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A Chromosome-Scale Reference Assembly of a Tibetan Loach, Triplophysa siluroides
Yang, Liandong1; Wang, Ying2; Wang, Tai3; Duan, Shengchang4; Dong, Yang4; Zhang, Yanping3; He, Shunping1,5
2019-10-16
Source PublicationFRONTIERS IN GENETICS
Volume10Issue:1Pages:7
Abstract

Cobitoidea is one of the two superfamilies in Cypriniformes; however, few genomes have been sequenced for Cobitoidea fishes. Here, we obtained a total of 252.90 Gb of short Illumina reads and 31.60 Gb of long PacBio Sequel reads, representing approximate genome coverage of 256x and 50x, respectively. The final assembled genome is about 583.47 Mb with contig N50 sizes of 2.87 Mb, which accounts for 91.44% of the estimated genome size of 638.07 Mb. Using Hi-C-based chromatin contact maps, 99.31% of the genome assembly was placed into 25 chromosomes, and the N50 is 22.3 Mb. The gene annotation completeness was evaluated by BUSCO, and 2,470 of the 2,586 conserved genes (95.5%) could be found in our assembly. Repetitive elements were calculated to reach 33.08% of the whole genome. Moreover, we identified 25,406 protein-coding genes, of which 92.59% have been functionally annotated. This genome assembly will be a valuable genomic resource to understand the biology of the Tibetan loaches and will also set a stage for comparative analysis of the classification, diversification, and adaptation of fishes in Cobitoidea.

KeywordTriplophysa siluroides PacBio sequencing genome assembly evolution adaptation
DOI10.3389/fgene.2019.00991
Indexed BySCI
Language英语
WOS Research AreaGenetics & Heredity
WOS SubjectGenetics & Heredity
WOS IDWOS:000497437100001
WOS KeywordCOBITOIDEA TELEOSTEI ; GENOME ; GENE ; CYPRINIFORMES ; PREDICTION ; EVOLUTION ; SEQUENCE ; INSIGHTS ; ADAPTATION ; ALIGNMENT
PublisherFRONTIERS MEDIA SA
Citation statistics
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/35301
Collection水生生物多样性与资源保护研究中心_期刊论文
Corresponding AuthorZhang, Yanping; He, Shunping
Affiliation1.Chinese Acad Sci, Key Lab Aquat Biodivers & Conservat, Inst Hydrobiol, Wuhan, Hubei, Peoples R China
2.Jianghan Univ, Sch Life Sci, Wuhan, Hubei, Peoples R China
3.Gansu Fishers Res Inst, Gansu Key Lab Cold Water Fishes Germplasm Resourc, Lanzhou, Gansu, Peoples R China
4.Nowbio Biotechnol Co, Kunming, Yunnan, Peoples R China
5.Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming, Yunnan, Peoples R China
Recommended Citation
GB/T 7714
Yang, Liandong,Wang, Ying,Wang, Tai,et al. A Chromosome-Scale Reference Assembly of a Tibetan Loach, Triplophysa siluroides[J]. FRONTIERS IN GENETICS,2019,10(1):7.
APA Yang, Liandong.,Wang, Ying.,Wang, Tai.,Duan, Shengchang.,Dong, Yang.,...&He, Shunping.(2019).A Chromosome-Scale Reference Assembly of a Tibetan Loach, Triplophysa siluroides.FRONTIERS IN GENETICS,10(1),7.
MLA Yang, Liandong,et al."A Chromosome-Scale Reference Assembly of a Tibetan Loach, Triplophysa siluroides".FRONTIERS IN GENETICS 10.1(2019):7.
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