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The gene-rich genome of the scallop Pecten maximus

BACKGROUND: The king scallop, Pecten maximus, is distributed in shallow waters along the Atlantic coast of Europe. It forms the basis of a valuable commercial fishery and plays a key role in coastal ecosystems and food webs. Like other filter feeding bivalves it can accumulate potent phytotoxins, to...

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Autores principales: Kenny, Nathan J, McCarthy, Shane A, Dudchenko, Olga, James, Katherine, Betteridge, Emma, Corton, Craig, Dolucan, Jale, Mead, Dan, Oliver, Karen, Omer, Arina D, Pelan, Sarah, Ryan, Yan, Sims, Ying, Skelton, Jason, Smith, Michelle, Torrance, James, Weisz, David, Wipat, Anil, Aiden, Erez L, Howe, Kerstin, Williams, Suzanne T
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7191990/
https://www.ncbi.nlm.nih.gov/pubmed/32352532
http://dx.doi.org/10.1093/gigascience/giaa037
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author Kenny, Nathan J
McCarthy, Shane A
Dudchenko, Olga
James, Katherine
Betteridge, Emma
Corton, Craig
Dolucan, Jale
Mead, Dan
Oliver, Karen
Omer, Arina D
Pelan, Sarah
Ryan, Yan
Sims, Ying
Skelton, Jason
Smith, Michelle
Torrance, James
Weisz, David
Wipat, Anil
Aiden, Erez L
Howe, Kerstin
Williams, Suzanne T
author_facet Kenny, Nathan J
McCarthy, Shane A
Dudchenko, Olga
James, Katherine
Betteridge, Emma
Corton, Craig
Dolucan, Jale
Mead, Dan
Oliver, Karen
Omer, Arina D
Pelan, Sarah
Ryan, Yan
Sims, Ying
Skelton, Jason
Smith, Michelle
Torrance, James
Weisz, David
Wipat, Anil
Aiden, Erez L
Howe, Kerstin
Williams, Suzanne T
author_sort Kenny, Nathan J
collection PubMed
description BACKGROUND: The king scallop, Pecten maximus, is distributed in shallow waters along the Atlantic coast of Europe. It forms the basis of a valuable commercial fishery and plays a key role in coastal ecosystems and food webs. Like other filter feeding bivalves it can accumulate potent phytotoxins, to which it has evolved some immunity. The molecular origins of this immunity are of interest to evolutionary biologists, pharmaceutical companies, and fisheries management. FINDINGS: Here we report the genome assembly of this species, conducted as part of the Wellcome Sanger 25 Genomes Project. This genome was assembled from PacBio reads and scaffolded with 10X Chromium and Hi-C data. Its 3,983 scaffolds have an N50 of 44.8 Mb (longest scaffold 60.1 Mb), with 92% of the assembly sequence contained in 19 scaffolds, corresponding to the 19 chromosomes found in this species. The total assembly spans 918.3 Mb and is the best-scaffolded marine bivalve genome published to date, exhibiting 95.5% recovery of the metazoan BUSCO set. Gene annotation resulted in 67,741 gene models. Analysis of gene content revealed large numbers of gene duplicates, as previously seen in bivalves, with little gene loss, in comparison with the sequenced genomes of other marine bivalve species. CONCLUSIONS: The genome assembly of P. maximus and its annotated gene set provide a high-quality platform for studies on such disparate topics as shell biomineralization, pigmentation, vision, and resistance to algal toxins. As a result of our findings we highlight the sodium channel gene Nav1, known to confer resistance to saxitoxin and tetrodotoxin, as a candidate for further studies investigating immunity to domoic acid.
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spelling pubmed-71919902020-05-05 The gene-rich genome of the scallop Pecten maximus Kenny, Nathan J McCarthy, Shane A Dudchenko, Olga James, Katherine Betteridge, Emma Corton, Craig Dolucan, Jale Mead, Dan Oliver, Karen Omer, Arina D Pelan, Sarah Ryan, Yan Sims, Ying Skelton, Jason Smith, Michelle Torrance, James Weisz, David Wipat, Anil Aiden, Erez L Howe, Kerstin Williams, Suzanne T Gigascience Data Note BACKGROUND: The king scallop, Pecten maximus, is distributed in shallow waters along the Atlantic coast of Europe. It forms the basis of a valuable commercial fishery and plays a key role in coastal ecosystems and food webs. Like other filter feeding bivalves it can accumulate potent phytotoxins, to which it has evolved some immunity. The molecular origins of this immunity are of interest to evolutionary biologists, pharmaceutical companies, and fisheries management. FINDINGS: Here we report the genome assembly of this species, conducted as part of the Wellcome Sanger 25 Genomes Project. This genome was assembled from PacBio reads and scaffolded with 10X Chromium and Hi-C data. Its 3,983 scaffolds have an N50 of 44.8 Mb (longest scaffold 60.1 Mb), with 92% of the assembly sequence contained in 19 scaffolds, corresponding to the 19 chromosomes found in this species. The total assembly spans 918.3 Mb and is the best-scaffolded marine bivalve genome published to date, exhibiting 95.5% recovery of the metazoan BUSCO set. Gene annotation resulted in 67,741 gene models. Analysis of gene content revealed large numbers of gene duplicates, as previously seen in bivalves, with little gene loss, in comparison with the sequenced genomes of other marine bivalve species. CONCLUSIONS: The genome assembly of P. maximus and its annotated gene set provide a high-quality platform for studies on such disparate topics as shell biomineralization, pigmentation, vision, and resistance to algal toxins. As a result of our findings we highlight the sodium channel gene Nav1, known to confer resistance to saxitoxin and tetrodotoxin, as a candidate for further studies investigating immunity to domoic acid. Oxford University Press 2020-04-30 /pmc/articles/PMC7191990/ /pubmed/32352532 http://dx.doi.org/10.1093/gigascience/giaa037 Text en © The Author(s) 2020. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://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 Note
Kenny, Nathan J
McCarthy, Shane A
Dudchenko, Olga
James, Katherine
Betteridge, Emma
Corton, Craig
Dolucan, Jale
Mead, Dan
Oliver, Karen
Omer, Arina D
Pelan, Sarah
Ryan, Yan
Sims, Ying
Skelton, Jason
Smith, Michelle
Torrance, James
Weisz, David
Wipat, Anil
Aiden, Erez L
Howe, Kerstin
Williams, Suzanne T
The gene-rich genome of the scallop Pecten maximus
title The gene-rich genome of the scallop Pecten maximus
title_full The gene-rich genome of the scallop Pecten maximus
title_fullStr The gene-rich genome of the scallop Pecten maximus
title_full_unstemmed The gene-rich genome of the scallop Pecten maximus
title_short The gene-rich genome of the scallop Pecten maximus
title_sort gene-rich genome of the scallop pecten maximus
topic Data Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7191990/
https://www.ncbi.nlm.nih.gov/pubmed/32352532
http://dx.doi.org/10.1093/gigascience/giaa037
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