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Chromosome-level genome and population genomic analysis provide insights into the evolution and environmental adaptation of Jinjiang oyster Crassostrea ariakensis

文献类型： 外文期刊

作者： Wu, Biao 1 ; Chen, Xi 1 ; Yu, Mengjun 4 ; Ren, Jianfeng 3 ; Hu, Jie 4 ; Shao, Changwei 1 ; Zhou, Liqing 1 ; Sun, Xiujun 1 ; Yu, Tao 5 ; Zheng, Yanxin 5 ; Wang, Yan 1 ; Wang, Zhenyuan 1 ; Zhang, He 4 ; Fan, Guangyi 4 ; Liu, Zhihong 1 ;

作者机构： 1.Chinese Acad Fishery Sci, Yellow Sea Fisheries Res Inst, Key Lab Sustainable Dev Marine Fisheries, Minist Agr & Rural Affairs, Qingdao, Peoples R China

2.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Fisheries Sci & Food Prod Proc, Qingdao, Peoples R China

3.Shanghai Ocean Univ, Natl Demonstrat Ctr Expt Fisheries Sci Educ, Shanghai, Peoples R China

4.BGI Shenzhen, BGI Qingdao, Qingdao, Peoples R China

5.Chinese Acad Fishery Sci, Changdao Enhancement & Expt Stn, Yantai, Peoples R China

6.BGI Shenzhen, State Key Lab Agr Genom, Shenzhen, Peoples R China

关键词： Crassostrea ariakensis; environmental adaptation; genetic structure; genome; WGS

期刊名称：MOLECULAR ECOLOGY RESOURCES （ 影响因子：8.678； 五年影响因子：8.984 ）

ISSN： 1755-098X

年卷期： 2022 年 22 卷 4 期

页码：

收录情况： SCI

摘要： The Jinjiang oyster Crassostrea ariakensis, naturally distributing in estuarine regions with low salinity, is an important economic and ecological species in China. However, studies on its genomics and population genetics remain lacking. Here, we assembled the chromosome-level genome of a female C. ariakensis and re-sequenced 261 individuals from five locations in China representing three typical habitats. The C. ariakensis genome was 662.9 Mb with contig N50 length of 5.9 Mb using PacBio HiFi-CCS long reads, and 99.83% sequences were anchored onto 10 pseudochromosomes using Hi-C data. A total of 26,354 protein-coding genes were predicted. We identified three significantly expanded gene families which are closely associated with osmotic pressure regulation, including CDO, SLC13 and SDR. Population structure analysis revealed that the C. ariakensis from five locations were clustered into three typical groups (northern, southern and Shanghai) (K = 3) and their phylogenetic relationship was consistently correlated to their geographical distribution. Furtherly, the differentiation between northern and southern groups was clearly demonstrated by estimated population differentiation coefficient (F-ST = 0.1154), and the PSMC distribution showed the two groups of effective population size separated at 0.1 Ma. Meanwhile gene flow from southern to Shanghai was detected. Selective sweep analysis between northern and southern group detected genes associated with heat response and salinity adaptation. This study could provide valuable genomic resources and information for further research on the molecular evolution, genetic breeding, biological function and evolutionary adaptation of C. ariakensis.

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