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143 results on '"Lopez-Roques, Céline"'

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

Kuhl, Heiner, Euclide, Peter T., Klopp, Christophe, Cabau, Cédric, Zahm, Margot, Lopez-Roques, Céline, Iampietro, Carole, Kuchly, Claire, Donnadieu, Cécile, Feron, Romain, Parrinello, Hugues, Poncet, Charles, Jaffrelo, Lydia, Confolent, Carole, Wen, Ming, Herpin, Amaury, Jouanno, Elodie, Bestin, Anastasia, Haffray, Pierrick, Morvezen, Romain, de Almeida, Taina Rocha, Lecocq, Thomas, Schaerlinger, Bérénice, Chardard, Dominique, Żarski, Daniel, Larson, Wesley A., Postlethwait, John H., Timirkhanov, Serik, Kloas, Werner, Wuertz, Sven, Stöck, Matthias, and Guiguen, Yann

Published
2024
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4. Complete Genome Sequence of the Type Strain Pectobacterium punjabense SS95, Isolated from a Potato Plant with Blackleg Symptoms.

Author

Sarfraz, Sohaib, Oulghazi, Saïd, Cigna, Jérémy, Sahi, Shahbaz, Riaz, Kashif, Tufail, Muhammad, Fayyaz, Amna, Naveed, Khalid, Hameed, Akhtar, Lopez-Roques, Céline, Vandecasteele, Céline, and Faure, Denis

Abstract

Pectobacterium punjabense is a newly described species causing blackleg disease in potato plants. Therefore, by the combination of long (Oxford Nanopore Technologies, MinION) and short (Illumina MiSeq) reads, we sequenced the complete genome of P. punjabense SS95T, which contains a circular chromosome of 4.793 Mb with a GC content of 50.7%.

Published
2020

6. A 180 Myr-old female-specific genome region in sturgeon reveals the oldest known vertebrate sex determining system with undifferentiated sex chromosomes

Author

Kuhl, Heiner, Guiguen, Yann, Höhne, Christin, Kreuz, Eva, Du, Kang, Klopp, Christophe, Lopez-Roques, Céline, Yebra-Pimentel, Elena Santidrian, Ciorpac, Mitica, Gessner, Jörn, Holostenco, Daniela, Kleiner, Wibke, Kohlmann, Klaus, Lamatsch, Dunja K., Prokopov, Dmitry, Bestin, Anastasia, Bonpunt, Emmanuel, Debeuf, Bastien, Haffray, Pierrick, Morvezen, Romain, Patrice, Pierre, Suciu, Radu, Dirks, Ron, Wuertz, Sven, Kloas, Werner, Schartl, Manfred, and Stöck, Matthias

Published
2021

7. A chromosome-level, haplotype-phased Vanilla planifolia genome highlights the challenge of partial endoreplication for accurate whole-genome assembly

Author

Piet, Quentin, Droc, Gaetan, Marande, William, Sarah, Gautier, Bocs, Stéphanie, Klopp, Christophe, Bourge, Mickael, Siljak-Yakovlev, Sonja, Bouchez, Olivier, Lopez-Roques, Céline, Lepers-Andrzejewski, Sandra, Bourgois, Laurent, Zucca, Joseph, Dron, Michel, Besse, Pascale, Grisoni, Michel, Jourda, Cyril, and Charron, Carine

Published
2022
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8. Increased Evolutionary Rate in the Z chromosome of Sympatric and Allopatric Species of Morpho Butterflies.

Author

Villavicencio, Manuela López, Ledamoisel, Joséphine, Poloni, Riccardo, Lopez-Roques, Céline, Debat, Vincent, and Llaurens, Violaine

Subjects
SEX chromosomes, CHROMOSOMAL rearrangement, CLOCK genes, GENOMICS, SYMPATRIC speciation, GENE flow
Abstract

Divergent evolution of genomes among closely related species is shaped by both neutral processes and ecological forces, such as local adaptation and reinforcement. These factors can drive accelerated evolution of sex chromosomes relative to autosomes. Comparative genomic analyses between allopatric and sympatric species with overlapping or divergent ecological niches offer insights into reinforcement and ecological specialization on genome evolution. In the butterfly genus Morpho , several species coexist in sympatry, with specialization across forest strata and temporal niches. We analyzed the genomes of eight Morpho species, along with previously published genomes of three others, to compare chromosomal rearrangements and signs of positive selection in the Z chromosome v s. autosomes. We found extensive chromosomal rearrangements in Z chromosome, particularly in sympatric species with similar ecological niches, suggesting a role for inversions in restricting gene flow at a postzygotic level. Z-linked genes also exhibited significantly higher dN/dS ratios than autosomal genes across the genus, with pronounced differences in closely related species living in sympatry. Additionally, we examined the evolution of eight circadian clock genes, detecting positive selection in Period, located on the Z chromosome. Our findings suggest that the Z chromosome evolves more rapidly than autosomes, particularly among closely related species, raising questions about its role in prezygotic and postzygotic isolation mechanisms. [ABSTRACT FROM AUTHOR]

Published
2024
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10. Changes in DNA methylation contribute to rapid adaptation in bacterial plant pathogen evolution.

Author

Gopalan-Nair, Rekha, Coissac, Aurore, Legrand, Ludovic, Lopez-Roques, Céline, Pécrix, Yann, Vandecasteele, Céline, Bouchez, Olivier, Barlet, Xavier, Lanois, Anne, Givaudan, Alain, Brillard, Julien, Genin, Stéphane, and Guidot, Alice

Subjects
DNA analysis, AGRICULTURE, BACTERIAL adaptation, GENETIC mutation, GENE expression
Abstract

Adaptation is usually explained by beneficial genetic mutations that are transmitted from parents to offspring and become fixed in the adapted population. However, genetic mutation analysis alone is not sufficient to fully explain the adaptive processes, and several studies report the existence of nongenetic (or epigenetic) inheritance that can enable adaptation to new environments. In the present work, we tested the hypothesis of the role of DNA methylation, a form of epigenetic modification, in adaptation of the plant pathogen Ralstonia pseudosolanacearum to the host during experimental evolution. Using SMRT-seq technology, we analyzed the methylomes of 31 experimentally evolved clones obtained after serial passages on 5 different plant species during 300 generations. Comparison with the methylome of the ancestral clone revealed a list of 50 differential methylated sites (DMSs) at the GTWWAC motif. Gene expression analysis of the 39 genes targeted by these DMSs revealed limited correlation between differential methylation and differential expression of the corresponding genes. Only 1 gene showed a correlation, the RSp0338 gene encoding the EpsR regulator protein. The MSRE-qPCR technology, used as an alternative approach for DNA methylation analysis, also found the 2 DMSs upstream RSp0338. Using site-directed mutagenesis, we demonstrated the contribution of these 2 DMSs in host adaptation. As these DMSs appeared very early in the experimental evolution, we hypothesize that such fast epigenetic changes can allow rapid adaptation to the plant stem environment. In addition, we found that the change in DNA methylation upstream RSp0338 remains stable at least for 100 generations outside the host and thus can contribute to long-term adaptation to the host plant. To our knowledge, this is the first study showing a direct link between bacterial epigenetic variation and adaptation to a new environment. Do epigenetic changes contribute to long-term bacterial adaptation? This study shows that changes in DNA methylation enable rapid adaptation of the major agricultural bacterial pathogen Ralstonia pseudosolanacearum to novel hosts, stable over 100 generations. [ABSTRACT FROM AUTHOR]

Published
2024
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14. A duplicated copy of id2b is an unusual sex-determining candidate gene on the Y chromosome of arapaima (Arapaima gigas)

Author

Adolfi, Mateus C., Du, Kang, Kneitz, Susanne, Cabau, Cédric, Zahm, Margot, Klopp, Christophe, Feron, Romain, Paixão, Rômulo V., Varela, Eduardo S., de Almeida, Fernanda L., de Oliveira, Marcos A., Nóbrega, Rafael H., Lopez-Roques, Céline, Iampietro, Carole, Lluch, Jérôme, Kloas, Werner, Wuertz, Sven, Schaefer, Fabian, Stöck, Matthias, Guiguen, Yann, and Schartl, Manfred

Published
2021
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15. Population genomics of apricots unravels domestication history and adaptive events

Author

Groppi, Alexis, Liu, Shuo, Cornille, Amandine, Decroocq, Stéphane, Bui, Quynh Trang, Tricon, David, Cruaud, Corinne, Arribat, Sandrine, Belser, Caroline, Marande, William, Salse, Jérôme, Huneau, Cécile, Rodde, Nathalie, Rhalloussi, Wassim, Cauet, Stéphane, Istace, Benjamin, Denis, Erwan, Carrère, Sébastien, Audergon, Jean-Marc, Roch, Guillaume, Lambert, Patrick, Zhebentyayeva, Tetyana, Liu, Wei-Sheng, Bouchez, Olivier, Lopez-Roques, Céline, Serre, Rémy-Félix, Debuchy, Robert, Tran, Joseph, Wincker, Patrick, Chen, Xilong, Pétriacq, Pierre, Barre, Aurélien, Nikolski, Macha, Aury, Jean-Marc, Abbott, Albert Glenn, Giraud, Tatiana, and Decroocq, Véronique

Published
2021
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18. Whole-genome landscape of Medicago truncatula symbiotic genes

Author

Pecrix, Yann, Staton, S. Evan, Sallet, Erika, Lelandais-Brière, Christine, Moreau, Sandra, Carrère, Sébastien, Blein, Thomas, Jardinaud, Marie-Françoise, Latrasse, David, Zouine, Mohamed, Zahm, Margot, Kreplak, Jonathan, Mayjonade, Baptiste, Satgé, Carine, Perez, Magali, Cauet, Stéphane, Marande, William, Chantry-Darmon, Céline, Lopez-Roques, Céline, Bouchez, Olivier, Bérard, Aurélie, Debellé, Frédéric, Muños, Stéphane, Bendahmane, Abdelhafid, Bergès, Hélène, Niebel, Andreas, Buitink, Julia, Frugier, Florian, Benhamed, Moussa, Crespi, Martin, Gouzy, Jérôme, and Gamas, Pascal

Published
2018
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19. The Rosa genome provides new insights into the domestication of modern roses

Author

Raymond, Olivier, Gouzy, Jérôme, Just, Jérémy, Badouin, Hélène, Verdenaud, Marion, Lemainque, Arnaud, Vergne, Philippe, Moja, Sandrine, Choisne, Nathalie, Pont, Caroline, Carrère, Sébastien, Caissard, Jean-Claude, Couloux, Arnaud, Cottret, Ludovic, Aury, Jean-Marc, Szécsi, Judit, Latrasse, David, Madoui, Mohammed-Amin, François, Léa, Fu, Xiaopeng, Yang, Shu-Hua, Dubois, Annick, Piola, Florence, Larrieu, Antoine, Perez, Magali, Labadie, Karine, Perrier, Lauriane, Govetto, Benjamin, Labrousse, Yoan, Villand, Priscilla, Bardoux, Claudia, Boltz, Véronique, Lopez-Roques, Céline, Heitzler, Pascal, Vernoux, Teva, Vandenbussche, Michiel, Quesneville, Hadi, Boualem, Adnane, Bendahmane, Abdelhafid, Liu, Chang, Le Bris, Manuel, Salse, Jérôme, Baudino, Sylvie, Benhamed, Moussa, Wincker, Patrick, and Bendahmane, Mohammed

Published
2018
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24. A pan-genome of 69 Arabidopsis thalianaaccessions reveals a conserved genome structure throughout the global species range

Author

Lian, Qichao, Huettel, Bruno, Walkemeier, Birgit, Mayjonade, Baptiste, Lopez-Roques, Céline, Gil, Lisa, Roux, Fabrice, Schneeberger, Korbinian, and Mercier, Raphael

Abstract

Although originally primarily a system for functional biology, Arabidopsis thalianahas, owing to its broad geographical distribution and adaptation to diverse environments, developed into a powerful model in population genomics. Here we present chromosome-level genome assemblies of 69 accessions from a global species range. We found that genomic colinearity is very conserved, even among geographically and genetically distant accessions. Along chromosome arms, megabase-scale rearrangements are rare and typically present only in a single accession. This indicates that the karyotype is quasi-fixed and that rearrangements in chromosome arms are counter-selected. Centromeric regions display higher structural dynamics, and divergences in core centromeres account for most of the genome size variations. Pan-genome analyses uncovered 32,986 distinct gene families, 60% being present in all accessions and 40% appearing to be dispensable, including 18% private to a single accession, indicating unexplored genic diversity. These 69 new Arabidopsis thalianagenome assemblies will empower future genetic research.

Published
2024
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25. A chromosome-level, haplotype-phased genome assembly for Vanilla planifolia highlights that partial endoreplication challenges accurate whole genome assembly

Author

Piet, Quentin, Droc, Gaëtan, Marande, William, Sarah, Gautier, Bocs, Stéphanie, Klopp, Christophe, Bourge, Mickael, Siljak-Yakovlev, Sonja, Bouchez, Olivier, Lopez-Roques, Céline, Lepers-Andrzejewski, Sandra, Bourgois, Laurent, Zucca, Joseph, Dron, Michel, Besse, Pascale, Grisoni, Michel, Jourda, Cyril, Charron, Carine, Piet, Quentin, Droc, Gaëtan, Marande, William, Sarah, Gautier, Bocs, Stéphanie, Klopp, Christophe, Bourge, Mickael, Siljak-Yakovlev, Sonja, Bouchez, Olivier, Lopez-Roques, Céline, Lepers-Andrzejewski, Sandra, Bourgois, Laurent, Zucca, Joseph, Dron, Michel, Besse, Pascale, Grisoni, Michel, Jourda, Cyril, and Charron, Carine

Abstract

Vanilla planifolia, the species cultivated to produce one of the world's most popular flavors, is highly prone to partial genome endoreplication, which leads to highly unbalanced DNA content in cells. We report here the first molecular evidence of partial endoreplication at the chromosome scale by the assembly and annotation of an accurate haplotype-phased genome of V. planifolia. Cytogenetic data demonstrated that the diploid genome size is 4.09 Gb, with 16 chromosome pairs, although aneuploid cells are frequently observed. Using PacBio HiFi and optical mapping, we assembled and phased a diploid genome of 3.4 Gb with a scaffold N50 of 1.2 Mb and 59 128 predicted protein-coding genes. The atypical k-mer frequencies and the uneven sequencing depth observed agreed with our expectation of unbalanced genome representation. Sixty-seven percent of the genes were scattered over only 30% of the genome, putatively linking gene-rich regions and the endoreplication phenomenon. By contrast, low-coverage regions (non-endoreplicated) were rich in repeated elements but also contained 33% of the annotated genes. Furthermore, this assembly showed distinct haplotype-specific sequencing depth variation patterns, suggesting complex molecular regulation of endoreplication along the chromosomes. This high-quality, anchored assembly represents 83% of the estimated V. planifolia genome. It provides a significant step toward the elucidation of this complex genome. To support post-genomics efforts, we developed the Vanilla Genome Hub, a user-friendly integrated web portal that enables centralized access to high-throughput genomic and other omics data and interoperable use of bioinformatics tools.

Published
2022

27. Suspicions of two bridgehead invasions ofXylella fastidiosasubsp.multiplexin France

Author

Dupas, Enora, primary, Durand, Karine, additional, Rieux, Adrien, additional, Briand, Martial, additional, Pruvost, Olivier, additional, Cunty, Amandine, additional, Denancé, Nicolas, additional, Donnadieu, Cécile, additional, Legendre, Bruno, additional, Lopez-Roques, Céline, additional, Cesbron, Sophie, additional, Ravigné, Virginie, additional, and Jacques, Marie-Agnès, additional

Published
2022
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29. Preliminary results from Nanopore Q20+ sequencing

Author

Kuchly, Claire, Sabban, Jules, Darnige, Eden, Eché, Camille, Suin, Amandine, Vandecasteele, Céline, Birbes, Clement, Dreau, Andreea, Klopp, Christophe, Gaspin, Christine, Milan, Denis, Donnadieu, Cécile, Salin, Gérald, Lopez-Roques, Céline, Kuchly, Claire, 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), 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), and Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE)

Subjects
[SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SDV.BIO] Life Sciences [q-bio]/Biotechnology
Abstract

International audience

Published
2022

30. A supernumerary “B-sex” chromosome drives male sex determination in the Pachón cavefish, Astyanax mexicanus

Author

Imarazene, Boudjema, Du, Kang, Beille, Séverine, Jouanno, Elodie, Feron, Romain, Pan, Qiaowei, Torres-Paz, Jorge, Lopez-Roques, Céline, Castinel, Adrien, Gil, Lisa, Kuchly, Claire, Donnadieu, Cécile, Parrinello, Hugues, Journot, Laurent, Cabau, Cédric, Zahm, Margot, Klopp, Christophe, Pavlica, Tomáš, Al-Rikabi, Ahmed, Liehr, Thomas, Simanovsky, Sergey A., Bohlen, Joerg, Sember, Alexandr, Perez, Julie, Veyrunes, Frédéric, Mueller, Thomas D., Postlethwait, John H., Schartl, Manfred, Herpin, Amaury, Rétaux, Sylvie, and Guiguen, Yann

Published
2021
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31. Convergent Rewiring of the Virulence Regulatory Network Promotes Adaptation of Ralstonia solanacearum on Resistant Tomato

Author

Gopalan-Nair, Rekha, Jardinaud, Marie-Françoise, Legrand, Ludovic, Landry, David, Barlet, Xavier, Lopez-Roques, Céline, Vandecasteele, Céline, Bouchez, Olivier, Genin, Stéphane, Guidot, Alice, Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-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), 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), French Research Federation 'FR AIB' (Agrobiosciences Interactions and Biodiversity), GET-PACBIO program (Programme Operationnel FEDER-FSE MIDI-PYRENEES ET GARONNE 2014-2020), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), ANR-17-CE20-0005,EPI-PATH,Rôle des modifications épigénétiques chez un pathogène de plante au cours de l'adaptation à l'hôte et des changements d'hôte(2017), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), SEGUIN, Nathalie, Initiative d'excellence - Université Fédérale de Toulouse - - UNITI2011 - ANR-11-IDEX-0002 - IDEX - VALID, Rôle des modifications épigénétiques chez un pathogène de plante au cours de l'adaptation à l'hôte et des changements d'hôte - - EPI-PATH2017 - ANR-17-CE20-0005 - AAPG2017 - VALID, Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID, 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
[SDV.BIO]Life Sciences [q-bio]/Biotechnology, bacterial plant pathogen, Adaptation, Biological, [SDV.GEN] Life Sciences [q-bio]/Genetics, AcademicSubjects/SCI01180, Regulon, [SDV.BV.BOT] Life Sciences [q-bio]/Vegetal Biology/Botanics, Solanum lycopersicum, transcriptomic variation, adaptive potential, genomic polymorphisms, experimental evolution, Discoveries, [SDV.GEN]Life Sciences [q-bio]/Genetics, AcademicSubjects/SCI01130, food and beverages, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, fitness measure, Biological Evolution, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.BIO] Life Sciences [q-bio]/Biotechnology, Gain of Function Mutation, Ralstonia solanacearum, Genetic Fitness, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Transcriptome
Abstract

International audience; Abstract The evolutionary and adaptive potential of a pathogen is a key determinant for successful host colonization and proliferation but remains poorly known for most of the pathogens. Here, we used experimental evolution combined with phenotyping, genomics, and transcriptomics to estimate the adaptive potential of the bacterial plant pathogen Ralstonia solanacearum to overcome the quantitative resistance of the tomato cultivar Hawaii 7996. After serial passaging over 300 generations, we observed pathogen adaptation to within-plant environment of the resistant cultivar but no plant resistance breakdown. Genomic sequence analysis of the adapted clones revealed few genetic alterations, but we provide evidence that all but one were gain of function mutations. Transcriptomic analyses revealed that even if different adaptive events occurred in independently evolved clones, there is convergence toward a global rewiring of the virulence regulatory network as evidenced by largely overlapping gene expression profiles. A subset of four transcription regulators, including HrpB, the activator of the type 3 secretion system regulon and EfpR, a global regulator of virulence and metabolic functions, emerged as key nodes of this regulatory network that are frequently targeted to redirect the pathogen’s physiology and improve its fitness in adverse conditions. Significant transcriptomic variations were also detected in evolved clones showing no genomic polymorphism, suggesting that epigenetic modifications regulate expression of some of the virulence network components and play a major role in adaptation as well.

Published
2021
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32. Transcriptional response to host chemical cues underpins the expansion of host range in a fungal plant pathogen lineage

Author

Kusch, Stefan, primary, Larrouy, Justine, additional, Ibrahim, Heba M. M., additional, Mounichetty, Shantala, additional, Gasset, Noémie, additional, Navaud, Olivier, additional, Mbengue, Malick, additional, Zanchetta, Catherine, additional, Lopez-Roques, Céline, additional, Donnadieu, Cécile, additional, Godiard, Laurence, additional, and Raffaele, Sylvain, additional

Published
2021
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33. Genome structure and content of the rice root‐knot nematode ( Meloidogyne graminicola )

Author

Phan, Ngan Thi, Orjuela, Julie, Danchin, Etienne, Klopp, Christophe, Perfus‐Barbeoch, Laetitia, Kozlowski, Djampa, Koutsovoulos, Georgios, Lopez‐Roques, Céline, Bouchez, Olivier, Zahm, Margot, Besnard, Guillaume, Bellafiore, Stéphane, Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), Plateforme Bio-Informatique - Génotoul, 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), 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), Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Consultative Group for International Agricultural Research Program on rice-agrifood systems, Université Nice Sophia Antipolis (1965 - 2019) (UNS), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), 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 Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), 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
cereals, Ecology, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, horizontal gene transfer, pest, root‐knot nematode, transposable element, QH540-549.5, reference genome
Abstract

International audience; Discovered in the 1960s,Meloidogyne graminicolais a root-knot nematode species considered as a major threat to rice production. Yet, its origin, genomic structure, and intraspecific diversity are poorly understood. So far, such studies have been limited by the unavailability of a sufficiently complete and well-assembled genome. In this study, using a combination of Oxford Nanopore Technologies and Illumina sequencing data, we generated a highly contiguous reference genome (283 scaffolds with an N50 length of 294 kb, totaling 41.5 Mb). The completeness scores of our assembly are among the highest currently published forMeloidogynegenomes. We predicted 10,284 protein-coding genes spanning 75.5% of the genome. Among them, 67 are identified as possibly originating from horizontal gene transfers (mostly from bacteria), which supposedly contribute to nematode infection, nutrient processing, and plant defense manipulation. Besides, we detected 575 canonical transposable elements (TEs) belonging to seven orders and spanning 2.61% of the genome. These TEs might promote genomic plasticity putatively related to the evolution ofM. graminicolaparasitism. This high-quality genome assembly constitutes a major improvement regarding previously available versions and represents a valuable molecular resource for future phylogenomic studies ofMeloidogynespecies. In particular, this will foster comparative genomic studies to trace back the evolutionary history ofM. graminicolaand its closest relatives.

Published
2020
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34. DNAModAnnot: A R toolbox for DNA modification filtering and annotation

Author

Hardy, Alexis, Matelot, Mélody, Touzeau, Amandine, Klopp, Christophe, Lopez-Roques, Céline, Duharcourt, Sandra, Defrance, Matthieu, Hardy, Alexis, Matelot, Mélody, Touzeau, Amandine, Klopp, Christophe, Lopez-Roques, Céline, Duharcourt, Sandra, and Defrance, Matthieu

Abstract

Motivation: Long-read sequencing technologies can be employed to detect and map DNA modifications at the nucleotide resolution on a genome-wide scale. However, published software packages neglect the integration of genomic annotation and comprehensive filtering when analyzing patterns of modified bases detected using Pacific Biosciences (PacBio) or Oxford Nanopore Technologies (ONT) data. Here, we present DNA Modification Annotation (DNAModAnnot), a R package designed for the global analysis of DNA modification patterns using adapted filtering and visualization tools. Results: We tested our package using PacBio sequencing data to analyze patterns of the 6-methyladenine (6mA) in the ciliate Paramecium tetraurelia, in which high 6mA amounts were previously reported. We found P. tetraurelia 6mA genome-wide distribution to be similar to other ciliates. We also performed 5-methylcytosine (5mC) analysis in human lymphoblastoid cells using ONT data and confirmed previously known patterns of 5mC. DNAModAnnot provides a toolbox for the genome-wide analysis of different DNA modifications using PacBio and ONT long-read sequencing data., SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2021

36. A Supernumerary “B-Sex” Chromosome Drives Male Sex Determination in the Pachón Cavefish, Astyanax mexicanus

Author

Imarazene, Boudjema, primary, Du, Kang, additional, Beille, Séverine, additional, Jouanno, Elodie, additional, Feron, Romain, additional, Pan, Qiaowei, additional, Torres-Paz, Jorge, additional, Lopez-Roques, Céline, additional, Castinel, Adrien, additional, Gil, Lisa, additional, Kuchly, Claire, additional, Donnadieu, Cécile, additional, Parrinello, Hugues, additional, Journot, Laurent, additional, Cabau, Cédric, additional, Zham, Margot, additional, Klopp, Christophe, additional, Pavlica, Tomáš, additional, Al-Rikabi, Ahmed, additional, Liehr, Thomas, additional, Simanovsky, Sergey, additional, Bohlen, Joerg, additional, Sember, Alexandr, additional, Perez, Julie, additional, Veyrunes, Frédéric, additional, Mueller, Thomas, additional, Postlethwait, John, additional, Schartl, Manfred, additional, Herpin, Amaury, additional, Rétaux, Sylvie, additional, and Guiguen, Yann, additional

Published
2021
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38. Complete Genome Sequence of Microbacterium sp. Strain Nx66, Isolated from Waters Contaminated with Petrochemicals in El Saf-Saf Valley, Algeria

Author

Chéraiti, Nardjess, primary, Plewniak, Frédéric, additional, Tighidet, Salima, additional, Sayeh, Amalia, additional, Gil, Lisa, additional, Malherbe, Ludivine, additional, Memmi, Yosr, additional, Zilliox, Laurence, additional, Vandecasteele, Céline, additional, Boyer, Pierre, additional, Lopez-Roques, Céline, additional, Jaulhac, Benoît, additional, Bensouilah, Mourad, additional, and Bertin, Philippe N., additional

Published
2020
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39. A 180 My-old female-specific genome region in sturgeon reveals the oldest known vertebrate sex determining system with undifferentiated sex chromosomes

Author

Kuhl, Heiner, primary, Guiguen, Yann, additional, Höhne, Christin, additional, Kreuz, Eva, additional, Du, Kang, additional, Klopp, Christophe, additional, Lopez-Roques, Céline, additional, Yebra-Pimentel, Elena Santidrian, additional, Ciorpac, Mitica, additional, Gessner, Jörn, additional, Holostenco, Daniela, additional, Kleiner, Wibke, additional, Kohlmann, Klaus, additional, Lamatsch, Dunja K., additional, Prokopov, Dmitry, additional, Bestin, Anastasia, additional, Bonpunt, Emmanuel, additional, Debeuf, Bastien, additional, Haffray, Pierrick, additional, Morvezen, Romain, additional, Patrice, Pierre, additional, Suciu, Radu, additional, Dirks, Ron, additional, Wuertz, Sven, additional, Kloas, Werner, additional, Schartl, Manfred, additional, and Stöck, Matthias, additional

Published
2020
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42. Long-Read Genome Sequence of the Sugar Beet Rhizosphere Mycoparasite Pythium oligandrum

Author

Faure, Charlène, primary, Veyssière, Marine, additional, Boëlle, Betty, additional, San Clemente, Hélène, additional, Bouchez, Olivier, additional, Lopez-Roques, Céline, additional, Chaubet, Adeline, additional, Martinez, Yves, additional, Bezouška, Karel, additional, Suchánek, Martin, additional, Gaulin, Elodie, additional, Rey, Thomas, additional, and Dumas, Bernard, additional

Published
2020
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43. The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird

Author

Gautier, Mathieu, Yamaguchi, Junichi, Foucaud, Julien, Loiseau, Anne, Ausset, Aurélien, Facon, Benoit, Gschloessl, Bernhard, Lagnel, Jacques, Loire, Etienne, Parrinello, Hugues, Severac, Dany, Lopez-Roques, Celine, Donnadieu, Cecile, Manno, Maxime, Berges, Helene, Gharbi, Karim, Lawson-Handley, Lori, Zang, Lian-Sheng, Vogel, Heiko, Estoup, Arnaud, and Prud’homme, Benjamin

Published
2018
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44. Independent Origin of XY and ZW Sex Determination Mechanisms in Mosquitofish Sister Species

Author

Kottler, Verena A, primary, Feron, Romain, additional, Nanda, Indrajit, additional, Klopp, Christophe, additional, Du, Kang, additional, Kneitz, Susanne, additional, Helmprobst, Frederik, additional, Lamatsch, Dunja K, additional, Lopez-Roques, Céline, additional, Lluch, Jerôme, additional, Journot, Laurent, additional, Parrinello, Hugues, additional, Guiguen, Yann, additional, and Schartl, Manfred, additional

Published
2020
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46. Accurate Identification and Quantification of DNA Species by Next-Generation Sequencing in Adeno-Associated Viral Vectors Produced in Insect Cells

Author

Penaud-Budloo, Magalie, primary, Lecomte, Emilie, additional, Guy-Duché, Aurélien, additional, Saleun, Sylvie, additional, Roulet, Alain, additional, Lopez-Roques, Céline, additional, Tournaire, Benoît, additional, Cogné, Benjamin, additional, Léger, Adrien, additional, Blouin, Véronique, additional, Lindenbaum, Pierre, additional, Moullier, Philippe, additional, and Ayuso, Eduard, additional

Published
2017
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47. Whole-genome landscape of Medicago truncatulasymbiotic genes

Author

Pecrix, Yann, Staton, S. Evan, Sallet, Erika, Lelandais-Brière, Christine, Moreau, Sandra, Carrère, Sébastien, Blein, Thomas, Jardinaud, Marie-Françoise, Latrasse, David, Zouine, Mohamed, Zahm, Margot, Kreplak, Jonathan, Mayjonade, Baptiste, Satgé, Carine, Perez, Magali, Cauet, Stéphane, Marande, William, Chantry-Darmon, Céline, Lopez-Roques, Céline, Bouchez, Olivier, Bérard, Aurélie, Debellé, Frédéric, Muños, Stéphane, Bendahmane, Abdelhafid, Bergès, Hélène, Niebel, Andreas, Buitink, Julia, Frugier, Florian, Benhamed, Moussa, Crespi, Martin, Gouzy, Jérôme, and Gamas, Pascal

Abstract

Advances in deciphering the functional architecture of eukaryotic genomes have been facilitated by recent breakthroughs in sequencing technologies, enabling a more comprehensive representation of genes and repeat elements in genome sequence assemblies, as well as more sensitive and tissue-specific analyses of gene expression. Here we show that PacBio sequencing has led to a substantially improved genome assembly of Medicago truncatulaA17, a legume model species notable for endosymbiosis studies1, and has enabled the identification of genome rearrangements between genotypes at a near-base-pair resolution. Annotation of the new M. truncatulagenome sequence has allowed for a thorough analysis of transposable elements and their dynamics, as well as the identification of new players involved in symbiotic nodule development, in particular 1,037 upregulated long non-coding RNAs (lncRNAs). We have also discovered that a substantial proportion (~35% and 38%, respectively) of the genes upregulated in nodules or expressed in the nodule differentiation zone colocalize in genomic clusters (270 and 211, respectively), here termed symbiotic islands. These islands contain numerous expressed lncRNA genes and display differentially both DNA methylation and histone marks. Epigenetic regulations and lncRNAs are therefore attractive candidate elements for the orchestration of symbiotic gene expression in the M. truncatulagenome.

Published
2018
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48. The Rosagenome provides new insights into the domestication of modern roses

Author

Raymond, Olivier, Gouzy, Jérôme, Just, Jérémy, Badouin, Hélène, Verdenaud, Marion, Lemainque, Arnaud, Vergne, Philippe, Moja, Sandrine, Choisne, Nathalie, Pont, Caroline, Carrère, Sébastien, Caissard, Jean-Claude, Couloux, Arnaud, Cottret, Ludovic, Aury, Jean-Marc, Szécsi, Judit, Latrasse, David, Madoui, Mohammed-Amin, François, Léa, Fu, Xiaopeng, Yang, Shu-Hua, Dubois, Annick, Piola, Florence, Larrieu, Antoine, Perez, Magali, Labadie, Karine, Perrier, Lauriane, Govetto, Benjamin, Labrousse, Yoan, Villand, Priscilla, Bardoux, Claudia, Boltz, Véronique, Lopez-Roques, Céline, Heitzler, Pascal, Vernoux, Teva, Vandenbussche, Michiel, Quesneville, Hadi, Boualem, Adnane, Bendahmane, Abdelhafid, Liu, Chang, Le Bris, Manuel, Salse, Jérôme, Baudino, Sylvie, Benhamed, Moussa, Wincker, Patrick, and Bendahmane, Mohammed

Abstract

Roses have high cultural and economic importance as ornamental plants and in the perfume industry. We report the rose whole-genome sequencing and assembly and resequencing of major genotypes that contributed to rose domestication. We generated a homozygous genotype from a heterozygous diploid modern rose progenitor, Rosa chinensis‘Old Blush’. Using single-molecule real-time sequencing and a meta-assembly approach, we obtained one of the most comprehensive plant genomes to date. Diversity analyses highlighted the mosaic origin of ‘La France’, one of the first hybrids combining the growth vigor of European species and the recurrent blooming of Chinese species. Genomic segments of Chinese ancestry identified new candidate genes for recurrent blooming. Reconstructing regulatory and secondary metabolism pathways allowed us to propose a model of interconnected regulation of scent and flower color. This genome provides a foundation for understanding the mechanisms governing rose traits and should accelerate improvement in roses, Rosaceae and ornamentals.

Published
2018
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49. A chromosome-level, haplotype-phased Vanilla planifoliagenome highlights the challenge of partial endoreplication for accurate whole-genome assembly

Author

Piet, Quentin, Droc, Gaetan, Marande, William, Sarah, Gautier, Bocs, Stéphanie, Klopp, Christophe, Bourge, Mickael, Siljak-Yakovlev, Sonja, Bouchez, Olivier, Lopez-Roques, Céline, Lepers-Andrzejewski, Sandra, Bourgois, Laurent, Zucca, Joseph, Dron, Michel, Besse, Pascale, Grisoni, Michel, Jourda, Cyril, and Charron, Carine

Abstract

Vanilla planifolia, the species cultivated to produce one of the world’s most popular flavors, is highly prone to partial genome endoreplication, which leads to highly unbalanced DNA content in cells. We report here the first molecular evidence of partial endoreplication at the chromosome scale by the assembly and annotation of an accurate haplotype-phased genome of V. planifolia. Cytogenetic data demonstrated that the diploid genome size is 4.09 Gb, with 16 chromosome pairs, although aneuploid cells are frequently observed. Using PacBio HiFi and optical mapping, we assembled and phased a diploid genome of 3.4 Gb with a scaffold N50 of 1.2 Mb and 59 128 predicted protein-coding genes. The atypical k-mer frequencies and the uneven sequencing depth observed agreed with our expectation of unbalanced genome representation. Sixty-seven percent of the genes were scattered over only 30% of the genome, putatively linking gene-rich regions and the endoreplication phenomenon. By contrast, low-coverage regions (non-endoreplicated) were rich in repeated elements but also contained 33% of the annotated genes. Furthermore, this assembly showed distinct haplotype-specific sequencing depth variation patterns, suggesting complex molecular regulation of endoreplication along the chromosomes. This high-quality, anchored assembly represents 83% of the estimated V. planifoliagenome. It provides a significant step toward the elucidation of this complex genome. To support post-genomics efforts, we developed the Vanilla Genome Hub, a user-friendly integrated web portal that enables centralized access to high-throughput genomic and other omics data and interoperable use of bioinformatics tools.

Published
2022
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50. Supplementary text S1-S5; Tables S1-S2; Figures S1-S16 from A 180 Myr-old female-specific genome region in sturgeon reveals the oldest known vertebrate sex determining system with undifferentiated sex chromosomes

Author

Kuhl, Heiner, Guiguen, Yann, Höhne, Christin, Kreuz, Eva, Du, Kang, Klopp, Christophe, Lopez-Roques, Céline, Yebra-Pimentel, Elena Santidrian, Ciorpac, Mitica, Gessner, Jörn, Holostenco, Daniela, Kleiner, Wibke, Kohlmann, Klaus, Lamatsch, Dunja K., Prokopov, Dmitry, Bestin, Anastasia, Bonpunt, Emmanuel, Debeuf, Bastien, Haffray, Pierrick, Morvezen, Romain, Patrice, Pierre, Suciu, Radu, Dirks, Ron, Wuertz, Sven, Kloas, Werner, Schartl, Manfred, and Stöck, Matthias

Subjects
14. Life underwater
Abstract

Several hypotheses explain the prevalence of undifferentiated sex chromosomes in poikilothermic vertebrates. Turnovers change the master sex determination gene, the sex chromosome or the sex determination system (e.g. XY to WZ). Jumping master genes stay main triggers but translocate to other chromosomes. Occasional recombination (e.g. in sex-reversed females) prevents sex chromosome degeneration. Recent research has uncovered conserved heteromorphic or even homomorphic sex chromosomes in several clades of non-avian and non-mammalian vertebrates. Sex determination in sturgeons (Acipenseridae) has been a long-standing basic biological question, linked to economical demands by the caviar-producing aquaculture. Here, we report the discovery of a sex-specific sequence from sterlet (Acipenser ruthenus). Using chromosome-scale assemblies and pool-sequencing, we first identified an approximately 16 kb female-specific region. We developed a PCR-genotyping test, yielding female-specific products in six species, spanning the entire phylogeny with the most divergent extant lineages (A. sturio, A. oxyrinchus versus A. ruthenus, Huso huso), stemming from an ancient tetraploidization. Similar results were obtained in two octoploid species (A. gueldenstaedtii, A. baerii). Conservation of a female-specific sequence for a long period, representing 180 Myr of sturgeon evolution, and across at least one polyploidization event, raises many interesting biological questions. We discuss a conserved undifferentiated sex chromosome system with a ZZ/ZW-mode of sex determination and potential alternatives.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)’.

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