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  6. 深海鱼类物种与基因组多样性的研究
Extensive sequence divergence between the reference genomes of two zebrafish strains, Tuebingen and AB

文献类型：期刊论文

作者Deng, Yu5,6,7; Qian, Yuting5,7; Meng, Minghui4; Jiang, Haifeng5,7; Dong, Yang3; Fang, Chengchi5,6; He, Shunping1,2,5,6; Yang, Liandong5,6
刊名MOLECULAR ECOLOGY RESOURCES
出版日期2022-03-06
页码10
ISSN号1755-098X
关键词AB strain reference genome structural variation zebrafish
DOI10.1111/1755-0998.13602
通讯作者He, Shunping ; Yang, Liandong
英文摘要The zebrafish (Danio rerio) is one of the most widely used model organisms for studying vertebrate gene function and human disease, given the 70% conserved protein-coding genes between zebrafish and human. Two of the most common laboratory zebrafish strains are Tuebingen and AB. Despite the fact that the zebrafish reference genome is derived from the Tuebingen strain, the AB strain is still widely used although a high-quality genome comparable to Tuebingen is lacking. Here, we report a 1.40-Gb representative de novo genome assembly of the AB strain (DrAB1), with contig N50 length of 21 Mb, by integrating Illumina short-read sequencing, Nanopore long-read sequencing and HiC-based chromatin mapping. Compared with the published zebrafish Zv11 reference genome (GRCz11), this genome assembly shows considerable improvements in both contiguity and completeness. In addition, substantial structural differences and extensive sequence divergence of unprecedented resolution have been uncovered, especially with respect to 9,029,929 single nucleotide polymorphisms, 2,376,812 InDels, 32,623 insertions, 22,089 deletions and 220 inversions, which constitute similar to 2.6% of the DrAB1 genome. Many of these variants may have potential functional effects on phenotype, which should be considered in further experimental designs. Consequently, our study provides additional genomic resources and a high-resolution structural variation map based on whole-genome alignment for the zebrafish community, which could also be an indispensable reference genome from a model species in future research on fish phylogenetic genomics, comparative genomics and adaptive evolution.
WOS关键词STRUCTURAL VARIATION ; VERTEBRATE ; ALIGNMENT
资助项目Strategic Priority Research Program of Chinese Academy of Sciences[XDB31000000] ; National Natural Science Foundation of China[32170480] ; National Natural Science Foundation of China[31972866] ; Youth Innovation Promotion Association, Chinese Academy of Sciences
WOS研究方向Biochemistry & Molecular Biology ; Environmental Sciences & Ecology ; Evolutionary Biology
语种英语
出版者WILEY
WOS记录号WOS:000765150400001
资助机构Strategic Priority Research Program of Chinese Academy of Sciences ; National Natural Science Foundation of China ; Youth Innovation Promotion Association, Chinese Academy of Sciences
源URL[http://ir.idsse.ac.cn/handle/183446/9248]  
专题深海科学研究部_深海生物学研究室_深海鱼类物种与基因组多样性的研究
通讯作者He, Shunping; Yang, Liandong
作者单位1.Chinese Acad Sci, Inst Deep Sea Sci & Engn, Sanya, Peoples R China
2.Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming, Yunnan, Peoples R China
3.Yunnan Agr Univ, State Key Lab Conservat & Utilizat Bioresources Y, Kunming, Yunnan, Peoples R China
4.Diggers Wuhan Biotechnol Co Ltd, Wuhan, Peoples R China
5.Chinese Acad Sci, Inst Hydrobiol, State Key Lab Freshwater Ecol & Biotechnol, Wuhan, Peoples R China
6.Qinghai Normal Univ, Acad Plateau Sci & Sustainabil, Xining, Peoples R China
7.Univ Chinese Acad Sci, Beijing, Peoples R China
推荐引用方式
GB/T 7714		 Deng, Yu,Qian, Yuting,Meng, Minghui,et al. Extensive sequence divergence between the reference genomes of two zebrafish strains, Tuebingen and AB[J]. MOLECULAR ECOLOGY RESOURCES,2022:10.
APA Deng, Yu.,Qian, Yuting.,Meng, Minghui.,Jiang, Haifeng.,Dong, Yang.,...&Yang, Liandong.(2022).Extensive sequence divergence between the reference genomes of two zebrafish strains, Tuebingen and AB.MOLECULAR ECOLOGY RESOURCES,10.
MLA Deng, Yu,et al."Extensive sequence divergence between the reference genomes of two zebrafish strains, Tuebingen and AB".MOLECULAR ECOLOGY RESOURCES (2022):10.

入库方式： OAI收割

来源：深海科学与工程研究所

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