Gene-associated markers as a genomic and transcriptomic resource for a highly migratory and apex predator shark (Isurus oxyrinchus)

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dc.contributor.authorDomingues, Rodrigo R.
dc.contributor.authorMastrochirico-Filho, Vito Antonio [UNESP]
dc.contributor.authorMendes, Natalia J. [UNESP]
dc.contributor.authorHashimoto, Diogo T. [UNESP]
dc.contributor.authorCoelho, Rui
dc.contributor.authorAntunes, Agostinho
dc.contributor.authorForesti, Fausto [UNESP]
dc.contributor.authorMendonça, Fernando F.
dc.contributor.institutionUniversidade Federal de São Paulo (UNIFESP)
dc.contributor.institutionUniversidade de São Paulo (USP)
dc.contributor.institutionUniversidade Estadual Paulista (UNESP)
dc.contributor.institutionInstituto Português do Mar e da Atmosfera–IPMA
dc.contributor.institutionUniversidade do Algarve
dc.contributor.institutionUniversity of Porto
dc.date.accessioned2023-03-01T21:04:49Z
dc.date.available2023-03-01T21:04:49Z
dc.date.issued2022-09-01
dc.description.abstractThe shortfin mako, Isurus oxyrinchus, is an oceanic pelagic shark species found worldwide in tropical and subtropical waters. It is frequently caught by pelagic longline fisheries, but despite its commercial importance and ecological significance, little is still known about its biology and ecology at the molecular level. Therefore, we combined two massive parallel sequencing approaches, double digest restriction site-associated DNA sequencing (ddRAD) and RNA sequencing (RNAseq), for single nucleotide polymorphism (SNP) discovery in the shortfin mako. The ddRAD yielded a total of 82,676 putative SNPs. For RNAseq, a total of 129,663 putative SNPs were found. After the stricter filtering procedure, 405 SNPs from ddRAD and 1165 SNPs from RNAseq were retained and suitable for further analysis. Annotation analysis of SNPs from ddRAD revealed a total of 55 gene associated SNP markers, of which 32 SNPs (58.2%) are associated with diseases and defense responses, 9 SNPs (16.4%) are associated with developmental process, and 3 SNPs (5.4%) are present in genes involved in the reproductive function. For RNAseq, 739 SNPs were annotated and associated to relevant functions amongst which 10 SNPs (0.53%) were related with reproduction, 6 SNPs (0.32%) with growth, and 9 (0.48%) with locomotion. Overall, the genotyping of the SNPs was followed by the validation of 255 SNPs from ddRAD and 646 for RNAseq in 31 individuals from the Atlantic and Indian oceans. Our results provide valuable sequence resources for future population genomics analysis, comparative genomics, phylogenomics, and molecular evolution of the globally endangered shortfin mako shark.en
dc.description.affiliationDepartamento de Ciências do Mar Instituto do Mar Universidade Federal de São Paulo-UNIFESP, Rua Carvalho de Mendonça, 144, São Paulo
dc.description.affiliationDepartamento de Oceanografia Biológica Instituto Oceanográfico Universidade de São Paulo, Praça do Oceanográfico, 191, Cidade Universitária
dc.description.affiliationDepartamento de Ciências Biológicas Faculdade de Ciências de Bauru Universidade Estadual Paulista–UNESP, Campus Bauru, Avenida Engenheiro Luiz Edmundo C. Coube, 14-01, São Paulo
dc.description.affiliationCentro de Aquicultura da UNESP Universidade Estadual Paulista–UNESP Jaboticabal, Via de Acesso Prof. Paulo Donato Castellane, s/n, São Paulo
dc.description.affiliationInstituto Português do Mar e da Atmosfera–IPMA, Av. 5 de Outubro
dc.description.affiliationCentro de Ciências do Mar do Algarve–CCMAR Universidade do Algarve, Campus de Gambelas
dc.description.affiliationCIIMAR/CIMAR Interdisciplinary Centre of Marine and Environmental Research University of Porto, Av. General Norton de Matos, s/n
dc.description.affiliationDepartment of Biology Faculty of Sciences University of Porto, Rua Do Campo Alegre, s/n
dc.description.affiliationLaboratório de Biologia e Genética de Peixes Instituto de Biociências de Botucatu Universidade Estadual Paulista–UNESP, Rua Prof. Antônio Celso Wagner Zanin, 250, São Paulo
dc.description.affiliationUnespDepartamento de Ciências Biológicas Faculdade de Ciências de Bauru Universidade Estadual Paulista–UNESP, Campus Bauru, Avenida Engenheiro Luiz Edmundo C. Coube, 14-01, São Paulo
dc.description.affiliationUnespCentro de Aquicultura da UNESP Universidade Estadual Paulista–UNESP Jaboticabal, Via de Acesso Prof. Paulo Donato Castellane, s/n, São Paulo
dc.description.affiliationUnespLaboratório de Biologia e Genética de Peixes Instituto de Biociências de Botucatu Universidade Estadual Paulista–UNESP, Rua Prof. Antônio Celso Wagner Zanin, 250, São Paulo
dc.description.sponsorshipFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
dc.description.sponsorshipFundação para a Ciência e a Tecnologia
dc.description.sponsorshipIdFAPESP: 2014/19740-7
dc.description.sponsorshipIdFAPESP: 2017/02420-8
dc.description.sponsorshipIdFAPESP: 2019/10201-0
dc.description.sponsorshipIdFundação para a Ciência e a Tecnologia: UIDB/04326/2020
dc.identifierhttp://dx.doi.org/10.1007/s00227-022-04094-z
dc.identifier.citationMarine Biology, v. 169, n. 9, 2022.
dc.identifier.doi10.1007/s00227-022-04094-z
dc.identifier.issn1432-1793
dc.identifier.issn0025-3162
dc.identifier.scopus2-s2.0-85135453428
dc.identifier.urihttp://hdl.handle.net/11449/241471
dc.language.isoeng
dc.relation.ispartofMarine Biology
dc.sourceScopus
dc.subjectMarine omics
dc.subjectNext-generation sequencing
dc.subjectShortfin mako shark
dc.subjectSingle nucleotide polymorphism
dc.titleGene-associated markers as a genomic and transcriptomic resource for a highly migratory and apex predator shark (Isurus oxyrinchus)en
dc.typeArtigo
unesp.author.orcid0000-0002-8979-645X[1]
unesp.author.orcid0000-0002-3550-2671[2]
unesp.author.orcid0000-0002-8808-2498[4]
unesp.author.orcid0000-0003-3813-5157[5]
unesp.author.orcid0000-0002-1328-1732[6]
unesp.author.orcid0000-0002-0862-0445[7]
unesp.author.orcid0000-0002-4806-9897[8]
unesp.departmentCiências Biológicas - FCpt

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Bauru - FC - Faculdade de Ciências
Artigos - Genética - IBB
Jaboticabal - CAUNESP - Centro de Aquicultura da Unesp