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Chromosome-level analysis of the Crassostrea hongkongensis genome reveals extensive duplication of immune-related genes in bivalves
Peng, Jinxia1; Li, Qiongzhen1; Xu, Lian2,3; Wei, Pinyuan1; He, Pingping1; Zhang, Xingzhi1; Zhang, Li1; Guan, Junliang1; Zhang, Xiaojuan4,5; Lin, Yong1; Gui, Jianfang4,5; Chen, Xiaohan1
2020-04-15
Source PublicationMOLECULAR ECOLOGY RESOURCES
ISSN1755-098X
Issue1Pages:15
Abstract

Crassostrea hongkongensis is a popular and important native oyster species that is cultured mainly along the coast of the South China Sea. However, the absence of a reference genome has restricted genetic studies and the development of molecular breeding schemes for this species. Here, we combined PacBio and 10 x Genomics technologies to create a C. hongkongensis genome assembly, which has a size of 610 Mb, and is close to that estimated by flow cytometry (similar to 650 Mb). Contig and scaffold N50 are 2.57 and 4.99 Mb, respectively, and BUSCO analysis indicates that 95.8% of metazoan conserved genes are completely represented. Using a high-density linkage map of its closest related species, C. gigas, a total of 521 Mb (85.4%) was anchored to 10 haploid chromosomes. Comparative genomic analyses with other molluscs reveal that several immune- or stress response-related genes extensively expanded in bivalves by tandem duplication, including C1q, Toll-like receptors and Hsp70, which are associated with their adaptation to filter-feeding and sessile lifestyles in shallow sea and/or deep-sea ecosystems. Through transcriptome sequencing, potential genes and pathways related to sex determination and gonad development were identified. The genome and transcriptome of C. hongkongensis provide valuable resources for future molecular studies, genetic improvement and genome-assisted breeding of oysters.

Keywordadaptation bivalve Crassostrea hongkongensis genome gonad development transcriptome
DOI10.1111/1755-0998.13157
Indexed BySCI
Language英语
WOS Research AreaBiochemistry & Molecular Biology ; Environmental Sciences & Ecology ; Evolutionary Biology
WOS SubjectBiochemistry & Molecular Biology ; Ecology ; Evolutionary Biology
WOS IDWOS:000525824400001
WOS KeywordSEX DETERMINATION ; DIVERGENCE TIMES ; IDENTIFICATION ; SEQUENCE ; ALIGNMENT ; OYSTERS ; EVOLUTION ; PROGRAM ; INVOLVEMENT ; PREDICTION
PublisherWILEY
Citation statistics
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/36092
Collection鱼类生物学及渔业生物技术研究中心_期刊论文
Corresponding AuthorLin, Yong; Gui, Jianfang; Chen, Xiaohan
Affiliation1.Guangxi Acad Fisheries Sci, Guangxi Key Lab Aquat Genet Breeding & Hlth Aquac, Nanning, Peoples R China
2.Nantong Univ, Coinnovat Ctr Neuroregenerat, Key Lab Neuroregenerat Jiangsu, Nantong, Peoples R China
3.Nantong Univ, Coinnovat Ctr Neuroregenerat, Minist Educ, Nantong, Peoples R China
4.Chinese Acad Sci, State Key Lab Freshwater Ecol & Biotechnol, Inst Hydrobiol, Wuhan, Peoples R China
5.Chinese Acad Sci, Innovat Acad Seed Design, Wuhan, Peoples R China
Recommended Citation
GB/T 7714
Peng, Jinxia,Li, Qiongzhen,Xu, Lian,et al. Chromosome-level analysis of the Crassostrea hongkongensis genome reveals extensive duplication of immune-related genes in bivalves[J]. MOLECULAR ECOLOGY RESOURCES,2020(1):15.
APA Peng, Jinxia.,Li, Qiongzhen.,Xu, Lian.,Wei, Pinyuan.,He, Pingping.,...&Chen, Xiaohan.(2020).Chromosome-level analysis of the Crassostrea hongkongensis genome reveals extensive duplication of immune-related genes in bivalves.MOLECULAR ECOLOGY RESOURCES(1),15.
MLA Peng, Jinxia,et al."Chromosome-level analysis of the Crassostrea hongkongensis genome reveals extensive duplication of immune-related genes in bivalves".MOLECULAR ECOLOGY RESOURCES .1(2020):15.
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