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A high-quality chromosome-level genome of the endangered roughskin sculpin provides insights into its evolution and adaptation
Xue, Dong-Xiu1,2,3; Xing, Teng-Fei1,2,3,4; Liu, Jin-Xian1,2,3
2022-01-21
Source PublicationMOLECULAR ECOLOGY RESOURCES
ISSN1755-098X
Pages14
Corresponding AuthorLiu, Jin-Xian(jinxianliu@gmail.com)
AbstractThe cottids (Cottidae) are a taxonomically diverse and ecologically important component of many marine and freshwater ecosystems. Despite recent breakthroughs in long-read sequencing, high quality genomic resources are still limited for studies of ecological and evolutionary processes in cottids. Here, we generated a high-quality, chromosome-scale genome assembly (521.26 Mb) of the catadromous roughskin sculpin (Trachidermus fasciatus Heckel) with a contig N50 of 2.93 Mb and a scaffold N50 of 24.06 Mb. Approximately 21.97% of the genome was composed of repetitive elements. A total of 21,872 protein-coding genes were predicted, of which 19,900 genes (90.98%) were functionally annotated. Phylogenetic analysis supported the validity of Scorpaenoidei and Cottioidei as two suborders of the Perciformes. Chromosome-scale collinearity analyses identified four chromosome fusions leading to the reduction of chromosome number in T. fasciatus. Gene families related to cell apoptosis and cell death were expanded and those related to immune system were contracted, suggesting that these gene families might be relevant to a host of phenotypic differences between T. fasciatus and other teleosts. Gene families associated with osmoregulation were also expanded, which might be associated with its catadromous life history. A total of 50 aging-associated genes were found to be under positive selection, which might be associated with the short lifespan of T. fasciatus. The high-quality genome assembly and annotation will promote researches into the evolution of catadromous life history and short lifespan for T. fasciatus and facilitate comparative genomic studies of cottids in the near future.
Keywordaging-associated genes catadromous life history chromosomal assembly karyotype evolution Trachidermus fasciatus
DOI10.1111/1755-0998.13582
Indexed BySCI
Language英语
Funding ProjectNational Natural Science Foundation of China[31972793]
WOS Research AreaBiochemistry & Molecular Biology ; Environmental Sciences & Ecology ; Evolutionary Biology
WOS SubjectBiochemistry & Molecular Biology ; Ecology ; Evolutionary Biology
WOS IDWOS:000744939000001
PublisherWILEY
Citation statistics
Document Type期刊论文
Identifierhttp://ir.qdio.ac.cn/handle/337002/177745
Collection海洋生态与环境科学重点实验室
Corresponding AuthorLiu, Jin-Xian
Affiliation1.Chinese Acad Sci, Inst Oceanol, CAS Key Lab Marine Ecol & Environm Sci, Qingdao, Peoples R China
2.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Ecol & Environm Sci, Qingdao, Peoples R China
3.Chinese Acad Sci, Ctr Ocean Mega Sci, Qingdao, Peoples R China
4.Univ Chinese Acad Sci, Beijing, Peoples R China
First Author AffilicationInstitute of Oceanology, Chinese Academy of Sciences
Corresponding Author AffilicationInstitute of Oceanology, Chinese Academy of Sciences
Recommended Citation
GB/T 7714
Xue, Dong-Xiu,Xing, Teng-Fei,Liu, Jin-Xian. A high-quality chromosome-level genome of the endangered roughskin sculpin provides insights into its evolution and adaptation[J]. MOLECULAR ECOLOGY RESOURCES,2022:14.
APA Xue, Dong-Xiu,Xing, Teng-Fei,&Liu, Jin-Xian.(2022).A high-quality chromosome-level genome of the endangered roughskin sculpin provides insights into its evolution and adaptation.MOLECULAR ECOLOGY RESOURCES,14.
MLA Xue, Dong-Xiu,et al."A high-quality chromosome-level genome of the endangered roughskin sculpin provides insights into its evolution and adaptation".MOLECULAR ECOLOGY RESOURCES (2022):14.
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