The gene-rich genome of the scallop Pecten maximus

doi:10.1093/gigascience/giaa037

KMS > 免疫化学研究所 > 特聘教授组 > Roger D. Kornberg组

	The gene-rich genome of the scallop Pecten maximus
	Kenny, Nathan J.1,2; McCarthy, Shane A.3; Dudchenko, Olga 4,5; James, Katherine 1,6; Betteridge, Emma 7; Corton, Craig 7; Dolucan, Jale 7,8; Mead, Dan 7; Oliver, Karen 7; Omer, Arina D.4; Pelan, Sarah 7; Ryan, Yan 9,10; Sims, Ying 7; Skelton, Jason 7; Smith, Michelle 7; Torrance, James 7; Weisz, David 4; Wipat, Anil 9; Aiden, Erez L.4,5,11,12 ; Howe, Kerstin 7; Williams, Suzanne T.1
	2020-05
发表期刊	GIGASCIENCE
ISSN	2047-217X
卷号	9 期号:5
发表状态	已发表
DOI	10.1093/gigascience/giaa037
摘要	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.
关键词	scallop bivalve mollusc genome domoic neurotoxin
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收录类别	SCI ; SCIE
语种	英语
资助项目	NHM DIF[SDR17012] ; European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant[750,937] ; Wellcome grant[WT207492] ; NSF Physics Frontiers Center Award[PHY1427654] ; Welch Foundation[Q-1866] ; USDA Agriculture and Food Research Initiative Grant[2017-05741] ; NIH 4D Nucleome Grant[U01HL130010] ; NIH Encyclopedia of DNA Elements Mapping Center Award[UM1HG009375]
WOS研究方向	Life Sciences & Biomedicine - Other Topics ; Science & Technology - Other Topics
WOS类目	Biology ; Multidisciplinary Sciences
WOS记录号	WOS:000537394700003
出版者	OXFORD UNIV PRESS
WOS关键词	DOMOIC-ACID ; WHOLE-GENOME ; BIVALVE ; OYSTER ; TRANSCRIPTOME ; ADAPTATION ; TOXICITY ; FISH ; TETRODOTOXIN ; DUPLICATION
原始文献类型	Article ; Data Paper
引用统计
文献类型	期刊论文
条目标识符	https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/121621
专题	免疫化学研究所_特聘教授组_结构生物化学实验室
通讯作者	Williams, Suzanne T.
作者单位	1.Nat Hist Museum, Dept Life Sci, Cromwell Rd, London SW7 5BD, England 2.Oxford Brookes Univ, Headington Rd, Oxford OX3 0BP, England 3.Univ Cambridge, Dept Genet, Cambridge CB2 3EH, England 4.Baylor Coll Med, Dept Mol & Human Genet, Ctr Genome Architecture, Houston, TX 77030 USA 5.Rice Univ, Ctr Theoret Biol Phys, 6100 Main St, Houston, TX 77005 USA 6.Northumbria Univ, Fac Hlth & Life Sci, Dept Appl Sci, Newcastle Upon Tyne NE1 8ST, Tyne & Wear, England 7.Wellcome Sanger Inst, Cambridge CB10 1SA, England 8.Freeline Therapeut Ltd, Stevenage Biosci Catalyst, Gunnels Wood Rd, Stevenage SG1 2FX, Herts, England 9.Newcastle Univ, Sch Comp, Newcastle Upon Tyne NE1 7RU, Tyne & Wear, England 10.Univ Liverpool, Inst Infect & Global Hlth, iC2,146 Brownlow Hill, Liverpool L3 5RF, Merseyside, England 11.Shanghai Tech Univ, Shanghai Inst Adv Immunochem Studies, Shanghai, Peoples R China 12.Univ Western Australia, Sch Agr & Environm, Perth, WA, Australia
推荐引用方式 GB/T 7714	Kenny, Nathan J.,McCarthy, Shane A.,Dudchenko, Olga,et al. The gene-rich genome of the scallop Pecten maximus[J]. GIGASCIENCE,2020,9(5).
APA	Kenny, Nathan J..,McCarthy, Shane A..,Dudchenko, Olga.,James, Katherine.,Betteridge, Emma.,...&Williams, Suzanne T..(2020).The gene-rich genome of the scallop Pecten maximus.GIGASCIENCE,9(5).
MLA	Kenny, Nathan J.,et al."The gene-rich genome of the scallop Pecten maximus".GIGASCIENCE 9.5(2020).