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 and Williams, Suzanne T. (2020) The gene-rich genome of the scallop Pecten maximus. GigaScience, 9 (5). giaa037. ISSN 2047-217X

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Abstract

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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