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

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...

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Autores principales: Gomes-dos-Santos, André, Lopes-Lima, Manuel, Machado, André M., Forest, Thomas, Achaz, Guillaume, Teixeira, Amílcar, Prié, Vincent, C. Castro, L. Filipe, Froufe, Elsa
Formato: Online Artículo Texto
Lenguaje:English
Publicado: GigaScience Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10189783/
https://www.ncbi.nlm.nih.gov/pubmed/37207176
http://dx.doi.org/10.46471/gigabyte.81
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author Gomes-dos-Santos, André
Lopes-Lima, Manuel
Machado, André M.
Forest, Thomas
Achaz, Guillaume
Teixeira, Amílcar
Prié, Vincent
C. Castro, L. Filipe
Froufe, Elsa
author_facet Gomes-dos-Santos, André
Lopes-Lima, Manuel
Machado, André M.
Forest, Thomas
Achaz, Guillaume
Teixeira, Amílcar
Prié, Vincent
C. Castro, L. Filipe
Froufe, Elsa
author_sort Gomes-dos-Santos, André
collection PubMed
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.
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spelling pubmed-101897832023-05-18 The Crown Pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758) Gomes-dos-Santos, André Lopes-Lima, Manuel Machado, André M. Forest, Thomas Achaz, Guillaume Teixeira, Amílcar Prié, Vincent C. Castro, L. Filipe Froufe, Elsa GigaByte Data Release 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. GigaScience Press 2023-05-15 /pmc/articles/PMC10189783/ /pubmed/37207176 http://dx.doi.org/10.46471/gigabyte.81 Text en © The Author(s) 2023. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Data Release
Gomes-dos-Santos, André
Lopes-Lima, Manuel
Machado, André M.
Forest, Thomas
Achaz, Guillaume
Teixeira, Amílcar
Prié, Vincent
C. Castro, L. Filipe
Froufe, Elsa
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)
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_short The Crown Pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)
title_sort crown pearl v2: an improved genome assembly of the european freshwater pearl mussel margaritifera margaritifera (linnaeus, 1758)
topic Data Release
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10189783/
https://www.ncbi.nlm.nih.gov/pubmed/37207176
http://dx.doi.org/10.46471/gigabyte.81
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