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The Sinocyclocheilus cavefish genome provides insights into cave adaptation

Overview of attention for article published in BMC Biology, January 2016
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The Sinocyclocheilus cavefish genome provides insights into cave adaptation
Published in
BMC Biology, January 2016
DOI 10.1186/s12915-015-0223-4
Pubmed ID

Junxing Yang, Xiaoli Chen, Jie Bai, Dongming Fang, Ying Qiu, Wansheng Jiang, Hui Yuan, Chao Bian, Jiang Lu, Shiyang He, Xiaofu Pan, Yaolei Zhang, Xiaoai Wang, Xinxin You, Yongsi Wang, Ying Sun, Danqing Mao, Yong Liu, Guangyi Fan, He Zhang, Xiaoyong Chen, Xinhui Zhang, Lanping Zheng, Jintu Wang, Le Cheng, Jieming Chen, Zhiqiang Ruan, Jia Li, Hui Yu, Chao Peng, Xingyu Ma, Junmin Xu, You He, Zhengfeng Xu, Pao Xu, Jian Wang, Huanming Yang, Jun Wang, Tony Whitten, Xun Xu, Qiong Shi


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. 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. 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.

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Geographical breakdown

Country Count As %
United States 1 <1%
Portugal 1 <1%
Unknown 132 99%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 26 19%
Researcher 20 15%
Student > Master 18 13%
Student > Bachelor 8 6%
Other 8 6%
Other 21 16%
Unknown 33 25%
Readers by discipline Count As %
Agricultural and Biological Sciences 48 36%
Biochemistry, Genetics and Molecular Biology 27 20%
Environmental Science 6 4%
Engineering 4 3%
Neuroscience 2 1%
Other 7 5%
Unknown 40 30%