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The crown pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

2023Journal article Open access
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dc.contributor.authorGomes-dos-Santos, André
dc.contributor.authorLopes-Lima, Manuel
dc.contributor.authorMachado, André M.
dc.contributor.authorForest, Thomas
dc.contributor.authorAchaz, Guillaume
dc.contributor.authorTeixeira, Amílcar
dc.contributor.authorPrié, Vincent
dc.contributor.authorCastro, L. Filipe C.
dc.contributor.authorFroufe, Elsa
dc.date.accessioned2024-02-05T14:18:53Z
dc.date.available2024-02-05T14:18:53Z
dc.date.issued2023
dc.description.abstractContiguous assemblies are fundamental to deciphering the composition of extant genomes. In molluscs, this is considerably challenging owing to the large size of their genomes, heterozygosity, and widespread repetitive content. Consequently, long-read sequencing technologies are fundamental for high contiguity and quality. The first genome assembly of Margaritifera margaritifera (Linnaeus, 1758) (Mollusca: Bivalvia: Unionida), a culturally relevant, widespread, and highly threatened species of freshwater mussels, was recently generated. However, the resulting genome is highly fragmented since the assembly relied on short-read approaches. Here, an improved reference genome assembly was generated using a combination of PacBio CLR long reads and Illumina paired-end short reads. This genome assembly is 2.4 Gb long, organized into 1,700 scaffolds with a contig N50 length of 3.4 Mbp. The ab initio gene prediction resulted in 48,314 protein-coding genes. Our new assembly is a substantial improvement and an essential resource for studying this species’ unique biological and evolutionary features, helping promote its conservation.pt_PT
dc.description.sponsorshipAGS was funded by the Portuguese Foundation for Science and Technology (FCT) under the grant SFRH/BD/137935/2018 and COVID/DB/152933/2022, which also supported MLL (2020.03608.CEECIND) and EF (CEECINST/00027/2021). This research was developed under the project EdgeOmics - Freshwater Bivalves at the Edge: Adaptation genomics under climate-change scenarios (PTDC/CTA-AMB/3065/2020) funded by FCT through national funds. Additional strategic funding was provided by FCT UIDB/04423/2020 and UIDP/04423/2020.pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationGomes-dos-Santos, André; Lopes-Lima, Manuel; Machado, André M.; Forest, Thomas; Achaz, Guillaume; Teixeira, Amílcar; Prié, Vincent; Castro, L. Filipe C.; Froufe, Elsa (2023). The crown pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758). Gigabyte. ISSN 2709-4715. p. 1-14pt_PT
dc.identifier.doi10.46471/gigabyte.81pt_PT
dc.identifier.issn2709-4715
dc.identifier.urihttp://hdl.handle.net/10198/29419
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherGigaScience Presspt_PT
dc.relationInferring phylogeny, demography and adaptive evolution in Margaritiferidae from High-throughput Sequencing data
dc.relationInferring phylogeny, demography and adaptive evolution in Margaritiferidae from High-throughput Sequencing data
dc.relationNot Available
dc.relationNot Available
dc.relationFreshwater Bivalves at the edge: Adaptation genomics under climate-change scenarios
dc.relationInterdisciplinary Centre of Marine and Environmental Research
dc.relationInterdisciplinary Centre of Marine and Environmental Research
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.subjectGenetics and genomicspt_PT
dc.subjectAnimal geneticspt_PT
dc.subjectFreshwater sciencept_PT
dc.titleThe crown pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)pt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleInferring phylogeny, demography and adaptive evolution in Margaritiferidae from High-throughput Sequencing data
oaire.awardTitleInferring phylogeny, demography and adaptive evolution in Margaritiferidae from High-throughput Sequencing data
oaire.awardTitleNot Available
oaire.awardTitleNot Available
oaire.awardTitleFreshwater Bivalves at the edge: Adaptation genomics under climate-change scenarios
oaire.awardTitleInterdisciplinary Centre of Marine and Environmental Research
oaire.awardTitleInterdisciplinary Centre of Marine and Environmental Research
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/POR_NORTE/SFRH%2FBD%2F137935%2F2018/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/POR_NORTE/COVID%2FBD%2F152933%2F2022/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/CEEC IND 3ed/2020.03608.CEECIND%2FCP1601%2FCP1649%2FCT0005/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/CEEC INST 2ed/CEECINST%2F00027%2F2021%2FCP2789%2FCT0001/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/Concurso para Financiamento de Projetos de Investigação Científica e Desenvolvimento Tecnológico em Todos os Domínios Científicos - 2020/PTDC%2FCTA-AMB%2F3065%2F2020/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDB%2F04423%2F2020/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDP%2F04423%2F2020/PT
oaire.citation.endPage14pt_PT
oaire.citation.startPage1pt_PT
oaire.citation.titleGigabytept_PT
oaire.citation.volume2023pt_PT
oaire.fundingStreamPOR_NORTE
oaire.fundingStreamPOR_NORTE
oaire.fundingStreamCEEC IND 3ed
oaire.fundingStreamCEEC INST 2ed
oaire.fundingStreamConcurso para Financiamento de Projetos de Investigação Científica e Desenvolvimento Tecnológico em Todos os Domínios Científicos - 2020
oaire.fundingStream6817 - DCRRNI ID
oaire.fundingStream6817 - DCRRNI ID
person.familyNameTeixeira
person.givenNameAmilcar
person.identifier2153193
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project.funder.nameFundação para a Ciência e a Tecnologia
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rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT
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