首页|Draft Genome of White-blotched River Stingray Provides Novel Clues for Niche Adaptation and Skeleton Formation

Draft Genome of White-blotched River Stingray Provides Novel Clues for Niche Adaptation and Skeleton Formation

扫码查看
原文链接
  • 万方数据
  • 维普
The white-blotched river stingray(Potamotrygon leopoldi)is a cartilaginous fish native to the Xingu River,a tributary of the Amazon River system.As a rare freshwater-dwelling cartilagi-nous fish in the Potamotrygonidae family in which no member has the genome sequencing informa-tion available,P.leopoldi provides the evolutionary details in fish phylogeny,niche adaptation,and skeleton formation.In this study,we present its draft genome of 4.11 Gb comprising 16,227 contigs and 13,238 scaffolds,with contig N50 of 3937 kb and scaffold N50 of 5675 kb in size.Our analysis shows that P.leopoldi is a slow-evolving fish that diverged from elephant sharks about 96 million years ago.Moreover,two gene families related to the immune system(immunoglobulin heavy con-stant delta genes and T-cell receptor alpha/delta variable genes)exhibit expansion in P.leopoldi only.We also identified the Hox gene clusters in P.leopoldi and discovered that seven Hox genes shared by five representative fish species are missing in P.leopoldi.The RNA sequencing data from P.leopoldi and other three fish species demonstrate that fishes have a more diversified tissue expres-sion spectrum when compared to mammals.Our functional studies suggest that lack of the gc gene encoding vitamin D-binding protein in cartilaginous fishes(both P.leopoldi and Callorhinchus milii)could partly explain the absence of hard bone in their endoskeleton.Overall,this genome resource provides new insights into the niche adaptation,body plan,and skeleton formation of P.leopoldi,as well as the genome evolution in cartilaginous fishes.

White-blotched river stingrayPotamotrygon leopoldiDe novo genome assemblyVitamin D-binding proteinNiche adaptation

Jingqi Zhou、Ake Liu、Funan He、Yunbin Zhang、Libing Shen、Jun Yu、Xiang Zhang

展开 >

School of Public Health,Shanghai Jiao Tong University School of Medicine,Shanghai 200025,China

Department of Life Sciences,Changzhi University,Changzhi 046011,China

Greehey Children's Cancer Research Institute,UT Health San Antonio,San Antonio,TX 78229,USA

State Key Laboratory of Cell Biology,Shanghai Key Laboratory of Molecular Andrology,Shanghai Institute of Biochemistry and Cell Biology,Center for Excellence in Molecular Cell Science,Chinese Academy of Sciences,Shanghai 200031,China

International Human Phenome Institutes(Shanghai),Shanghai 200433,China

Institute of Neuroscience,Center for Excellence in Brain Science and Intelligence Technology,Chinese Academy of Sciences,Shanghai 200031,China

Beijing Institute of Genomics,Chinese Academy of Sciences and China National Center for Bioinformation,Beijing 100101,China

University of Chinese Academy of Sciences,Beijing 100049,China

Shanghai Nanmulin Biotechnology Company Limited,Shanghai 200031,China

展开 >

National Natural Science Foundation of ChinaMajor Science and Technology Innovation Program of Shanghai Municipal Education Commission,ChinaShanghai Nanmulin Biotechnology Company Limited

318010492019-01-07-00-01-E00059

2023

10.1016/j.gpb.2022.11.005

基因组蛋白质组与生物信息学报(英文版)
中国科学院北京基因组研究所

基因组蛋白质组与生物信息学报(英文版)

CSTPCDCSCD
影响因子：0.495
ISSN：1672-0229
年,卷(期)：2023.21(3)
  • 79