Extensive sequence divergence between the reference genomes of two zebrafish strains, Tuebingen and AB | |
Deng, Yu3,4,6; Qian, Yuting3,4; Meng, Minghui5; Jiang, Haifeng3,4; Dong, Yang2; Fang, Chengchi4,6; He, Shunping1,4,6,7; Yang, Liandong4,6 | |
刊名 | MOLECULAR ECOLOGY RESOURCES |
2022-03-06 | |
页码 | 10 |
关键词 | AB strain reference genome structural variation zebrafish |
ISSN号 | 1755-098X |
DOI | 10.1111/1755-0998.13602 |
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. |
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关键词 | STRUCTURAL VARIATION ; VERTEBRATE ; ALIGNMENT |
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 |
内容类型 | 期刊论文 |
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.Yunnan Agr Univ, State Key Lab Conservat & Utilizat Bioresources Y, Kunming, Yunnan, Peoples R China 3.Univ Chinese Acad Sci, Beijing, Peoples R China 4.Chinese Acad Sci, Inst Hydrobiol, State Key Lab Freshwater Ecol & Biotechnol, Wuhan, Peoples R China 5.Diggers Wuhan Biotechnol Co Ltd, Wuhan, Peoples R China 6.Qinghai Normal Univ, Acad Plateau Sci & Sustainabil, Xining, Peoples R China 7.Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming, Yunnan, 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. |
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