The Sinocyclocheilus cavefish genome provides insights into cave adaptation

BMC Biology

Research Article

Hui Yuan¹  Jintu Wang¹  Danqing Mao¹  Xiaoli Chen¹  Yong Liu¹  Guangyi Fan¹  Yongsi Wang¹  Xun Xu¹  He Zhang¹  Dongming Fang²  Ying Sun³  Shiyang He⁴  Jiang Lu⁴  Jun Wang⁵  Jian Wang⁶  Huanming Yang⁶  Yaolei Zhang⁷  Xinxin You⁸  Jieming Chen⁸  Zhiqiang Ruan⁸  Xinhui Zhang⁸  Chao Peng⁸  Chao Bian⁸  Ying Qiu⁹  Hui Yu^1,10  Jia Li^1,10  Jie Bai^1,11  Qiong Shi^1,12  Le Cheng^1,13  Tony Whitten^1,14  Pao Xu^1,15  You He^1,16  Junmin Xu^1,17  Xingyu Ma^1,17  Xiaoyong Chen^1,18  Xiaofu Pan^1,18  Junxing Yang^1,18  Wansheng Jiang^1,18  Xiaoai Wang^1,18  Lanping Zheng^1,18  Zhengfeng Xu^1,19 

[1] BGI-Shenzhen, 518083, Shenzhen, China;BGI-Shenzhen, 518083, Shenzhen, China;Agricultural Genomes Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China;BGI-Shenzhen, 518083, Shenzhen, China;China National Genebank, 518083, Shenzhen, China;BGI-Shenzhen, 518083, Shenzhen, China;College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China;BGI-Shenzhen, 518083, Shenzhen, China;Department of Biology, Ole Maaløes Vej 5, University of Copenhagen, DK-2200, Copenhagen, Denmark;BGI-Shenzhen, 518083, Shenzhen, China;James D. Watson Institute of Genome Science, 310008, Hangzhou, China;BGI-Shenzhen, 518083, Shenzhen, China;School of Life Science and Technology, University of Electronic Science and Technology of China, 610054, Chengdu, China;BGI-Shenzhen, 518083, Shenzhen, China;Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, 518083, Shenzhen, China;BGI-Shenzhen, 518083, Shenzhen, China;Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, 518083, Shenzhen, China;China National Genebank, 518083, Shenzhen, China;BGI-Shenzhen, 518083, Shenzhen, China;Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, 518083, Shenzhen, China;College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China;BGI-Shenzhen, 518083, Shenzhen, China;Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, 518083, Shenzhen, China;Fauna & Flora International, CB1 2JD, Cambridge, UK;BGI-Shenzhen, 518083, Shenzhen, China;Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, 518083, Shenzhen, China;Shenzhen BGI Fisheries Sci & Tech Co. Ltd., 518083, Shenzhen, China;Zhenjiang BGI Fisheries Science & Technology Industrial Co. Ltd., 212000, Zhenjiang, China;China National Genebank, 518083, Shenzhen, China;BGI-Yunnan, 650106, Kunming, China;Fauna & Flora International, CB1 2JD, Cambridge, UK;Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, 214081, Wuxi, China;Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 201204, Shanghai, China;Shenzhen BGI Fisheries Sci & Tech Co. Ltd., 518083, Shenzhen, China;Zhenjiang BGI Fisheries Science & Technology Industrial Co. Ltd., 212000, Zhenjiang, China;State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China;State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, 210029, Nanjing, China;

关键词: Cavefish;    Genome;    Adaptation;    Evolution;    Qinghai-Tibetan Plateau;    Sinocyclocheilus;   

DOI  :  10.1186/s12915-015-0223-4

 received in 2015-10-08, accepted in 2015-12-17,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundAn 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.ResultsThe 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.ConclusionAs 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.

【 授权许可】

CC BY   
© Yang et al. 2016