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

Registro completo de metadados
MetadadosDescriçãoIdioma
Autor(es): dc.contributorIINRAE-
Autor(es): dc.contributorUniv Lausanne-
Autor(es): dc.contributorSwiss Inst Bioinformat-
Autor(es): dc.contributorHunan Normal Univ-
Autor(es): dc.contributorUppsala Univ-
Autor(es): dc.contributorUniv Montpellier-
Autor(es): dc.contributorINRAE-
Autor(es): dc.contributorUniv Wurzburg-
Autor(es): dc.contributorTexas State Univ-
Autor(es): dc.contributorUniv Oregon-
Autor(es): dc.contributorNOAA-
Autor(es): dc.contributorSophia Univ-
Autor(es): dc.contributorNortheastern Univ-
Autor(es): dc.contributorUniversidade Estadual Paulista (Unesp)-
Autor(es): dc.contributorTokyo Univ Marine Sci & Technol-
Autor(es): dc.contributorInst Marine Res-
Autor(es): dc.contributorChinese Acad Sci-
Autor(es): dc.contributorIGB-
Autor(es): dc.contributorMichigan State Univ-
Autor(es): dc.creatorFeron, Romain-
Autor(es): dc.creatorPan, Qiaowei-
Autor(es): dc.creatorWen, Ming-
Autor(es): dc.creatorImarazene, Boudjema-
Autor(es): dc.creatorJouanno, Elodie-
Autor(es): dc.creatorAnderson, Jennifer-
Autor(es): dc.creatorHerpin, Amaury-
Autor(es): dc.creatorJournot, Laurent-
Autor(es): dc.creatorParrinello, Hugues-
Autor(es): dc.creatorKlopp, Christophe-
Autor(es): dc.creatorKottler, Verena A.-
Autor(es): dc.creatorRoco, Alvaro S.-
Autor(es): dc.creatorDu, Kang-
Autor(es): dc.creatorKneitz, Susanne-
Autor(es): dc.creatorAdolfi, Mateus-
Autor(es): dc.creatorWilson, Catherine A.-
Autor(es): dc.creatorMcCluskey, Braedan-
Autor(es): dc.creatorAmores, Angel-
Autor(es): dc.creatorDesvignes, Thomas-
Autor(es): dc.creatorGoetz, Frederick W.-
Autor(es): dc.creatorTakanashi, Ato-
Autor(es): dc.creatorKawaguchi, Mari-
Autor(es): dc.creatorDetrich, Harry William-
Autor(es): dc.creatorOliveira, Marcos A. [UNESP]-
Autor(es): dc.creatorNobrega, Rafael H.-
Autor(es): dc.creatorSakamoto, Takashi-
Autor(es): dc.creatorNakamoto, Masatoshi-
Autor(es): dc.creatorWargelius, Anna-
Autor(es): dc.creatorKarlsen, Orjan-
Autor(es): dc.creatorWang, Zhongwei-
Autor(es): dc.creatorStoeck, Matthias-
Autor(es): dc.creatorWaterhouse, Robert M.-
Autor(es): dc.creatorBraasch, Ingo-
Autor(es): dc.creatorPostlethwait, John H.-
Autor(es): dc.creatorSchartl, Manfred-
Autor(es): dc.creatorGuiguen, Yann-
Data de aceite: dc.date.accessioned2022-02-22T00:55:49Z-
Data de disponibilização: dc.date.available2022-02-22T00:55:49Z-
Data de envio: dc.date.issued2021-06-25-
Data de envio: dc.date.issued2021-06-25-
Data de envio: dc.date.issued2021-03-09-
Fonte completa do material: dc.identifierhttp://dx.doi.org/10.1111/1755-0998.13360-
Fonte completa do material: dc.identifierhttp://hdl.handle.net/11449/209254-
Fonte: dc.identifier.urihttp://educapes.capes.gov.br/handle/11449/209254-
Descrição: dc.descriptionThe study of sex determination and sex chromosome organization in nonmodel species has long been technically challenging, but new sequencing methodologies now enable precise and high-throughput identification of sex-specific genomic sequences. In particular, restriction site-associated DNA sequencing (RAD-Seq) is being extensively applied to explore sex determination systems in many plant and animal species. However, software specifically designed to search for and visualize sex-biased markers using RAD-Seq data is lacking. Here, we present RADSex, a computational analysis workflow designed to study the genetic basis of sex determination using RAD-Seq data. RADSex is simple to use, requires few computational resources, makes no prior assumptions about the type of sex-determination system or structure of the sex locus, and offers convenient visualization through a dedicated R package. To demonstrate the functionality of RADSex, we re-analysed a published data set of Japanese medaka, Oryzias latipes, where we uncovered a previously unknown Y chromosome polymorphism. We then used RADSex to analyse new RAD-Seq data sets from 15 fish species spanning multiple taxonomic orders. We identified the sex determination system and sex-specific markers in six of these species, five of which had no known sex-markers prior to this study. We show that RADSex greatly facilitates the study of sex determination systems in nonmodel species thanks to its speed of analyses, low resource usage, ease of application and visualization options. Furthermore, our analysis of new data sets from 15 species provides new insights on sex determination in fish.-
Descrição: dc.descriptionNational Institute of Health (USA)-
Descrição: dc.descriptionDeutsche Forschungsgemeinschaft-
Descrição: dc.descriptionNational Science Foundation (USA) Office of Polar Programs-
Descrição: dc.descriptionAgence Nationale de la Recherche-
Descrição: dc.descriptionSchweizerischer Nationalfonds zur Forderung der Wissenschaftlichen Forschung-
Descrição: dc.descriptionIINRAE, LPGP, Rennes, France-
Descrição: dc.descriptionUniv Lausanne, Dept Ecol & Evolut, Lausanne, Switzerland-
Descrição: dc.descriptionSwiss Inst Bioinformat, Lausanne, Switzerland-
Descrição: dc.descriptionHunan Normal Univ, Coll Life Sci, State Key Lab Dev Biol Freshwater Fish, Changsha, Peoples R China-
Descrição: dc.descriptionUppsala Univ, Dept Organismal Biol, Systemat Biol, Uppsala, Sweden-
Descrição: dc.descriptionUniv Montpellier, Inst Genom Fonct, INSERM, IGF,CNRS, Montpellier, France-
Descrição: dc.descriptionINRAE, Math & Informat Appl Toulouse, SIGENAE, Castanet Tolosan, France-
Descrição: dc.descriptionUniv Wurzburg, Physiol Chem, Bioctr, Wurzburg, Germany-
Descrição: dc.descriptionTexas State Univ, Xiphophorus Genet Stock Ctr, Dept Chem & Biochem, San Marcos, TX USA-
Descrição: dc.descriptionUniv Wurzburg, Dev Biochem, Bioctr, Wurzburg, Germany-
Descrição: dc.descriptionUniv Oregon, Inst Neurosci, Eugene, OR USA-
Descrição: dc.descriptionNOAA, Environm & Fisheries Sci Div, Northwest Fisheries Sci Ctr, Natl Marine Fisheries Serv, Seattle, WA USA-
Descrição: dc.descriptionSophia Univ, Fac Sci & Technol, Dept Mat & Life Sci, Tokyo, Japan-
Descrição: dc.descriptionNortheastern Univ, Ctr Marine Sci, Dept Marine & Environm Sci, Nahant, MA 01908 USA-
Descrição: dc.descriptionSao Paulo State Univ, Inst Biosci, Dept Struct & Funct Biol, Reprod & Mol Biol Grp, Botucatu, SP, Brazil-
Descrição: dc.descriptionTokyo Univ Marine Sci & Technol, Dept Aquat Marine Biosci, Tokyo, Japan-
Descrição: dc.descriptionInst Marine Res, Bergen, Norway-
Descrição: dc.descriptionChinese Acad Sci, Inst Hydrobiol, Beijing, Peoples R China-
Descrição: dc.descriptionIGB, Leibniz Inst Freshwater Ecol & Inland Fishe, Berlin, Germany-
Descrição: dc.descriptionMichigan State Univ, Dept Integrat Biol, Ecol Evolut & Behav Program, E Lansing, MI 48824 USA-
Descrição: dc.descriptionSao Paulo State Univ, Inst Biosci, Dept Struct & Funct Biol, Reprod & Mol Biol Grp, Botucatu, SP, Brazil-
Descrição: dc.descriptionNational Institute of Health (USA): R01GM085318-
Descrição: dc.descriptionNational Institute of Health (USA): R35GM139635-
Descrição: dc.descriptionDeutsche Forschungsgemeinschaft: SCHA 408/10-1-
Descrição: dc.descriptionNational Science Foundation (USA) Office of Polar Programs: OPP-1543383-
Descrição: dc.descriptionNational Science Foundation (USA) Office of Polar Programs: PLR-1247510-
Descrição: dc.descriptionNational Science Foundation (USA) Office of Polar Programs: PLR-1444167-
Descrição: dc.descriptionAgence Nationale de la Recherche: SCHA 408/10-1-
Descrição: dc.descriptionAgence Nationale de la Recherche: ANR-10-INBS-09-
Descrição: dc.descriptionSchweizerischer Nationalfonds zur Forderung der Wissenschaftlichen Forschung: PP00P3_170664-
Formato: dc.format17-
Idioma: dc.languageen-
Publicador: dc.publisherWiley-Blackwell-
Relação: dc.relationMolecular Ecology Resources-
???dc.source???: dc.sourceWeb of Science-
Palavras-chave: dc.subjectcomputational workflow-
Palavras-chave: dc.subjectfish-
Palavras-chave: dc.subjectRAD&#8208-
Palavras-chave: dc.subjectSequencing-
Palavras-chave: dc.subjectsex determination-
Palavras-chave: dc.subjectvisualization-
Título: dc.titleRADSex: A computational workflow to study sex determination using restriction site-associated DNA sequencing data-
Tipo de arquivo: dc.typelivro digital-
Aparece nas coleções:Repositório Institucional - Unesp

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