The gene-rich genome of the scallop Pecten maximus
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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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Now published in GigaScience doi: 10.1093/gigascience/giaa037
Nathan J Kenny 1Natural History Museum, Department of Life Sciences, Cromwell Road, London SW7 5BD, UK2Oxford Brookes University, Headington Rd, Oxford OX3 0BP, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Nathan J KennyShane A McCarthy 3Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteOlga Dudchenko 4The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA5The Center for Theoretical Biological Physics, Rice University, Houston, TX, USAFind this author on Google ScholarFind this author on PubMedSearch for this author …
Now published in GigaScience doi: 10.1093/gigascience/giaa037
Nathan J Kenny 1Natural History Museum, Department of Life Sciences, Cromwell Road, London SW7 5BD, UK2Oxford Brookes University, Headington Rd, Oxford OX3 0BP, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Nathan J KennyShane A McCarthy 3Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteOlga Dudchenko 4The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA5The Center for Theoretical Biological Physics, Rice University, Houston, TX, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKatherine James 1Natural History Museum, Department of Life Sciences, Cromwell Road, London SW7 5BD, UK6Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteEmma Betteridge 7Wellcome Sanger Institute, Cambridge CB10 1SA, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteCraig Corton 7Wellcome Sanger Institute, Cambridge CB10 1SA, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJale Dolucan 7Wellcome Sanger Institute, Cambridge CB10 1SA, UK8Freeline Therapeutics Limited, Stevenage Bioscience Catalyst, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2FX, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDan Mead 7Wellcome Sanger Institute, Cambridge CB10 1SA, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKaren Oliver 7Wellcome Sanger Institute, Cambridge CB10 1SA, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteArina D Omer 4The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSarah Pelan 7Wellcome Sanger Institute, Cambridge CB10 1SA, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteYan Ryan 9School of Computing, Newcastle University, Newcastle upon Tyne NE1 7RU, UK10Institute of Infection and Global Health, Liverpool University, iC2, 146 Brownlow Hill, L3 5RFFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteYing Sims 7Wellcome Sanger Institute, Cambridge CB10 1SA, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJason Skelton 7Wellcome Sanger Institute, Cambridge CB10 1SA, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMichelle Smith 7Wellcome Sanger Institute, Cambridge CB10 1SA, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJames Torrance 7Wellcome Sanger Institute, Cambridge CB10 1SA, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDavid Weisz 4The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAnil Wipat 9School of Computing, Newcastle University, Newcastle upon Tyne NE1 7RU, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteErez L Aiden 4The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA5The Center for Theoretical Biological Physics, Rice University, Houston, TX, USA11Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China12School of Agriculture and Environment, University of Western Australia, Perth, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKerstin Howe 7Wellcome Sanger Institute, Cambridge CB10 1SA, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSuzanne T Williams 1Natural History Museum, Department of Life Sciences, Cromwell Road, London SW7 5BD, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Suzanne T WilliamsFor correspondence: s.williams@nhm.ac.uk
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa037 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102199 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102200 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.102201
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