Among major drivers of genome dynamics are the transposable elements but, surprisingly, their potential role in insect gustatory receptor expansion has not been considered yet. In this work, we hypothesized that transposable elements and possibly positive selection would be involved in the highly dynamic evolution of gustatory receptor in Spodoptera spp. We first sequenced de novo the full 465 Mb genome of S. littoralis, and manually annotated the main chemosensory genes, including a large repertoire of 373 gustatory receptor genes (including 19 pseudogenes). We also improved the completeness of S. frugiperda and S. litura gustatory receptor gene repertoires. Then, we annotated transposable elements and revealed that a particular category of class I retrotransposons, the SINE transposons, was significantly enriched in the vicinity of gustatory receptor gene clusters, suggesting a transposon-mediated mechanism for the formation of these clusters. Selection pressure analyses indicated that positive selection within the gustatory receptor gene family is cryptic, only 7 receptors being identified as positively selected. Altogether, our data provide a new good quality Spodoptera genome, pinpoint interesting gustatory receptor candidates for further functional studies and bring valuable genomic information on the mechanisms of gustatory receptor expansions in polyphagous insect species.

Published
2022

39. The evolutionary process of invasion in the fall armyworm (Spodoptera frugiperda)

Author

Yainna Kumarihami, Sudeeptha, Tay, Wee Tek, Durand, Karine, Fiteni, Estelle, Hilliou, Frédérique, Legeai, Fabrice, Clamens, Anne-Laure, Gimenez, Sylvie, Asokan, R., Kalleshwaraswamy, C.M., Deshmukh, Sharanabasappa S., Meagher Jr., Robert L., Blanco, Carlos A., Silvie, Pierre, Brévault, Thierry, Dassou, Gbèblonoudo Anicet, Kergoat, Gael J., Walsh, Thomas, Gordon, Karl H.J., Nègre, Nicolas, D'Alençon, Emmanuelle, Nam, Kiwoong, Yainna Kumarihami, Sudeeptha, Tay, Wee Tek, Durand, Karine, Fiteni, Estelle, Hilliou, Frédérique, Legeai, Fabrice, Clamens, Anne-Laure, Gimenez, Sylvie, Asokan, R., Kalleshwaraswamy, C.M., Deshmukh, Sharanabasappa S., Meagher Jr., Robert L., Blanco, Carlos A., Silvie, Pierre, Brévault, Thierry, Dassou, Gbèblonoudo Anicet, Kergoat, Gael J., Walsh, Thomas, Gordon, Karl H.J., Nègre, Nicolas, D'Alençon, Emmanuelle, and Nam, Kiwoong

Abstract

The fall armyworm (FAW; Spodoptera frugiperda) is one of the major agricultural pest insects. FAW is native to the Americas, and its invasion was first reported in West Africa in 2016. Then it quickly spread through Africa, Asia, and Oceania, becoming one of the main threats to corn production. We analyzed whole genome sequences of 177 FAW individuals from 12 locations on four continents to infer evolutionary processes of invasion. Principal component analysis from the TPI gene and whole genome sequences shows that invasive FAW populations originated from the corn strain. Ancestry coefficient and phylogenetic analyses from the nuclear genome indicate that invasive populations are derived from a single ancestry, distinct from native populations, while the mitochondrial phylogenetic tree supports the hypothesis of multiple introductions. Adaptive evolution specific to invasive populations was observed in detoxification, chemosensory, and digestion genes. We concluded that extant invasive FAW populations originated from the corn strain with potential contributions of adaptive evolution.

Published
2022

42. First chromosome scale genomes of ithomiine butterflies (Nymphalidae: Ithomiini): comparative models for mimicry genetic studies

Author

GAUTHIER, Jérémy, primary, Meier, Joana, additional, Legeai, Fabrice, additional, McClure, Melanie, additional, Whibley, Annabel, additional, Bretaudeau, Anthony, additional, Boulain, Hélène, additional, Parrinello, Hugues, additional, Mugford, Sam, additional, Durbin, Richard, additional, Zhou, Chenxi, additional, McCarthy, Shane, additional, Wheat, Christopher, additional, Piron-Prunier, Florence, additional, Monsempes, Christelle, additional, François, Marie-Christine, additional, Jay, Paul, additional, Nous, Camille, additional, Persyn, Emma, additional, Jacquin-Joly, Emmanuelle, additional, Meslin, Camille, additional, Montagné, Nicolas, additional, Lemaitre, Claire, additional, and Elias, Marianne, additional

Published
2022
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43. Spodoptera littoralis genome mining brings insights on the dynamic of expansion of gustatory receptors in polyphagous noctuidae

Author

Meslin, Camille, primary, Mainet, Pauline, additional, Montagné, Nicolas, additional, Robin, Stéphanie, additional, Legeai, Fabrice, additional, Bretaudeau, Anthony, additional, Johnston, J Spencer, additional, Koutroumpa, Fotini, additional, Persyn, Emma, additional, Monsempès, Christelle, additional, François, Marie-Christine, additional, and Jacquin-Joly, Emmanuelle, additional

Published
2022
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45. Additional file 1 of Host-plant adaptation as a driver of incipient speciation in the fall armyworm (Spodoptera frugiperda)

Author

Fiteni, Estelle, Durand, Karine, Gimenez, Sylvie, Meagher, Robert L., Legeai, Fabrice, Kergoat, Gael J., Nègre, Nicolas, d’Alençon, Emmanuelle, and Nam, Kiwoong

Abstract

Additional file 1: Table S1. Summary statistics of genome assemblies showing contiguity and correctness of the assemblies (BUSCO) generated in this study and other published assemblies. Table S2. The information of each sample used in this study. Table S3. Position of targets of selective sweeps specific to the corn or grass group. Table S5. Summary statistics of genome assemblies showing contiguity and correctness of the assemblies generated using SALSA2 and 3D-DNA. Table S6. The list of samples used in this study. Figure S1. Identification of strains. Figure S2. The result of the principal component analysis from whole nuclear genome sequences with the information of sampling locations. Figure S3. Ancestry coefficient analysis using the samples from Florida. Figure S4. The composite likelihood of being targeted by selection on chromosome 12 and Z chromosomes. Figure S5. Forward simulation to test increased DXY and FST at divergently selected loci causing reproductive isolation.

Published
2022
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47. RNA sequencing data for responses to drought stress and/or clubroot infection in developing seeds of Brassica napus

Author

Bianchetti, Grégoire, Clouet, Vanessa, Legeai, Fabrice, Baron, Cécile, Gazengel, Kévin, Carrillo, Aurélien, Manzanares-Dauleux, Maria, Buitink, Julia, Nesi, Nathalie, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, IRHS - Équipe SEED (Semences, Environnement et Développement) (IRHS-SEED), Université d'Angers (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université d'Angers (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, This research was funded through an ANR grant (ANR-14-JFAC-007-01) in the framework of the SYBRACLIM project (FACCE-JPI-ERA-NET+ CLIMATE SMART AGRICULTURE project call) and a grant from INRAE to J. Buitink and N. Nesi (INRAE-BAP-IB2017-SQUAL). G. Bianchetti was supported by INRAE and the Région de Bretagne through a 3 years PhD grant., ANR-14-JFAC-0007,SYBRACLIM,Securing yield stability of Brassica crops in changing climate conditions(2014), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), and Université d'Angers (UA)-AGROCAMPUS OUEST

Subjects
Drought stress, Science (General), Clubroot infection, [SDE.MCG]Environmental Sciences/Global Changes, Computer applications to medicine. Medical informatics, fungi, R858-859.7, food and beverages, Q1-390, Plasmodiophora brassicae, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Seed development, RNA-seq, Oilseed rape
Abstract

International audience; Oilseed rape (Brassica napus L.) is the third largest oil crop worldwide. Like other crops, oilseed rape faces unfavorable environmental conditions resulting from multiple and combined actions of abiotic and biotic constraints that occur throughout the growing season. In particular drought severely reduces seed yield but also impacts seed quality in oilseed rape. In addition, clubroot disease, caused by the pathogen Plasmodiophora brassicae, limits the yield of the oilseed rape crops grown in infected areas. Clubroot induces swellings or galls on the roots that decrease the flow of water and nutrients within the plant. Furthermore, combinations of different stresses lead to complex plant responses that can not be predicted by the simple addition of individual stress responses. Indeed, an abiotic constraint can either reduce or stimulate the plant response to a pathogen or pest. Transcriptome datasets from different conditions are key resources to improve our knowledge of environmental stress-resistance mechanisms in plant organs. Here, we describe a RNA-seq dataset consisting of 72 samples of immature B. napus seeds from plants grown either under drought, infected with P. brassicae, or a combination of both stresses. A total of 67.6 Gb of transcriptome paired-end reads were filtered, mapped onto the B. napus reference genome Darmor-bzh and used for identification of differentially expressed genes and gene ontology enrichment. The raw reads are available under accession PRJNA738318 at NCBI Sequence Read Archive (SRA) repository. The dataset is a resource for the scientific community exploring seed plasticity.

Published
2021
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48. Des analyses protéotrancriptomiques révèlent une grande expansion des protéines de type métalloprotéase dans les vésicules atypiques de venin de la guêpe parasitoide Meteorus pulchricornis (Braconidae)

Author

Gatti, Jean-Luc, Belghazi, Maya, Legeai, Fabrice, Ravallec, Marc, Frayssinet, Marie, Robin, Stéphanie, Aboubakar-Souna, Djibril, Srinivasan, Ramasamy, Tamò, Manuele, Poirié, Marylène, Volkoff, Anne-Nathalie, Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Institut de neurophysiopathologie (INP), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] (DGIMI), Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), World Vegetable Center (WorldVeg), International Institute of Tropical Agriculture (IITA-Benin), International Institute of Tropical Agriculture [Nigeria] (IITA), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Department of Plant Health (SPE) from the French National Institute for Research in Agriculture, Food and Environment (INRAE) and from the French Government, ANR-12-ADAP-0001,ABC - PaPoGen,Adaptation en lutte biologique - Génomique des populations de parasitoïdes(2012), ANR-11-LABX-0028,SIGNALIFE,Réseau d'Innovation sur les Voies de Signalisation en Sciences de la Vie(2011), ANR-15-IDEX-0001,UCA JEDI,Idex UCA JEDI(2015), Université Nice Sophia Antipolis (1965 - 2019) (UNS), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique)

Subjects
Meteorus pulchricornis, venomics, DUF-4803 proteins, Braconidae, [SDV]Life Sciences [q-bio], virus-like particles (VLPs), transcriptomic, metalloproteases, parasitoid wasp, complex mixtures, proteomic
Abstract

International audience; Meteorus pulchricornis (Ichneumonoidea, Braconidae) is an endoparasitoid wasp of lepidopteran caterpillars. Its parasitic success relies on vesicles (named M. pulchricornis Virus-Like Particles or MpVLPs) that are synthesized in the venom gland and injected into the parasitoid host along with the venom during oviposition. In order to define the content and understand the biogenesis of these atypical vesicles, we performed a transcriptome analysis of the venom gland and a proteomic analysis of the venom and purified MpVLPs. About half of the MpVLPs and soluble venom proteins identified were unknown and no similarity with any known viral sequence was found. However, MpVLPs contained a large number of proteins labelled as metalloproteinases while the most abundant protein family in the soluble venom was that of proteins containing the Domain of Unknown Function DUF-4803. The high number of these proteins identified suggests that a large expansion of these two protein families occurred in M. pulchricornis. Therefore, although the exact mechanism of MpVLPs formation remains to be elucidated, these vesicles appear to be “metalloproteinase bombs” that may have several physiological roles in the host including modifying the functions of its immune cells. The role of DUF4803 proteins, also present in the venom of other braconids, remains to be clarified.

Published
2021
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49. MTG-Link: filling gaps in draft genome assemblies with linked read data

Author

Guichard, Anne, Legeai, Fabrice, Tagu, Denis, Lemaitre, Claire, Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
Genome assembly, Linked reads, Gap-filling, High throughput sequencing, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

National audience; De novo genome assembly is a challenging task, especially for large non-model organism genomes. Low sequence coverage, genomic repeats and heterozygosity often create ambiguities in the assembly, and result in undefined sequences between contigs called "gaps". Hence, filling gaps in draft genomes has become a natural sub-problem of many de novo genome assembly projects. Even though there are several tools for closing gaps, to our knowledge none uses the long-range information of the linked read data. Linked read technologies have a great potential for filling gaps in draft genomes as they provide long-range information while maintaining the power and accuracy of short-read sequencing. In this work, we present MTG-Link, a novel gap-filling tool dedicated to linked read data. Taking advantage of the barcode information contained in the linked read dataset, a subsample of reads is first selected for each gap. These reads are then locally assembled and the resulting gap-filled sequences are automatically evaluated. We validated our approach on a real 10X genomics linked read dataset, on a set of simulated gaps, and showed that the read subsampling step of MTG-Link enables to get better gap assemblies in a time/memory efficient manner. We also applied MTG-Link on individual genomes of a mimetic butterfly (Heliconius numata), where it significantly improved the contiguity of a 1.3 Mb locus of biological interest. MTG-Link is freely available at https://github.com/anne-gcd/MTG-Link.

Published
2021

50. Spodoptera littoralis genome mining brings insights on the dynamic of expansion of gustatory receptors in polyphagous noctuidae

Author

Meslin, Camille, primary, Mainet, Pauline, additional, Montagné, Nicolas, additional, Robin, Stéphanie, additional, Legeai, Fabrice, additional, Bretaudeau, Anthony, additional, Johnston, J. Spencer, additional, Koutroumpa, Fotini, additional, Persyn, Emma, additional, Monsempès, Christelle, additional, François, Marie-Christine, additional, and Jacquin-Joly, Emmanuelle, additional

Published
2021
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