The Sinocyclocheilus cavefish genome provides insights into cave adaptation

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

来源：BMC Biology, 2016, 14: 1.

DOI：10.1186/s12915-015-0223-4

• Cavefish
• Genome
• Adaptation
• Evolution
• Qinghai-Tibetan Plateau
• Sinocyclocheilus

Background: 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.

• 单位
  南京医科大学; 深圳华大基因研究院; 中国农业科学院; 中国水产科学研究院; 中国水产科学研究院淡水渔业研究中心; 中国科学院昆明动物研究所; 中国科学院研究生院; 中国科学院上海应用物理研究所