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The Sinocyclocheilus cavefish genome provides insights into cave adaptation
Yang, JX; Chen, XL; Bai, J; Fang, DM; Qiu, Y; Jiang, WS; Yuan, H; Bian, C; Lu, J; He, SY; Pan, XF; Zhang, YL; Wang, XA; You, XX; Wang, YS; Sun, Y; Mao, DQ; Liu, Y; Fan, GY; Zhang, H; Chen, XY; Zhang, XH; Zheng, LP; Wang, JT; Cheng, L; Chen, JM; Ruan, ZQ; Li, J; Yu, H; Peng, C; Ma, XY; Xu, JM; He, Y; Xu, ZF; Xu, P; Wang, J; Yang, HM; Wang, J; Whitten, T; Xu, X; Shi, Q; Yang, JX (reprint author), Chinese Acad Sci, Kunming Inst Zool, State Key Lab Genet Resources & Evolut, Kunming 650223, Peoples R China.
2016
Source PublicationBMC BIOLOGY
ISSN1741-7007
Volume14Issue:-Pages:
Subtype期刊文献
AbstractBackground: An emerging cavefish model, the cyprinid genus Sinocyclocheilus, is endemic to the massive southwestern karst area adjacent to the Qinghai-Tibetan Plateau of China. In order to understand whether orogeny influenced the evolution of these species, and how genomes change under isolation, especially in subterranean habitats, we performed whole-genome sequencing and comparative analyses of three species in this genus, S. grahami, S. rhinocerous and S. anshuiensis. These species are surface-dwelling, semi-cave-dwelling and cave-restricted, respectively. Results: The assembled genome sizes of S. grahami, S. rhinocerous and S. anshuiensis are 1.75 Gb, 1.73 Gb and 1.68 Gb, respectively. Divergence time and population history analyses of these species reveal that their speciation and population dynamics are correlated with the different stages of uplifting of the Qinghai-Tibetan Plateau. We carried out comparative analyses of these genomes and found that many genetic changes, such as gene loss (e.g. opsin genes), pseudogenes (e.g. crystallin genes), mutations (e.g. melanogenesis-related genes), deletions (e.g. scale-related genes) and down-regulation (e.g. circadian rhythm pathway genes), are possibly associated with the regressive features (such as eye degeneration, albinism, rudimentary scales and lack of circadian rhythms), and that some gene expansion (e.g. taste-related transcription factor gene) may point to the constructive features (such as enhanced taste buds) which evolved in these cave fishes. Conclusion: As the first report on cavefish genomes among distinct species in Sinocyclocheilus, our work provides not only insights into genetic mechanisms of cave adaptation, but also represents a fundamental resource for a better understanding of cavefish biology.
KeywordMaximum-likelihood Phylogenies Gene Family Evolution Molecular Phylogeny Blind Cavefish Oculocutaneous Albinism Epidermolysis-bullosa Stripe Formation Tibetan Plateau Candidate Genes Dna-sequences
DOI10.1186/s12915-015-0223-4
Indexed BySCI
Language英语
WOS IDWOS:000367435000001
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Document Type期刊论文
Identifierhttp://ir.sinap.ac.cn/handle/331007/25872
Collection中科院上海应用物理研究所2011-2018年
Corresponding AuthorYang, JX (reprint author), Chinese Acad Sci, Kunming Inst Zool, State Key Lab Genet Resources & Evolut, Kunming 650223, Peoples R China.
Recommended Citation
GB/T 7714
Yang, JX,Chen, XL,Bai, J,et al. The Sinocyclocheilus cavefish genome provides insights into cave adaptation[J]. BMC BIOLOGY,2016,14(-):—.
APA Yang, JX.,Chen, XL.,Bai, J.,Fang, DM.,Qiu, Y.,...&Yang, JX .(2016).The Sinocyclocheilus cavefish genome provides insights into cave adaptation.BMC BIOLOGY,14(-),—.
MLA Yang, JX,et al."The Sinocyclocheilus cavefish genome provides insights into cave adaptation".BMC BIOLOGY 14.-(2016):—.
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