Journal Article
The Sinocyclocheilus cavefish genome provides insights into cave adaptation
Yang,J., Chen,X., Bai,J., Fang,D., Qiu,Y., Jiang,W., Yuan,H., Bian,C., Lu,J., He,S., Pan,X., Zhang,Y., Wang,X., You,X., Wang,Y., Sun,Y., Mao,D., Liu,Y., Fan,G., Zhang,H., Chen,X., Zhang,X., Zheng,L., Wang,J., Cheng,L.
Record Number:
2891
Year:
2016
Journal:
BMC Biology
Pages:
1-13
Volume:
14
Abstract:
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.
Times Cited:
13
Relevent Species:
Sinocyclocheilus hyalinus Chen and Yang 1993Sinocyclocheilus furcodorsalis Chen, Yang and Lan 1997Sinocyclocheilus angularis Zheng and Wang 1990Sinocyclocheilus tianlinensis Zhou, Zhang and He 2004Sinocyclocheilus xunlensis Lan, Zhao and Zhang, 2004Sinocyclocheilus aquihornes Li and Yang 2007Sinocyclocheilus broadihornes Li and Mao 2007Sinocyclocheilus rhinocerous Li and Tao 1994Pseudosinocyclocheilus jinxiensis (Zheng, Xiu and Yang 2013) Zhang and Zhao 2016Sinocyclocheilus anshuiensis Gan, Wu, Wei and Yang 2013Sinocyclocheilus anatirostris Lin and Luo 1986Sinocyclocheilus bicornutus Wang and Liao 1997Triplophysa xiangxiensis (Yang, Yuan and Liao 1986) Chen, Yang and Xu 1992