Whole genome sequencing of Crassostrea ariakensis (Mollusca: Ostreidae) and C. hongkongensis expands understandings of stress resistance in sessile oysters

Xingzhi Zhang; Junliang Guan; Ming Zou; Pingping He; Li Zhang; Yongxian Chen; Wei Li; Dapeng Wang; Ermeng Yu; Fangjie Zhong; Peng Zhu; Xueyu Yan; Youhou Xu; Bang Luo; Ting Huang; Linyuan Jiang; Pinyuan Wei; Jinxia Peng

doi:10.1016/j.ygeno.2023.110757

Whole genome sequencing of Crassostrea ariakensis (Mollusca: Ostreidae) and C. hongkongensis expands understandings of stress resistance in sessile oysters

Genomics. 2024 Jan;116(1):110757. doi: 10.1016/j.ygeno.2023.110757. Epub 2023 Dec 6.

Authors

Xingzhi Zhang¹, Junliang Guan¹, Ming Zou², Pingping He¹, Li Zhang¹, Yongxian Chen³, Wei Li¹, Dapeng Wang¹, Ermeng Yu⁴, Fangjie Zhong⁵, Peng Zhu⁵, Xueyu Yan⁶, Youhou Xu⁵, Bang Luo¹, Ting Huang¹, Linyuan Jiang⁷, Pinyuan Wei⁸, Jinxia Peng⁹

Affiliations

¹ Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China.
² Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
³ Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China. Electronic address: yohnsonchen@foxtail.com.
⁴ Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China. Electronic address: yem@prfri.ac.cn.
⁵ Beibu Gulf University, Qinzhou 535000, China.
⁶ Beibu Gulf University, Qinzhou 535000, China. Electronic address: yanxueyu@bbgu.edu.cn.
⁷ Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China. Electronic address: 253346541@qq.com.
⁸ Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China. Electronic address: weipinyuan@hotmail.com.
⁹ Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China. Electronic address: pengjinxia@gmail.com.

PMID: 38061482
DOI: 10.1016/j.ygeno.2023.110757

Abstract

To understand the environmental adaptations among sessile bivalves lacking adaptive immunity, a series of analyses were conducted, with special emphasis on the widely distributed C. ariakensis. Employing Pacbio sequencing and Hi-C technologies, whole genome for each of a C. ariakensis (southern China) and C. hongkongensis individual was generated, with the contig N50 reaching 6.2 and 13.0 Mb, respectively. Each genome harbored over 30,000 protein-coding genes, with approximately half of each genome consisting of repeats. Genome alignment suggested possible introgression between C. gigas and C. ariakensis (northern China), and re-sequencing data corroborated this result and indicated significant gene flow between C. gigas and C. ariakensis. These introgressed candidates, well-represented by genes related to immunity and osmotic pressure, may be associated with environmental stresses. Gene family dynamics modeling suggested immune-related genes were well represented among the expanded genes in C. ariakensis. These outcomes could be attributed to the spread of C. ariakensis.

Keywords: Adaptive introgression; C. ariakensis; Gene family expansion; Genome; Oysters.

MeSH terms

Animals
China
Crassostrea* / genetics
Whole Genome Sequencing