Author: "Lemaitre, Claire" - Searchworks@Jio Institute Digital Library Search Results

Your search keyword '"Lemaitre, Claire"' showing total 270 results

Start Over Author "Lemaitre, Claire"

270 results on '"Lemaitre, Claire"'

1. MTG-Link: leveraging barcode information from linked-reads to assemble specific loci

Author: Guichard, Anne, Legeai, Fabrice, Tagu, Denis, and Lemaitre, Claire
Published: 2023
Full Text: View/download PDF

2. Critical Assessment of Metagenome Interpretation: the second round of challenges

Author: Meyer, Fernando, Fritz, Adrian, Deng, Zhi-Luo, Koslicki, David, Lesker, Till Robin, Gurevich, Alexey, Robertson, Gary, Alser, Mohammed, Antipov, Dmitry, Beghini, Francesco, Bertrand, Denis, Brito, Jaqueline J, Brown, C Titus, Buchmann, Jan, Buluç, Aydin, Chen, Bo, Chikhi, Rayan, Clausen, Philip TLC, Cristian, Alexandru, Dabrowski, Piotr Wojciech, Darling, Aaron E, Egan, Rob, Eskin, Eleazar, Georganas, Evangelos, Goltsman, Eugene, Gray, Melissa A, Hansen, Lars Hestbjerg, Hofmeyr, Steven, Huang, Pingqin, Irber, Luiz, Jia, Huijue, Jørgensen, Tue Sparholt, Kieser, Silas D, Klemetsen, Terje, Kola, Axel, Kolmogorov, Mikhail, Korobeynikov, Anton, Kwan, Jason, LaPierre, Nathan, Lemaitre, Claire, Li, Chenhao, Limasset, Antoine, Malcher-Miranda, Fabio, Mangul, Serghei, Marcelino, Vanessa R, Marchet, Camille, Marijon, Pierre, Meleshko, Dmitry, Mende, Daniel R, Milanese, Alessio, Nagarajan, Niranjan, Nissen, Jakob, Nurk, Sergey, Oliker, Leonid, Paoli, Lucas, Peterlongo, Pierre, Piro, Vitor C, Porter, Jacob S, Rasmussen, Simon, Rees, Evan R, Reinert, Knut, Renard, Bernhard, Robertsen, Espen Mikal, Rosen, Gail L, Ruscheweyh, Hans-Joachim, Sarwal, Varuni, Segata, Nicola, Seiler, Enrico, Shi, Lizhen, Sun, Fengzhu, Sunagawa, Shinichi, Sørensen, Søren Johannes, Thomas, Ashleigh, Tong, Chengxuan, Trajkovski, Mirko, Tremblay, Julien, Uritskiy, Gherman, Vicedomini, Riccardo, Wang, Zhengyang, Wang, Ziye, Wang, Zhong, Warren, Andrew, Willassen, Nils Peder, Yelick, Katherine, You, Ronghui, Zeller, Georg, Zhao, Zhengqiao, Zhu, Shanfeng, Zhu, Jie, Garrido-Oter, Ruben, Gastmeier, Petra, Hacquard, Stephane, Häußler, Susanne, Khaledi, Ariane, Maechler, Friederike, Mesny, Fantin, Radutoiu, Simona, Schulze-Lefert, Paul, Smit, Nathiana, and Strowig, Till
Subjects: Biological Sciences, Bioinformatics and Computational Biology, Networking and Information Technology R&D (NITRD), Archaea, Metagenome, Metagenomics, Reproducibility of Results, Sequence Analysis, DNA, Software, Technology, Medical and Health Sciences, Developmental Biology, Biological sciences
Abstract: Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilers markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses.
Published: 2022

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

4. Métagénomique et métatranscriptomique

Author: GUYOMAR, Cervin, primary and LEMAITRE, Claire, additional
Published: 2023
Full Text: View/download PDF

5. Chromosome-Level Assembly and Annotation of the Pearly Heath Coenonympha arcania Butterfly Genome

Author: Legeai, Fabrice, primary, Romain, Sandra, additional, Capblancq, Thibaut, additional, Doniol-Valcroze, Paul, additional, Joron, Mathieu, additional, Lemaitre, Claire, additional, and Després, Laurence, additional
Published: 2024
Full Text: View/download PDF

6. Multiple Comparative Metagenomics using Multiset k-mer Counting

Author: Benoit, Gaëtan, Peterlongo, Pierre, Mariadassou, Mahendra, Drezen, Erwan, Schbath, Sophie, Lavenier, Dominique, and Lemaitre, Claire
Subjects: Quantitative Biology - Genomics
Abstract: Background. Large scale metagenomic projects aim to extract biodiversity knowledge between different environmental conditions. Current methods for comparing microbial communities face important limitations. Those based on taxonomical or functional assignation rely on a small subset of the sequences that can be associated to known organisms. On the other hand, de novo methods, that compare the whole sets of sequences, either do not scale up on ambitious metagenomic projects or do not provide precise and exhaustive results. Methods. These limitations motivated the development of a new de novo metagenomic comparative method, called Simka. This method computes a large collection of standard ecological distances by replacing species counts by k-mer counts. Simka scales-up today's metagenomic projects thanks to a new parallel k-mer counting strategy on multiple datasets. Results. Experiments on public Human Microbiome Project datasets demonstrate that Simka captures the essential underlying biological structure. Simka was able to compute in a few hours both qualitative and quantitative ecological distances on hundreds of metagenomic samples (690 samples, 32 billions of reads). We also demonstrate that analyzing metagenomes at the k-mer level is highly correlated with extremely precise de novo comparison techniques which rely on all-versus-all sequences alignment strategy or which are based on taxonomic profiling.
Published: 2016

7. Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

Author: Sczyrba, Alexander, Hofmann, Peter, Belmann, Peter, Koslicki, David, Janssen, Stefan, Dröge, Johannes, Gregor, Ivan, Majda, Stephan, Fiedler, Jessika, Dahms, Eik, Bremges, Andreas, Fritz, Adrian, Garrido-Oter, Ruben, Jørgensen, Tue Sparholt, Shapiro, Nicole, Blood, Philip D, Gurevich, Alexey, Bai, Yang, Turaev, Dmitrij, DeMaere, Matthew Z, Chikhi, Rayan, Nagarajan, Niranjan, Quince, Christopher, Meyer, Fernando, Balvočiūtė, Monika, Hansen, Lars Hestbjerg, Sørensen, Søren J, Chia, Burton KH, Denis, Bertrand, Froula, Jeff L, Wang, Zhong, Egan, Robert, Don Kang, Dongwan, Cook, Jeffrey J, Deltel, Charles, Beckstette, Michael, Lemaitre, Claire, Peterlongo, Pierre, Rizk, Guillaume, Lavenier, Dominique, Wu, Yu-Wei, Singer, Steven W, Jain, Chirag, Strous, Marc, Klingenberg, Heiner, Meinicke, Peter, Barton, Michael D, Lingner, Thomas, Lin, Hsin-Hung, Liao, Yu-Chieh, Silva, Genivaldo Gueiros Z, Cuevas, Daniel A, Edwards, Robert A, Saha, Surya, Piro, Vitor C, Renard, Bernhard Y, Pop, Mihai, Klenk, Hans-Peter, Göker, Markus, Kyrpides, Nikos C, Woyke, Tanja, Vorholt, Julia A, Schulze-Lefert, Paul, Rubin, Edward M, Darling, Aaron E, Rattei, Thomas, and McHardy, Alice C
Subjects: Biological Sciences, Networking and Information Technology R&D (NITRD), Algorithms, Benchmarking, Metagenomics, Sequence Analysis, DNA, Software, Technology, Medical and Health Sciences, Developmental Biology, Biological sciences
Abstract: Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome data, but a lack of consensus about benchmarking complicates performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on highly complex and realistic data sets, generated from ∼700 newly sequenced microorganisms and ∼600 novel viruses and plasmids and representing common experimental setups. Assembly and genome binning programs performed well for species represented by individual genomes but were substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below family level. Parameter settings markedly affected performance, underscoring their importance for program reproducibility. The CAMI results highlight current challenges but also provide a roadmap for software selection to answer specific research questions.
Published: 2017

8. Compression of high throughput sequencing data with probabilistic de Bruijn graph

Author: Benoit, Gaëtan, Lemaitre, Claire, Lavenier, Dominique, and Rizk, Guillaume
Subjects: Computer Science - Data Structures and Algorithms, Quantitative Biology - Quantitative Methods
Abstract: Motivation: Data volumes generated by next-generation sequencing technolo- gies is now a major concern, both for storage and transmission. This triggered the need for more efficient methods than general purpose compression tools, such as the widely used gzip. Most reference-free tools developed for NGS data compression still use general text compression methods and fail to benefit from algorithms already designed specifically for the analysis of NGS data. The goal of our new method Leon is to achieve compression of DNA sequences of high throughput sequencing data, without the need of a reference genome, with techniques derived from existing assembly principles, that possibly better exploit NGS data redundancy. Results: We propose a novel method, implemented in the software Leon, for compression of DNA sequences issued from high throughput sequencing technologies. This is a lossless method that does not need a reference genome. Instead, a reference is built de novo from the set of reads as a probabilistic de Bruijn Graph, stored in a Bloom filter. Each read is encoded as a path in this graph, storing only an anchoring kmer and a list of bifurcations indicating which path to follow in the graph. This new method will allow to have compressed read files that also already contain its underlying de Bruijn Graph, thus directly re-usable by many tools relying on this structure. Leon achieved encoding of a C. elegans reads set with 0.7 bits/base, outperforming state of the art reference-free methods. Availability: Open source, under GNU affero GPL License, available for download at http://gatb.inria.fr/software/leon/, Comment: 21 pages
Published: 2014

9. TheSilene latifoliagenome and its giant Y chromosome

Author: Moraga, Carol, primary, Branco, Catarina, additional, Rougemont, Quentin, additional, Veltsos, Paris, additional, Jedlička, Pavel, additional, Muyle, Aline, additional, Hanique, Melissa, additional, Tannier, Eric, additional, Liu, Xiaodong, additional, Mendoza-Galindo, Eddy, additional, Lemaitre, Claire, additional, Fields, Peter D., additional, Cruaud, Corinne, additional, Labadie, Karine, additional, Belser, Caroline, additional, Briolay, Jerome, additional, Santoni, Sylvain, additional, Cegan, Radim, additional, Linheiro, Raquel, additional, de la Vega, Ricardo C. Rodríguez, additional, Adam, Gabriele, additional, Filali, Adil El, additional, Mossion, Vinciane, additional, Boualem, Adnane, additional, Tavares, Raquel, additional, Chebbi, Amine, additional, Cordaux, Richard, additional, Fruchard, Cécile, additional, Prentout, Djivan, additional, Velt, Amandine, additional, Spataro, Bruno, additional, Delmotte, Stephane, additional, Weingartner, Laura, additional, Toegelová, Helena, additional, Tulpová, Zuzana, additional, Cápal, Petr, additional, Šimková, Hana, additional, Štorchová, Helena, additional, Krüger, Manuela, additional, Abeyawardana, Oushadee A. J., additional, Taylor, Douglas R., additional, Olson, Matthew S., additional, Sloan, Daniel B., additional, Karrenberg, Sophie, additional, Delph, Lynda F., additional, Charlesworth, Deborah, additional, Giraud, Tatiana, additional, Bendahmane, Abdelhafid, additional, Genova, Alex Di, additional, Madoui, Amin, additional, Hobza, Roman, additional, and Marais, Gabriel A. B., additional
Published: 2023
Full Text: View/download PDF

10. De Novo NGS Data Compression

Author: Benoit, Gaetan, Lemaitre, Claire, Rizk, Guillaume, Drezen, Erwan, Lavenier, Dominique, and Elloumi, Mourad, editor
Published: 2017
Full Text: View/download PDF

11. SVJedi-graph: improving the genotyping of close and overlapping structural variants with long reads using a variation graph

Author: Romain, Sandra, primary and Lemaitre, Claire, additional
Published: 2023
Full Text: View/download PDF

12. Towards a better understanding of the low recall of insertion variants with short-read based variant callers

Author: Delage, Wesley J., Thevenon, Julien, and Lemaitre, Claire
Published: 2020
Full Text: View/download PDF

13. Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps

Author: Legeai, Fabrice, Santos, Bernardo F., Robin, Stéphanie, Bretaudeau, Anthony, Dikow, Rebecca B., Lemaitre, Claire, Jouan, Véronique, Ravallec, Marc, Drezen, Jean-Michel, Tagu, Denis, Baudat, Frédéric, Gyapay, Gabor, Zhou, Xin, Liu, Shanlin, Webb, Bruce A., Brady, Seán G., and Volkoff, Anne-Nathalie
Published: 2020
Full Text: View/download PDF

14. Parasitoid Mating Structures When Hosts Are Patchily Distributed: Field and Laboratory Experiments with Leptopilina boulardi and L. heterotoma

Author: Fauvergue, Xavier, Fleury, Frédéric, Lemaitre, Claire, and Allemand, Rolland
Published: 1999
Full Text: View/download PDF

15. Le SARS-CoV-2 : une expérience inédite de surveillance génomique mondiale

Author: Touzet, Hélène, Salson, Mikaël, Lemaitre, Claire, Débarre, Florence, and Lemaitre, Claire
Subjects: [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: Depuis le début de la pandémie de SARS-CoV-2, la surveillance de l’évolution du génome du virus avec son séquençage en continu est devenue un élément clé de santé publique. En effet, le génome d’un virus est par nature très dynamique, avec une évolution qui se manifeste par l’accumulation rapide de mutations. Disposer au fil du temps de nombreux génomes d’origines géographiques variées est donc nécessaire pour identifier l’émergence de variants, des lignées porteuses de mutations clés susceptibles d’affecter la pathogénicité et la transmissibilité du virus, voire de mener à un échappement vaccinal. Ce type de surveillance a pu être expérimenté ces dernières années avec la grippe saisonnière, les virus Ebola ou Zika, et a atteint une ampleur inédite avec le suivi du SARS-CoV-2. Une telle tâche requiert des moyens de génération, d’analyse bio-informatique et de partage des données particulièrement optimisés et ambitieux. Comment cela se passe-t-il ?
Published: 2023

16. 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
Full Text: View/download PDF

17. Mapping-Free and Assembly-Free Discovery of Inversion Breakpoints from Raw NGS Reads

Author: Lemaitre, Claire, Ciortuz, Liviu, Peterlongo, Pierre, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Kobsa, Alfred, editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Weikum, Gerhard, editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael S., editor, Dediu, Adrian-Horia, editor, Martín-Vide, Carlos, editor, and Truthe, Bianca, editor
Published: 2014
Full Text: View/download PDF

18. 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
Full Text: View/download PDF

19. Comment la bioinformatique a résolu le puzzle du génome du SARS-CoV-2

Author: Lemaitre, Claire, Salson, Mikaël, Touzet, Hélène, 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), Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Lemaitre, Claire, Scalable, Optimized and Parallel Algorithms for Genomics [GenScale], and Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]
Subjects: [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: International audience; Connaître le génome du SARS-CoV-2 a été une étape fondamentale dans la lutte contre l'épidémie de Covid-19. Cela a permis de rapidement identifier ses protéines, développer des tests, étudier son origine, suivre son évolution, etc. Mais comment à partir d'un simple écouvillon recouvert d'organismes variés, arrive-t-on à déterminer le génome du virus qui nous intéresse ? La bioinformatique propose des méthodes adaptées pour y arriver de manière très efficace.
Published: 2022

20. MTG-Link: leveraging barcode information from linked-reads to assemble specific loci

Author: Guichard, Anne, primary, Legeai, Fabrice, additional, Tagu, Denis, additional, and Lemaitre, Claire, additional
Published: 2022
Full Text: View/download PDF

21. Metagenomics and Metatranscriptomics

Author: Guyomar, Cervin, primary and Lemaitre, Claire, additional
Published: 2022
Full Text: View/download PDF

22. Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches

Author: Guyomar, Cervin, Legeai, Fabrice, Jousselin, Emmanuelle, Mougel, Christophe, Lemaitre, Claire, and Simon, Jean-Christophe
Published: 2018
Full Text: View/download PDF

23. Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems

Author: Richter, Daniel J., Watteaux, Romain, Vannier, Thomas, Leconte, Jade, Frémont, Paul, Reygondeau, Gabriel, Maillet, Nicolas, Henry, Nicolas, Benoit, Gaëtan, da Silva, Ophélie, Delmont, Tom O., Fernández-Guerra, Antonio, Suweis, Samir, Narci, Romain, Berney, Cedric, Eveillard, Damien, Gavory, Frederick, Guidi, Lionel, Labadie, Karine, Mahieu, Eric, Poulain, Julie, Romac, Sarah, Roux, Simon, Dimier, Céline, Kandels‐Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Oceans, Tara, Pesant, Stéphane, Aury, Jean-Marc, Brum, Jennifer R., Lemaitre, Claire, Pelletier, Eric, Bork, Peer, Sunagawa, Shinichi, Lombard, Fabien, Karp-Boss, Lee, Bowler, Chris, Sullivan, Matthew B., Karsenti, Eric, Mariadassou, Mahendra, Probert, Ian, Peterlongo, Pierre, Wincker, Patrick, Vargas, Colomban de, Ribera d’Alcalà, Maurizio, Iudicone, Daniele, Jaillon, Olivier, Tara Oceans Coordinators, Centre National de la Recherche Scientifique (France), European Molecular Biology Laboratory, Centre National de Séquençage (France), National Fund for Scientific Research (Belgium), Stazione Zoologica Anton Dohrn, Università degli Studi di Milano, Université Paris Sciences & Lettres, Agence Nationale de la Recherche (France), National Science Foundation (US), Veolia Foundation, Région Bretagne, World Courier, Illumina, Cap L’Orient, Fondation EDF, Fondation pour la Recherche sur la Biodiversité, Fondation Prince Albert II de Monaco, Ministère de l'Europe et des Affaires étrangères (France), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Stazione Zoologica Anton Dohrn (SZN), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), University of British Columbia (UBC), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes 1 (UR1), 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 (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Dipartimento di Fisica e Astronomia 'Galileo Galilei', Università degli Studi di Padova = University of Padua (Unipd), Consorzio Nazionale Interuniversitario per le Scienze FIsiche della Materia (CNISM), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Combinatoire et Bioinformatique (LS2N - équipe COMBI), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Institut de Biologie François JACOB (JACOB), Ohio State University [Columbus] (OSU), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Ecology and Evolutionary Biology [Tucson] (EEB), University of Arizona, 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 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 (IMT Atlantique), European Molecular Biology Laboratory [Heidelberg] (EMBL), University of Maine, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Fédération de recherche de Roscoff (FR2424), 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 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), French National Research Agency (ANR)HYDROGEN/ANR-14CE23-0001, National Science Foundation (NSF)OCE-1536989, OCE-1829831, Commissariat a l'Energie Atomique et aux Energies Alternatives, Graphene Flagship, European Project: 634486,H2020,H2020-BG-2014-2,INMARE(2015), European Project: 287589,EC:FP7:KBBE,FP7-OCEAN-2011,MICRO B3(2012), Adaptation et diversité en milieu marin (AD2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, 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), Universita degli Studi di Padova, Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Combinatoire et Bioinformatique (COMBI), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut 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), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Centre de Mathématiques et de Leurs Applications (CMLA), École normale supérieure - Cachan (ENS Cachan)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Infectiologie Santé Publique (ISP-311), Institut National de la Recherche Agronomique (INRA)-Université de Tours, Institut Pprime (PPRIME), Université de Poitiers-ENSMA-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Laboratoire d'Informatique de Nantes Atlantique (LINA), Mines Nantes (Mines Nantes)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), 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), IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and 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)
Subjects: 010504 meteorology & atmospheric sciences, Biogeography, Oceans and Seas, Context (language use), 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, plankton biogeography, genomics, Ecosystem, genetics, 14. Life underwater, microbial oceanography, 030304 developmental biology, 0105 earth and related environmental sciences, Seascape, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, metagenomics, General Immunology and Microbiology, Geography, General Neuroscience, Ocean current, fungi, Community structure, General Medicine, 15. Life on land, Plankton, Oceanography, 13. Climate action, Metagenomics, metabarcoding, ecology, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated. Here we assessed the global structure of plankton geography and its relation to the biological, chemical, and physical context of the ocean (the ‘seascape’) by analyzing metagenomes of plankton communities sampled across oceans during the Tara Oceans expedition, in light of environmental data and ocean current transport. Using a consistent approach across organismal sizes that provides unprecedented resolution to measure changes in genomic composition between communities, we report a pan-ocean, size-dependent plankton biogeography overlying regional heterogeneity. We found robust evidence for a basin-scale impact of transport by ocean currents on plankton biogeography, and on a characteristic timescale of community dynamics going beyond simple seasonality or life history transitions of plankton., We thank the commitment of the following people and sponsors who made this expedition possible: CNRS (in particular Groupement de Recherche GDR3280), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, Fund for Scientific Research – Flanders, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, Paris Sciences et Lettres (PSL) Research University (ANR-11-IDEX-0001–02), the French Government ANR (projects FRANCE GENOMIQUE/ANR-10-INBS-09, MEMO LIFE/ANR-10-LABX-54, POSEIDON/ANR-09-BLAN-0348, PROMETHEUS/ANR-09-PCS-GENM-217, MAPPI/ANR-2010-COSI-004, TARA-GIRUS/ANR-09-PCS-GENM-218), US NSF grant DEB-1031049, FWO, BIO5, Biosphere 2, Agnès b., the Veolia Environment Foundation, Région Bretagne, World Courier, Illumina, Cap L’Orient, the EDF Foundation EDF Diversiterre, FRB, the Prince Albert II de Monaco Foundation, Etienne Bourgois, the Tara schooner and its captain and crew. We thank MERCATOR-CORIOLIS and ACRI-ST for providing daily satellite data during the expedition. The bulk of genomic computations were performed using the Airain HPC machine provided through GENCI- [TGCC/CINES/IDRIS] (grants t2011076389, t2012076389, t2013036389, t2014036389, t2015036389 and t2016036389). We are also grateful to the French Ministry of Foreign Affairs for supporting the expedition and to the countries who granted us sampling permissions.
Published: 2022

24. 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
Full Text: View/download PDF

25. Décoder le génome : vers la compréhension du fonctionnement du SARS-CoV-2

Author: Touzet, Hélène, Salson, Mikaël, Lemaitre, Claire, Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), 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), and Interstices, inria
Subjects: protéine, génome, Modèle de Markov caché, Bio-informatique, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: International audience; Une longue suite de lettres. C'est ainsi qu'un génome, comme celui-du SARS-CoV-2 est représenté. Mais comment donner du sens à cette succession cryptique de A, C, G et T ? Où se trouvent les gènes ? Quels rôles jouent-ils ? Les outils de la bioinformatique permettent de bénéficier des connaissances acquises sur d'autres coronavirus pour les transférer au SARS-CoV-2.
Published: 2022

26. SVJedi-graph: Structural Variant genotyping with long-reads using a variation graph

Author: Romain, Sandra, 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 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 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 Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Lemaitre, Claire, 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: [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: International audience; Structural variants (SVs) are genomic segments of more than 50 bp that have been rearranged in the genome. The advent of third generation sequencing technologies has increased and enhanced their study, and a great number of SVs has already been discovered in the human genome. Complementary to their discovery, the genotyping of known SVs in newly sequenced individuals is of particular interest for several applications such as trait association and clinical diagnosis. Most of the SV genotypers currently available are designed for second generation sequencing data, although third generation sequencing data is more suited to study SVs due to their large range of sizes (up to few mega bases). As such, our team previously released SVJedi, the first SV genotyper dedicated to long read data[1]. The method is based on linear representations of the allelic sequences of each SV and each SV is represented and genotyped independently of the other ones. While this is very efficient for distant SVs, the method fails to genotype some closely located or overlapping SVs due to redundancy in representative allelic sequences.
Published: 2021

27. Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems

Author: Centre National de la Recherche Scientifique (France), European Molecular Biology Laboratory, Centre National de Séquençage (France), National Fund for Scientific Research (Belgium), Stazione Zoologica Anton Dohrn, Università degli Studi di Milano, Université Paris Sciences & Lettres, Agence Nationale de la Recherche (France), National Science Foundation (US), Veolia Foundation, Région Bretagne, World Courier, Illumina, Cap L’Orient, Fondation EDF, Fondation pour la Recherche sur la Biodiversité, Fondation Prince Albert II de Monaco, Ministère de l'Europe et des Affaires étrangères (France), Richter, Daniel J., Watteaux, Romain, Vannier, Thomas, Leconte, Jade, Frémont, Paul, Reygondeau, Gabriel, Maillet, Nicolas, Henry, Nicolas, Benoit, Gaëtan, da Silva, Ophélie, Delmont, Tom O., Fernández-Guerra, Antonio, Suweis, Samir, Narci, Romain, Berney, Cedric, Eveillard, Damien, Gavory, Frederick, Guidi, Lionel, Labadie, Karine, Mahieu, Eric, Poulain, Julie, Romac, Sarah, Roux, Simon, Dimier, Céline, Kandels‐Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Oceans, Tara, Pesant, Stéphane, Aury, Jean‐Marc, Brum, Jennifer R., Lemaitre, Claire, Pelletier, Eric, Bork, Peer, Sunagawa, Shinichi, Lombard, Fabien, Karp-Boss, Lee, Bowler, Chris, Sullivan, Matthew B., Karsenti, Eric, Mariadassou, Mahendra, Probert, Ian, Peterlongo, Pierre, Wincker, Patrick, Vargas, Colomban de, Ribera d’Alcalà, Maurizio, Iudicone, Daniele, Jaillon, Olivier, Tara Oceans Coordinators, Centre National de la Recherche Scientifique (France), European Molecular Biology Laboratory, Centre National de Séquençage (France), National Fund for Scientific Research (Belgium), Stazione Zoologica Anton Dohrn, Università degli Studi di Milano, Université Paris Sciences & Lettres, Agence Nationale de la Recherche (France), National Science Foundation (US), Veolia Foundation, Région Bretagne, World Courier, Illumina, Cap L’Orient, Fondation EDF, Fondation pour la Recherche sur la Biodiversité, Fondation Prince Albert II de Monaco, Ministère de l'Europe et des Affaires étrangères (France), Richter, Daniel J., Watteaux, Romain, Vannier, Thomas, Leconte, Jade, Frémont, Paul, Reygondeau, Gabriel, Maillet, Nicolas, Henry, Nicolas, Benoit, Gaëtan, da Silva, Ophélie, Delmont, Tom O., Fernández-Guerra, Antonio, Suweis, Samir, Narci, Romain, Berney, Cedric, Eveillard, Damien, Gavory, Frederick, Guidi, Lionel, Labadie, Karine, Mahieu, Eric, Poulain, Julie, Romac, Sarah, Roux, Simon, Dimier, Céline, Kandels‐Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Oceans, Tara, Pesant, Stéphane, Aury, Jean‐Marc, Brum, Jennifer R., Lemaitre, Claire, Pelletier, Eric, Bork, Peer, Sunagawa, Shinichi, Lombard, Fabien, Karp-Boss, Lee, Bowler, Chris, Sullivan, Matthew B., Karsenti, Eric, Mariadassou, Mahendra, Probert, Ian, Peterlongo, Pierre, Wincker, Patrick, Vargas, Colomban de, Ribera d’Alcalà, Maurizio, Iudicone, Daniele, Jaillon, Olivier, and Tara Oceans Coordinators
Abstract: Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated. Here we assessed the global structure of plankton geography and its relation to the biological, chemical, and physical context of the ocean (the ‘seascape’) by analyzing metagenomes of plankton communities sampled across oceans during the Tara Oceans expedition, in light of environmental data and ocean current transport. Using a consistent approach across organismal sizes that provides unprecedented resolution to measure changes in genomic composition between communities, we report a pan-ocean, size-dependent plankton biogeography overlying regional heterogeneity. We found robust evidence for a basin-scale impact of transport by ocean currents on plankton biogeography, and on a characteristic timescale of community dynamics going beyond simple seasonality or life history transitions of plankton.
Published: 2022

28. Critical Assessment of Metagenome Interpretation:the second round of challenges

Author: Meyer, Fernando, Fritz, Adrian, Deng, Zhi-Luo, Koslicki, David, Lesker, Till Robin, Gurevich, Alexey, Robertson, Gary, Alser, Mohammed, Antipov, Dmitry, Beghini, Francesco, Bertrand, Denis, Brito, Jaqueline J., Brown, C. Titus, Buchmann, Jan, Buluç, Aydin, Chen, Bo, Chikhi, Rayan, Clausen, Philip T.L.C., Cristian, Alexandru, Dabrowski, Piotr Wojciech, Darling, Aaron E., Egan, Rob, Eskin, Eleazar, Georganas, Evangelos, Goltsman, Eugene, Gray, Melissa A., Hansen, Lars Hestbjerg, Hofmeyr, Steven, Huang, Pingqin, Irber, Luiz, Jia, Huijue, Jørgensen, Tue Sparholt, Kieser, Silas D., Klemetsen, Terje, Kola, Axel, Kolmogorov, Mikhail, Korobeynikov, Anton, Kwan, Jason, LaPierre, Nathan, Lemaitre, Claire, Li, Chenhao, Limasset, Antoine, Malcher-Miranda, Fabio, Mangul, Serghei, Marcelino, Vanessa R., Marchet, Camille, Marijon, Pierre, Meleshko, Dmitry, Mende, Daniel R., Milanese, Alessio, Nagarajan, Niranjan, Nissen, Jakob, Nurk, Sergey, Oliker, Leonid, Paoli, Lucas, Peterlongo, Pierre, Piro, Vitor C., Porter, Jacob S., Rasmussen, Simon, Rees, Evan R., Reinert, Knut, Renard, Bernhard, Robertsen, Espen Mikal, Rosen, Gail L., Ruscheweyh, Hans-Joachim, Sarwal, Varuni, Segata, Nicola, Seiler, Enrico, Shi, Lizhen, Sun, Fengzhu, Sunagawa, Shinichi, Sørensen, Søren Johannes, Thomas, Ashleigh, Tong, Chengxuan, Trajkovski, Mirko, Tremblay, Julien, Uritskiy, Gherman, Vicedomini, Riccardo, Wang, Zhengyang, Wang, Ziye, Wang, Zhong, Warren, Andrew, Willassen, Nils Peder, Yelick, Katherine, You, Ronghui, Zeller, Georg, Zhao, Zhengqiao, Zhu, Shanfeng, Zhu, Jie, Garrido-Oter, Ruben, Gastmeier, Petra, Hacquard, Stephane, Häußler, Susanne, Khaledi, Ariane, Maechler, Friederike, Mesny, Fantin, Radutoiu, Simona, Schulze-Lefert, Paul, Smit, Nathiana, Strowig, Till, Bremges, Andreas, Sczyrba, Alexander, McHardy, Alice Carolyn, Meyer, Fernando, Fritz, Adrian, Deng, Zhi-Luo, Koslicki, David, Lesker, Till Robin, Gurevich, Alexey, Robertson, Gary, Alser, Mohammed, Antipov, Dmitry, Beghini, Francesco, Bertrand, Denis, Brito, Jaqueline J., Brown, C. Titus, Buchmann, Jan, Buluç, Aydin, Chen, Bo, Chikhi, Rayan, Clausen, Philip T.L.C., Cristian, Alexandru, Dabrowski, Piotr Wojciech, Darling, Aaron E., Egan, Rob, Eskin, Eleazar, Georganas, Evangelos, Goltsman, Eugene, Gray, Melissa A., Hansen, Lars Hestbjerg, Hofmeyr, Steven, Huang, Pingqin, Irber, Luiz, Jia, Huijue, Jørgensen, Tue Sparholt, Kieser, Silas D., Klemetsen, Terje, Kola, Axel, Kolmogorov, Mikhail, Korobeynikov, Anton, Kwan, Jason, LaPierre, Nathan, Lemaitre, Claire, Li, Chenhao, Limasset, Antoine, Malcher-Miranda, Fabio, Mangul, Serghei, Marcelino, Vanessa R., Marchet, Camille, Marijon, Pierre, Meleshko, Dmitry, Mende, Daniel R., Milanese, Alessio, Nagarajan, Niranjan, Nissen, Jakob, Nurk, Sergey, Oliker, Leonid, Paoli, Lucas, Peterlongo, Pierre, Piro, Vitor C., Porter, Jacob S., Rasmussen, Simon, Rees, Evan R., Reinert, Knut, Renard, Bernhard, Robertsen, Espen Mikal, Rosen, Gail L., Ruscheweyh, Hans-Joachim, Sarwal, Varuni, Segata, Nicola, Seiler, Enrico, Shi, Lizhen, Sun, Fengzhu, Sunagawa, Shinichi, Sørensen, Søren Johannes, Thomas, Ashleigh, Tong, Chengxuan, Trajkovski, Mirko, Tremblay, Julien, Uritskiy, Gherman, Vicedomini, Riccardo, Wang, Zhengyang, Wang, Ziye, Wang, Zhong, Warren, Andrew, Willassen, Nils Peder, Yelick, Katherine, You, Ronghui, Zeller, Georg, Zhao, Zhengqiao, Zhu, Shanfeng, Zhu, Jie, Garrido-Oter, Ruben, Gastmeier, Petra, Hacquard, Stephane, Häußler, Susanne, Khaledi, Ariane, Maechler, Friederike, Mesny, Fantin, Radutoiu, Simona, Schulze-Lefert, Paul, Smit, Nathiana, Strowig, Till, Bremges, Andreas, Sczyrba, Alexander, and McHardy, Alice Carolyn
Abstract: Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilers markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses.
Published: 2022

29. Spodoptera frugiperda (Lepidoptera: Noctuidae) host-plant variants: two host strains or two distinct species?

Author: Dumas, Pascaline, Legeai, Fabrice, Lemaitre, Claire, Scaon, Erwan, Orsucci, Marion, Labadie, Karine, Gimenez, Sylvie, Clamens, Anne-Laure, Henri, Hélène, Vavre, Fabrice, Aury, Jean-Marc, Fournier, Philippe, Kergoat, Gael J., and d’Alençon, Emmanuelle
Published: 2015
Full Text: View/download PDF

30. SVJedi-graph: genotyping close and overlapping structural variants with a variation graph and long-reads

Author: Romain, Sandra, Lemaitre, Claire, Romain, Sandra, 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), and Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)
Subjects: [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: International audience; Structural variants (SVs) are genomic segments of more than 50 bp that have been rearranged in the genome. The advent of long-read sequencing technologies has increased and enhanced their study, and a great number of SVs has already been discovered in many species. Complementary to their discovery, the genotyping of known SVs in newly sequenced individuals is of particular interest for several applications such as trait association and clinical diagnosis. Due to SVs' large size range (up to a few megabases), long-reads are more suited for their study than short-reads. As such, our team previously released SVJedi [1], one of the first SV genotypers using long-read data. SVJedi's method of representing independently both SV's allelic sequences reduced reference bias in genotyping and showed improved genotyping performances. However, the method failed to genotype closely located or overlapping SVs due to redundancy in representative allelic sequences.To overcome this limitation, we present SVJedi-graph, a long-read SV genotyper based on a variation graph to represent SV alleles. The use of sequence graphs to represent SVs for genotyping is fairly recent [2,3,4,5], but existing methods are restricted to short-read data, and SVJedi-graph is the first graph-based SV genotyper using long-reads. In our method, we build the variation graph from a reference genome and a given set of SVs. The genome sequence is split in fragments at each SV’s start and end positions, and each fragment becomes a node in the graph. Edges are added between nodes to indicate reference and alternative paths for each SV, and additional nodes are added for insertions. Then, the long reads are mapped on the variation graph using GraphAligner [6] and the resulting alignments are filtered on their quality and mapping localization. Finally, the most likely genotype for each SV is predicted from the ratio between the number of reads supporting each allele.SVJedi-graph can genotype four SV types as of now, namely deletions, insertions, inversions and translocations. Running SVJedi-graph on simulated sets of deletions showed that the use of a variation graph was able to restore the genotyping quality on close and overlapping SVs. For instance, with asimulated set of deletions that had another close deletion 0 to 50 bp apart, we obtained a genotyping rate (proportion of SVs with a predicted genotype) of 99.9% and an accuracy (proportion of accurate genotype predicted among all predicted genotypes) of 99.0%, compared to a genotyping rate of 78.9% and an accuracy of 97.3% with SVJedi on the same dataset. We also tested our method on the real gold standard dataset of Genome In A Bottle (human individual HG002), and were able to obtain a higher genotyping rate than SVJedi on the same data (97.4% against 90.2%), with a similar or slightly better accuracy (92.9% against 92.2%). SVJedi-graph is distributed under an AGPL license and available on GitHub at https://github.com/SandraLouise/SVJedi-graph.
Published: 2022

31. Méthodes bioinformatiques pour l'étude des Variants de Structure avec des données de séquençages génomiques

Author: 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), Université Rennes 1, Dominique Lavenier(lavenier@irisa.fr), 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), and 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)
Subjects: Assemblage de séquences, High throughput DNA sequencing, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Structural Variation, Variants génomiques, Genomic variants, Variants de structure, Sequence assembly, Séquençage ADN haut-Débit
Published: 2021

32. Towards a better understanding of the low discovery rate of short-read based insertion variant callers

Author: Delage, Wesley, Thevenon, Julien, Lemaitre, Claire, 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), Institute for Advanced Biosciences / Institut pour l'Avancée des Biosciences (Grenoble) (IAB), Centre Hospitalier Universitaire [Grenoble] (CHU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Etablissement français du sang - Auvergne-Rhône-Alpes (EFS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Pôle Couple-Enfant, Département de Génétique et Procréation, 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), and 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)
Subjects: [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], ComputingMilieux_MISCELLANEOUS, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: National audience
Published: 2020

33. 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

34. Reference-free detection of isolated SNPs

Author: Uricaru, Raluca, Rizk, Guillaume, Lacroix, Vincent, Quillery, Elsa, Plantard, Olivier, Chikhi, Rayan, Lemaitre, Claire, and Peterlongo, Pierre
Published: 2015
Full Text: View/download PDF

35. MindTheGap: integrated detection and assembly of short and long insertions

Author: Rizk, Guillaume, Gouin, Anaïs, Chikhi, Rayan, and Lemaitre, Claire
Published: 2014
Full Text: View/download PDF

36. Mapping-Free and Assembly-Free Discovery of Inversion Breakpoints from Raw NGS Reads

Author: Lemaitre, Claire, primary, Ciortuz, Liviu, additional, and Peterlongo, Pierre, additional
Published: 2014
Full Text: View/download PDF

37. Data from: Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems

Author: Richter, Daniel J., Watteaux, Romain, Vannier, Thomas, Leconte, Jade, Frémont, Paul, Reygondeau, Gabriel, Maillet, Nicolas, Henry, Nicolas, Benoit, Gaëtan, da Silva, Ophélie, Delmont, Tom O., Fernández-Guerra, Antonio, Suweis, Samir, Narci, Romain, Berney, Cedric, Eveillard, Damien, Gavory, Frederick, Guidi, Lionel, Labadie, Karine, Mahieu, Eric, Poulain, Julie, Romac, Sarah, Roux, Simon, Dimier, Céline, Kandels‐Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Oceans, Tara, Pesant, Stéphane, Aury, Jean‐Marc, Brum, Jennifer R., Lemaitre, Claire, Pelletier, Eric, Bork, Peer, Sunagawa, Shinichi, Lombard, Fabien, Karp-Boss, Lee, Bowler, Chris, Sullivan, Matthew B., Karsenti, Eric, Mariadassou, Mahendra, Probert, Ian, Peterlongo, Pierre, Wincker, Patrick, Vargas, Colomban de, Ribera d’Alcalà, Maurizio, Iudicone, Daniele, Jaillon, Olivier, Tara Oceans Coordinators, Richter, Daniel J., Watteaux, Romain, Vannier, Thomas, Leconte, Jade, Frémont, Paul, Reygondeau, Gabriel, Maillet, Nicolas, Henry, Nicolas, Benoit, Gaëtan, da Silva, Ophélie, Delmont, Tom O., Fernández-Guerra, Antonio, Suweis, Samir, Narci, Romain, Berney, Cedric, Eveillard, Damien, Gavory, Frederick, Guidi, Lionel, Labadie, Karine, Mahieu, Eric, Poulain, Julie, Romac, Sarah, Roux, Simon, Dimier, Céline, Kandels‐Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Oceans, Tara, Pesant, Stéphane, Aury, Jean‐Marc, Brum, Jennifer R., Lemaitre, Claire, Pelletier, Eric, Bork, Peer, Sunagawa, Shinichi, Lombard, Fabien, Karp-Boss, Lee, Bowler, Chris, Sullivan, Matthew B., Karsenti, Eric, Mariadassou, Mahendra, Probert, Ian, Peterlongo, Pierre, Wincker, Patrick, Vargas, Colomban de, Ribera d’Alcalà, Maurizio, Iudicone, Daniele, Jaillon, Olivier, and Tara Oceans Coordinators
Abstract: Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated. Here we assessed the global structure of plankton geography and its relation to the biological, chemical and physical context of the ocean (the 'seascape') by analyzing metagenomes of plankton communities sampled across oceans during the Tara Oceans expedition, in light of environmental data and ocean current transport. Using a consistent approach across organismal sizes that provides unprecedented resolution to measure changes in genomic composition between communities, we report a pan-ocean, size-dependent plankton biogeography overlying regional heterogeneity. We found robust evidence for a basin-scale impact of transport by ocean currents on plankton biogeography, and on a characteristic timescale of community dynamics going beyond simple seasonality or life history transitions of plankton.
Published: 2021

38. A small trip in the untranquil world of genomes: A survey on the detection and analysis of genome rearrangement breakpoints

Author: Lemaitre, Claire and Sagot, Marie-France
Published: 2008
Full Text: View/download PDF

39. GATB: Genome Assembly & Analysis Tool Box

Author: Drezen, Erwan, Rizk, Guillaume, Chikhi, Rayan, Deltel, Charles, Lemaitre, Claire, Peterlongo, Pierre, and Lavenier, Dominique
Published: 2014
Full Text: View/download PDF

40. LEVIATHAN: efficient discovery of large structural variants by leveraging long-range information from Linked-Reads data

Author: Morisse, Pierre, primary, Legeai, Fabrice, additional, and Lemaitre, Claire, additional
Published: 2021
Full Text: View/download PDF

41. MTG-Link: filling gaps in draft genome assemblies with linked read data

Author: Guichard, Anne, Legeai, Fabrice, Le Bars, Arthur, Jay, Paul Yann, Joron, Mathieu, 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), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (ABIMS), Fédération de recherche de Roscoff (FR2424), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), 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, 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 Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (FR2424)
Subjects: [INFO]Computer Science [cs], [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: International audience; Current advancements of both second and third generation sequencing technologies contribute to the improvement of the assembly of most genomes. However, complete and accurate reconstruction of large non-model organism genomes remains challenging. In particular, the scaffolding step orders and orients contigs but generates undefined sequences between them, called gaps. Linked read technologies, such as the 10X Genomics Chromium platform, have a great potential for filling the gaps in draft genomes as they provide long-range information while maintaining the power and accuracy of short-read sequencing [1][2]. With these technologies, reads that have been sequenced from the same long DNA molecule (around 30-50 Kb) can be identified thanks to a small barcode sequence. Several tools have been developed for gap-filling with short or long read data [3][4], but to our knowledge, none uses the long-range information of the linked read data.Here, we present MTG-Link, a novel gap-filling tool dedicated to linked read data generated by 10X Genomics Chromium technology. MTG-Link is a Python pipeline combining the local assembly tool MindTheGap [5] and an efficient read subsampling based on the barcode information. For each gap, it extracts the linked reads whose barcode is observed in the gap flanking sequences, and assembles them into contigs by traversing their de Bruijn graph. MTG-Link automatically tests different parameter values for gap-filling, in both forward and reverse orientations, and produces for each, whenever it is possible, a sequence assembly. After automatic qualitative evaluation of the best sequence assembly, it returns a GFA file, containing the gap-filled sequences of each gap. In order to speed up the process, MTG-Link uses a trivial parallelization scheme by giving each gap to a separate thread. We validated our approach on a set of simulated gaps from real datasets with various genome complexities, and showed that the read subsampling step of MTG-Link enables to get better gap assemblies in less CPU time than using MindTheGap on its own. We then applied MTG-Link on several individual genomes of a mimetic butterfly (Heliconius numata), where it significantly improved the contiguity of a 1.3 Mblocus of biological interest.MTG-Link is freely available at https://github.com/anne-gcd/MTG-Link.
Published: 2020

42. DiscoSnp-RAD: de novo detection of small variants for RAD-Seq population genomics

Author: Gauthier, Jérémy, Mouden, Charlotte, Suchan, Tomasz, Alvarez, Nadir, Arrigo, Nils, Riou, Chloé, Lemaitre, Claire, Peterlongo, Pierre, 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 1 (UR1), 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), W. Szafer Institute of Botany, Polska Akademia Nauk = Polish Academy of Sciences (PAN), Natural History Museum [Geneva], Department of Ecology and Evolution [Lausanne], Université de Lausanne (UNIL), 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 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), Université de Lausanne = University of Lausanne (UNIL), CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-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)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Université de Rennes (UNIV-RENNES)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Université de Rennes (UNIV-RENNES), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Polska Akademia Nauk (PAN), and Dpt of Ecology and Evolution [Lausanne]
Subjects: Insertions, Bioinformatics, Reference-free, lcsh:R, Variants, lcsh:Medicine, Genomics, De novo variant calling, RAD-seq, Next-generation sequencing, Deletions, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Population genomics, Molecular Biology, SNPs
Abstract: International audience; Restriction site Associated DNA Sequencing (RAD-Seq) is a technique characterized by the sequencing of specific loci along the genome that is widely employed in the field of evolutionary biology since it allows to exploit variants (mainly Single Nucleotide Polymorphism—SNPs) information from entire populations at a reduced cost. Common RAD dedicated tools, such as STACKS or IPyRAD, are based on all-vs-all read alignments, which require consequent time and computing resources. We present an original method, DiscoSnp-RAD, that avoids this pitfall since variants are detected by exploiting specific parts of the assembly graph built from the reads, hence preventing all-vs-all read alignments. We tested the implementation on simulated datasets of increasing size, up to 1,000 samples, and on real RAD-Seq data from 259 specimens of Chiastocheta flies, morphologically assigned to seven species. All individuals were successfully assigned to their species using both STRUCTURE and Maximum Likelihood phylogenetic reconstruction. Moreover, identified variants succeeded to reveal a within-species genetic structure linked to the geographic distribution. Furthermore, our results show that DiscoSnp-RAD is significantly faster than state-of-the-art tools. The overall results show that DiscoSnp-RAD is suitable to identify variants from RAD-Seq data, it does not require time-consuming parameterization steps and it stands out from other tools due to its completely different principle, making it substantially faster, in particular on large datasets.
Published: 2020

43. Additional file 8 of Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps

Author: Legeai, Fabrice, Santos, Bernardo F., Robin, Stéphanie, Bretaudeau, Anthony, Dikow, Rebecca B., Lemaitre, Claire, Jouan, Véronique, Ravallec, Marc, Jean-Michel Drezen, Tagu, Denis, Baudat, Frédéric, Gabor Gyapay, Zhou, Xin, Shanlin Liu, Webb, Bruce A., Brady, Seán G., and Volkoff, Anne-Nathalie
Abstract: Additional file 8: Table S9. Transposable elements (TE) found in Hyposter didymator segments, IVSPERs and neighboring regions. The LOLA package [86] was used to assess if some particular TE were enriched close to viral circles or IVSPER. Genomics positions were enlarged to 10 kbp at each segments ends and sampled against 1000 other similar regions from the genome, then used it a random reference. LOLA identifies overlaps and calculates enrichment for each TE. For each pairwise comparison, a series of columns describe the results of the statistical test (pvalueLog: -log10(pvalue) from the fisher’s exact result; oddsRatio: result from the fisher’s exact test; q-value transformation to provide false discovery rate (FDR) scores automatically). Some TE are enriched around viral locations, but after FDR correction, nothing was significant.
Published: 2020
Full Text: View/download PDF

44. Additional file 10 of Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps

Author: Legeai, Fabrice, Santos, Bernardo F., Robin, Stéphanie, Bretaudeau, Anthony, Dikow, Rebecca B., Lemaitre, Claire, Jouan, Véronique, Ravallec, Marc, Jean-Michel Drezen, Tagu, Denis, Baudat, Frédéric, Gabor Gyapay, Zhou, Xin, Shanlin Liu, Webb, Bruce A., Brady, Seán G., and Volkoff, Anne-Nathalie
Abstract: Additional file 10:. DRJs analysis. Figure S3. Examples of the different types of DRJ position. a. Proviral segment with two copies of a single direct repeat (DRJ1L and DRJ1R), one at each end of the segment. b. Proviral segment with two distinct repeated sequences (DRJ1, in yellow and DRJ2, in green), each present in two copies (DRJ1L and DRJ1R, DRJ2L and DRJ2R). c. Proviral segment with two repeated sequences, each present in two or more copies. DRJ1s in yellow, DRJ2s in green, HdIV genes represented by arrows. Table S11. DNA motifs found in the direct repeated sequences flanking the IV segments inserted in wasp genomes. Analysis was performed using the DNAMINDA2 webserver ( http://bmbl.sdstate.edu/DMINDA2/annotate.php ); the input dataset was composed of 99 DRJ sequences (right junctions of HdIV and CsIV segments). A total of 89 motifs were obtained; only those whose occurrence exceed 70% of the DRJs are reported. Table S12. Result of genome search using motifs predicted with DMINDA 2.0 webserver. Occurrence rate of motifs predicted with DMINDA 2.0 webserver in DRJs and whole genome sequences. Each of the two motifs was search among the 6 bp kmers present in the whole genome (201,969,604) and in the DRJs (33,930). The significance was evaluated using a Chi2 (taking into account the ratio of these motifs / all the other motifs in the DRJS and in the genome).
Published: 2020
Full Text: View/download PDF

45. Additional file 9 of Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps

Author: Legeai, Fabrice, Santos, Bernardo F., Robin, Stéphanie, Bretaudeau, Anthony, Dikow, Rebecca B., Lemaitre, Claire, Jouan, Véronique, Ravallec, Marc, Jean-Michel Drezen, Tagu, Denis, Baudat, Frédéric, Gabor Gyapay, Zhou, Xin, Shanlin Liu, Webb, Bruce A., Brady, Seán G., and Volkoff, Anne-Nathalie
Abstract: Additional file 9: Table S10. List of direct repeat junctions (DRJ) found at the ends or within proviral segments genes identified in Hyposoter didymator and Campoletis sonorensis genome scaffolds. Are indicated the scaffold name, the name of the proviral segment, its length and position in the scaffold, the name of the DRJ, its size and position in the scaffold and the DRJ sequence. Nucleotide identities are indicated for each pair of DRJ.
Published: 2020
Full Text: View/download PDF

46. Additional file 6 of Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps

Author: Legeai, Fabrice, Santos, Bernardo F., Robin, Stéphanie, Bretaudeau, Anthony, Dikow, Rebecca B., Lemaitre, Claire, Jouan, Véronique, Ravallec, Marc, Jean-Michel Drezen, Tagu, Denis, Baudat, Frédéric, Gabor Gyapay, Zhou, Xin, Shanlin Liu, Webb, Bruce A., Brady, Seán G., and Volkoff, Anne-Nathalie
Abstract: Additional file 6: Figure S1. H. didymator proviral loci corresponding to two segments previously described as “distinct” but sharing part of their sequence [36]. Segments Hd2a (GenBank: KJ586332.1) and Hd2b (GenBank: KJ586327.1) co-localize in the same genome locus here named Hd2; segments Hd11a (KJ586322.1) and Hd11b (KJ586302.1) co-localize in the same genome locus here named Hd11; Hd17a (KJ586314.1) and Hd17b (KJ586316.1) co-localize in the same genome locus here named Hd17; Hd20a (KJ586312.1) and Hd20b (KJ586297.1) co-localize in the same genome locus here named Hd20; Hd26a (KJ586301.1) and Hd26b (KJ586306.1) co-localize in the same genome locus here named Hd26; and finally, Hd31 (KJ586299.1) and Hd34 (KJ586295.1) co-localize in the same genome locus here named Hd31-34. Each proviral locus was characterized by the presence of two different direct repeated sequences (DRJ1 and DRJ2) at the extremities of each of the overlapping segments. Scale bar: 1000 nt.
Published: 2020
Full Text: View/download PDF

47. Additional file 5 of Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps

Author: Legeai, Fabrice, Santos, Bernardo F., Robin, Stéphanie, Bretaudeau, Anthony, Dikow, Rebecca B., Lemaitre, Claire, Jouan, Véronique, Ravallec, Marc, Jean-Michel Drezen, Tagu, Denis, Baudat, Frédéric, Gabor Gyapay, Zhou, Xin, Shanlin Liu, Webb, Bruce A., Brady, Seán G., and Volkoff, Anne-Nathalie
Abstract: Additional file 5: Table S7. List of ichnoviral genes identified in Hyposoter didymator and Campoletis sonorensis genome scaffolds containing at least on ichnovirus sequence. Are indicated the scaffold name, the name of the proviral segment or of the Ichnovirus structural protein encoding region (IVSPER) found in the scaffold, its length and position in the scaffold, the name of the gene, its position in the scaffold, if it contains or not introns, the size of the predicted protein, then the NCBI blast P search results (NCBI accession number and ID of the best match, the blast P e-value and the percentage of identities). Last column indicates comments, or notes reporting discrepancies in the genomic sequence compared with the original CDS sequence in NCBI database.
Published: 2020
Full Text: View/download PDF

48. Additional file 4 of Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps

Author: Legeai, Fabrice, Santos, Bernardo F., Robin, Stéphanie, Bretaudeau, Anthony, Dikow, Rebecca B., Lemaitre, Claire, Jouan, Véronique, Ravallec, Marc, Jean-Michel Drezen, Tagu, Denis, Baudat, Frédéric, Gabor Gyapay, Zhou, Xin, Shanlin Liu, Webb, Bruce A., Brady, Seán G., and Volkoff, Anne-Nathalie
Abstract: Additional file 4: Table S6. List of scaffolds in Hyposoter didymator and Campoletis sonorensis genomes containing at least on ichnovirus sequence. Are indicated the scaffold name and length, the name of the proviral segment or of the Ichnovirus structural protein encoding region (IVSPER) found in the scaffold, its length and position in the scaffold, the name of the direct repeats flanking the segment or within the segment, and the name of the genes predicted in each viral locus. DRJ, direct repeat junction; R, right; L, left; int, internal.
Published: 2020
Full Text: View/download PDF

49. Additional file 2 of Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps

Author: Legeai, Fabrice, Santos, Bernardo F., Robin, Stéphanie, Bretaudeau, Anthony, Dikow, Rebecca B., Lemaitre, Claire, Jouan, Véronique, Ravallec, Marc, Jean-Michel Drezen, Tagu, Denis, Baudat, Frédéric, Gabor Gyapay, Zhou, Xin, Shanlin Liu, Webb, Bruce A., Brady, Seán G., and Volkoff, Anne-Nathalie
Abstract: Additional file 2:. Orthogroups analyses. Table S2. Orthofinder clustering metrics. G50: cluster size at which 50% of genes are in an orthogroup (OG) of that size or greater. O50: fewest number of orthogroups required to reach G50; G50 (assigned genes) = 16; G50 (all genes) = 14; O50 (assigned genes) = 3063; O50 (all genes) = 4112. Species carrying a PDV are indicated with an asterisk. Species carrying polydnaviruses are indicated by asterisks. Table S3. Number of orthogroups shared by each species-pair (i.e. the number of orthogroups which contain at least one gene from each of the species-pairs). Species carrying a PDV are indicated with an asterisk. Table S4. Number of species-specific orthogroups. Number of orthogroups specific to one or groups of species.
Published: 2020
Full Text: View/download PDF

50. Additional file 3 of Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps

Author: Legeai, Fabrice, Santos, Bernardo F., Robin, Stéphanie, Bretaudeau, Anthony, Dikow, Rebecca B., Lemaitre, Claire, Jouan, Véronique, Ravallec, Marc, Jean-Michel Drezen, Tagu, Denis, Baudat, Frédéric, Gabor Gyapay, Zhou, Xin, Shanlin Liu, Webb, Bruce A., Brady, Seán G., and Volkoff, Anne-Nathalie
Abstract: Additional file 3:. Table S5. Synteny blocks between pairwise comparisons of multiple parasitoid genomes. Synteny blocks were computed using SynChro [89], a tool based on a simple algorithm that computes Reciprocal Best-Hits (RBH) to reconstruct the backbones of the synteny blocks. Species carrying polydnaviruses are indicated by asterisks. [Ichn.]: Ichneumonid; [Braco.]: Braconid.
Published: 2020
Full Text: View/download PDF

Catalog

Books, media, physical & digital resources

See catalog results

Searchworks

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

Search

Search Constraints

Refine your results

Search Limiters

Topic

Publication Year Range

Language

Publication Type

Journal

Region

Database

Publisher

270 results on '"Lemaitre, Claire"'

Search Results

Catalog

Select search scope, currently: Articles

Catalog

books, media & more in Jio Institute collections

Articles

journal articles & other e-resources