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

Detalhes bibliográficos
Autor(a) principal: Gomes-dos-Santos, André
Data de Publicação: 2023
Outros Autores: Lopes-Lima, Manuel, Machado, André M., Forest, Thomas, Achaz, Guillaume, Teixeira, Amílcar, Prié, Vincent, Castro, L. Filipe C., Froufe, Elsa
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10198/29419
Resumo: Contiguous 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.
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spelling The crown pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)Genetics and genomicsAnimal geneticsFreshwater scienceContiguous 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.AGS 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.GigaScience PressBiblioteca Digital do IPBGomes-dos-Santos, AndréLopes-Lima, ManuelMachado, André M.Forest, ThomasAchaz, GuillaumeTeixeira, AmílcarPrié, VincentCastro, L. Filipe C.Froufe, Elsa2024-02-05T14:18:53Z20232023-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10198/29419engGomes-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. 1-142709-471510.46471/gigabyte.81info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-02-07T01:19:32Zoai:bibliotecadigital.ipb.pt:10198/29419Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T02:36:32.824064Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv The crown pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)
title The crown pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)
spellingShingle The crown pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)
Gomes-dos-Santos, André
Genetics and genomics
Animal genetics
Freshwater science
title_short The crown pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)
title_full The crown pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)
title_fullStr The crown pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)
title_full_unstemmed The crown pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)
title_sort The crown pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)
author Gomes-dos-Santos, André
author_facet Gomes-dos-Santos, André
Lopes-Lima, Manuel
Machado, André M.
Forest, Thomas
Achaz, Guillaume
Teixeira, Amílcar
Prié, Vincent
Castro, L. Filipe C.
Froufe, Elsa
author_role author
author2 Lopes-Lima, Manuel
Machado, André M.
Forest, Thomas
Achaz, Guillaume
Teixeira, Amílcar
Prié, Vincent
Castro, L. Filipe C.
Froufe, Elsa
author2_role author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Biblioteca Digital do IPB
dc.contributor.author.fl_str_mv Gomes-dos-Santos, André
Lopes-Lima, Manuel
Machado, André M.
Forest, Thomas
Achaz, Guillaume
Teixeira, Amílcar
Prié, Vincent
Castro, L. Filipe C.
Froufe, Elsa
dc.subject.por.fl_str_mv Genetics and genomics
Animal genetics
Freshwater science
topic Genetics and genomics
Animal genetics
Freshwater science
description Contiguous 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.
publishDate 2023
dc.date.none.fl_str_mv 2023
2023-01-01T00:00:00Z
2024-02-05T14:18:53Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10198/29419
url http://hdl.handle.net/10198/29419
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Gomes-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. 1-14
2709-4715
10.46471/gigabyte.81
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv GigaScience Press
publisher.none.fl_str_mv GigaScience Press
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
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collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
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