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Draft Genome of White-blotched River Stingray Provides Novel Clues for niche adaptation and Skeleton Formation

Genomics, Proteomics & Bioinformatics 2023年第3期21卷 501-514页

作者： Jingqi Zhou Ake Liu Funan He Yunbin Zhang Libing Shen Jun Yu Xiang Zhang School of Public Health Shanghai Jiao Tong University School of MedicineShanghai 200025China Department of Life Sciences Changzhi UniversityChangzhi 046011China Greehey Children’s Cancer Research Institute UT Health San AntonioSan AntonioTX 78229USA State Key Laboratory of Cell Biology Shanghai Key Laboratory of Molecular AndrologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghai 200031China International Human Phenome Institutes(Shanghai) Shanghai 200433China Institute of Neuroscience Center for Excellence in Brain Science and Intelligence TechnologyChinese Academy of SciencesShanghai 200031China Beijing Institute of Genomics Chinese Academy of Sciences and China National Center for BioinformationBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Shanghai Nanmulin Biotechnology Company Limited Shanghai 200031China

The white-blotched river stingray(Potamotrygon leopoldi)is a cartilaginous fish native to the Xingu River,a tributary of the Amazon River *** a rare freshwater-dwelling cartilaginous fish in the Potamotrygonidae family in which no member has the genome sequencing information available,*** provides the evolutionary details in fish phylogeny,niche adaptation,and skeleton *** 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 *** analysis shows that *** is a slow-evolving fish that diverged from elephant sharks about 96 million years ***,two gene families related to the immune system(immunoglobulin heavy constant delta genes and T-cell receptor alpha/delta variable genes)exhibit expansion in *** *** also identified the Hox gene clusters in *** and discovered that seven Hox genes shared by five representative fish species are missing in *** RNA sequencing data from *** and other three fish species demonstrate that fishes have a more diversified tissue expression spectrum when compared to *** functional studies suggest that lack of the gc gene encoding vitamin D-binding protein in cartilaginous fishes(both *** and Callorhinchus milii)could partly explain the absence of hard bone in their ***,this genome resource provides new insights into the niche adaptation,body plan,and skeleton formation of ***,as well as the genome evolution in cartilaginous fishes.

关键词： White-blotched river stingray Potamotrygon leopoldi De novo genome assembly Vitamin D-binding protein niche adaptation

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