The crown pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)
Autor(a) principal: | |
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Data de Publicação: | 2023 |
Outros Autores: | , , , , , , , |
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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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 instacron:RCAAP |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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RCAAP |
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RCAAP |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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1799137416771010560 |