Chromosome-level genome assembly of the Pacific geoduck <i>Panopea generosa</i> reveals major inter- and intrachromosomal rearrangements and substantial expansion of the copine gene family

doi:10.1093/gigascience/giad105

YIC-IR

	*Chromosome-level genome assembly of the Pacific geoduck Panopea generosa* reveals major inter- and intrachromosomal rearrangements and substantial expansion of the copine gene family**
	Wang, Jing 1,2,3; Xu, Qing 1,2,3; Chen, Min4 ; Chen, Yang 1,2,3; Wang, Chunde 4,5; Chen, Nansheng 1,2,3,6
发表期刊	GIGASCIENCE
ISSN	2047-217X
	2023-12-19
卷号	12 页码:13
关键词	Panopea generosa chromosome-level genome assembly genetic breeding evolutionary adaptation
DOI	10.1093/gigascience/giad105
通讯作者	Wang, Chunde([email protected]) ; Chen, Nansheng([email protected])
英文摘要	The Pacific geoduck Panopea generosa (class Bivalvia, order Adapedonta, family Hiatellidae, genus Panopea) is the largest known burrowing bivalve with considerable commercial value. Pacific geoduck and other geoduck clams play important roles in maintaining ecosystem health for their filter feeding habit and coupling pelagic and benthic processes. Here, we report a high-quality chromosome-level genome assembly of P. generosa to characterize its phylogeny and molecular mechanisms of its life strategies. The assembled P. generosa genome consists of 19 chromosomes with a size of 1.47 Gb, a contig N50 length of 1.6 Mb, and a scaffold N50 length of 73.8 Mb. The BUSCO test of the genome assembly showed 93.0% completeness. Constructed chromosome synteny revealed many occurrences of inter- and intrachromosomal rearrangements between P. generosa and Sinonovacula constricta. Of the 35,034 predicted protein-coding genes, 30,700 (87.6%) could be functionally annotated in public databases, indicating the high quality of genome annotation. Comparison of gene copy numbers of gene families among P. generosa and 11 selected species identified 507 rapidly expanded P. generosa gene families that are functionally enriched in immune and gonad development and may be involved in its complex survival strategies. In particular, genes carrying the copine domains underwent additional duplications in P. generosa, which might be important for neuronal development and immune response. The availability of a fully annotated chromosome-level genome provides a valuable dataset for genetic breeding of P. generosa.
资助机构	Taishan Scholar Project Special Fund ; Strategic Priority Research Program of Chinese Academy of Sciences ; Chinese Academy of Sciences Pioneer Hundred Talents Program
收录类别	SCI
语种	英语
关键词[WOS]	ANNOTATION ; ALIGNMENT ; IDENTIFICATION ; INFORMATION ; EVOLUTION ; PROVIDES ; PROGRAM ; SYSTEM ; RATES ; CLAMS
研究领域[WOS]	Life Sciences & Biomedicine - Other Topics ; Science & Technology - Other Topics
WOS记录号	WOS:001185158300001
引用统计
文献类型	期刊论文
条目标识符	http://ir.yic.ac.cn/handle/133337/34898
专题	中国科学院烟台海岸带研究所
通讯作者	Wang, Chunde; Chen, Nansheng
作者单位	1.Chinese Acad Sci, Inst Oceanol, CAS Key Lab Marine Ecol & Environm Sci, Qingdao 266071, Peoples R China 2.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Ecol & Environm Sci, Qingdao 266237, Peoples R China 3.Chinese Acad Sci, Ctr Ocean Mega Sci, Qingdao 266071, Peoples R China 4.Chinese Acad Sci, Yantai Inst Coastal Zone Res, Res & Dev Ctr Efficient Utilizat Coastal Bioresou, Yantai 264003, Peoples R China 5.Qingdao Agr Univ, Marine Sci & Engn Coll, Qingdao 266109, Peoples R China 6.Simon Fraser Univ, Dept Mol Biol & Biochem, Burnaby, BC V5A IS6, Canada
推荐引用方式 GB/T 7714	Wang, Jing,Xu, Qing,Chen, Min,et al. Chromosome-level genome assembly of the Pacific geoduck Panopea generosa reveals major inter- and intrachromosomal rearrangements and substantial expansion of the copine gene family[J]. GIGASCIENCE,2023,12:13.
APA	Wang, Jing,Xu, Qing,Chen, Min,Chen, Yang,Wang, Chunde,&Chen, Nansheng.(2023).Chromosome-level genome assembly of the Pacific geoduck Panopea generosa reveals major inter- and intrachromosomal rearrangements and substantial expansion of the copine gene family.GIGASCIENCE,12,13.
MLA	Wang, Jing,et al."Chromosome-level genome assembly of the Pacific geoduck Panopea generosa reveals major inter- and intrachromosomal rearrangements and substantial expansion of the copine gene family".GIGASCIENCE 12(2023):13.