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., Chen, J., R

Record Number:
2891
Year:
2016
Journal:
BMC Biol
Pages:
1
Volume:
14
Short Title:
The Sinocyclocheilus cavefish genome provides insights into cave adaptation
Notes:
Yang, Junxing
PMCID:
PMC4698820
Accession Number:
26728391
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.
ISSN:
1741-7007 (Electronic)
Times Cited:
13
Author Address:
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. yangjx@mail.kiz.ac.cn.
Related Records:
Yijing, Jie (1541)Yang, G., Yuan, F. and Liao, Y. (1986)Lin, R. D. and Luo, Z. (1986)Zhu, S. Q. (1989)Zheng, J. Z. and Wang, J. (1990)Chen, Y. R., Yang, J. X. and Xu, G. C. (1992)Chen, Y. R. and Yang, J. X. (1993)Chen, Y. R. and Yang, J. X. (1993)Yang, J. X. and Chen, Y. R. (1993)Zhou, W. and Cui, G. H. (1993)Chen, Y. R. and Yang, J. X. (1993)Chen, Y. R. and Yang, J. X. (1993)Chen, Y. R. and Yang, J. X. (1993)Chen, Y. R. and Yang, J. X. (1993)Chen, Y. R., Yang, J. X. and Zhu, Z. G. (1994)Li, W.X and Tao, J.N. (1994)Durand, J., Keller, N., Laumont, C. and Delprat, B. (1996)Chen, Y..R., Yang, J.X and Lan, J. H. (1997)Wang, DH and Liao, JW (1997)Wang, D and Chen, YY (1998)Wang, D and Chen, YY (1998)Wang, D and Chen, YY (1998)Wang, D and Chen, YY (1998)Wang, D and Chen, YY (1998)Kottelat, M. and Brehier, F. (1999)Chen, YR, Yang, JX and Chen, ZM (2001)Xiao, H, Zhang, R, Feng, J, Ou, Y., M, Li, W, Chen, S and Zan, R (2002)Xiao, H, Zhang, R, Feng, J, Ou, Y., M, Li, W, Chen, S and Zan, R (2002)Xiao, H, Zhang, R, Feng, J, Ou, Y., M, Li, W, Chen, S and Zan, R (2002)Xiao, H, Zhang, R, Feng, J, Ou, Y., M, Li, W, Chen, S and Zan, R (2002)Xiao, H, Zhang, R, Feng, J, Ou, Y., M, Li, W, Chen, S and Zan, R (2002)Zhou, J, Zhang, CG and He, AY (2004)Lan, JH, Zhao, YH and Zhang, CG (2004)Li, WX, Yang, HF, Han, F, Tao, CP, Hong, Y and Chen, H (2007)Li, WX and Mao, WN (2007)Li, ZQ, Guo, BC, Li, JuB, He, SP and Chen, YY (2008)Zhao, YH and Zhang, CG (2009)Romero, A, Zhao, YH and Cheng, XY (2009)Zhao, YH and Zhang, CG (2009)Romero, A, Zhao, YH and Cheng, XY (2009)Romero, A, Zhao, YH and Cheng, XY (2009)Zhao, YH and Zhang, CG (2009)Zhao, YH and Zhang, CG (2009)Romero, A, Zhao, YH and Cheng, XY (2009)Zhao, YH and Zhang, CG (2009)Zhao, YH and Zhang, CG (2009)Romero, A, Zhao, YH and Cheng, XY (2009)Zhao, YH and Zhang, CG (2009)Zhao, YH and Zhang, CG (2009)Romero, A, Zhao, YH and Cheng, XY (2009)Romero, A, Zhao, YH and Cheng, XY (2009)Zhao, YH and Zhang, CG (2009)Zhao, YH and Zhang, CG (2009)Romero, A, Zhao, YH and Cheng, XY (2009)Romero, A, Zhao, YH and Cheng, XY (2009)Zhao, YH and Zhang, CG (2009)Romero, A, Zhao, YH and Cheng, XY (2009)Zhao, YH and Zhang, CG (2009)Zhao, YH, Gozlan, R. E. and Zhang, C. G. (2011)Zhao, YH, Gozlan, R. E. and Zhang, C. G. (2011)Zhao, YH, Gozlan, R. E. and Zhang, C. G. (2011)Zhao, YH, Gozlan, R. E. and Zhang, C. G. (2011)Zhao, YH, Gozlan, R. E. and Zhang, C. G. (2011)Zhao, YH, Gozlan, R. E. and Zhang, C. G. (2011)Zhao, YH, Gozlan, R. E. and Zhang, C. G. (2011)Zhao, YH, Gozlan, R. E. and Zhang, C. G. (2011)Zhao, YH, Gozlan, R. E. and Zhang, C. G. (2011)Zhao, YH, Gozlan, R. E. and Zhang, C. G. (2011)Zhao, YH, Gozlan, R. E. and Zhang, C. G. (2011)He,S., Liang,X.F., Chu, W.Y. and Chen, D.X (2012)Kottelat, M (2012)Waryani, B., Zhao, Y. H., Zhang, C. G., Dai, R. J. and Abbasi, A. R. (2013)Lan, JH, Gan, Xi, Wu, TJ and Yang, J (2013)Zheng, Hui-Fang, Xiu, LH and Yang, J (2013)He, Y, Chen, XY, Xiao, TQ and Yang, JX (2013)Fenolio, Dante B., Zhao, Yahui, Niemiller, Matthew L. and Stout, Jim F. (2013)Gan, X., Wu, T.J., Wei, M.L. and Yang, J. (2013)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., Chen, J., R (2016)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., Chen, J., R (2016)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., Chen, J., R (2016)Xing, YC, Zhang, CG, Fan, EY and Zhao, YH (2016)Zhang, C. G. and Zhou, YH (2016)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., Chen, J., R (2016)Zhang, C. G. and Zhou, YH (2016)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., Chen, J., R (2016)Xing, YC, Zhang, CG, Fan, EY and Zhao, YH (2016)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., Chen, J., R (2016)Zhang, C. G. and Zhou, YH (2016)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., Chen, J., R (2016)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., Chen, J., R (2016)Xing, YC, Zhang, CG, Fan, EY and Zhao, YH (2016)Zhang, C. G. and Zhou, YH (2016)Zhang, C. G. and Zhou, YH (2016)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., Chen, J., R (2016)Zhang, C. G. and Zhou, YH (2016)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., Chen, J., R (2016)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., Chen, J., R (2016)Zhang, C. G. and Zhou, YH (2016)Xing, YC, Zhang, CG, Fan, EY and Zhao, YH (2016)Zhang, C. G. and Zhou, YH (2016)Zhang, C. G. and Zhou, YH (2016)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., Chen, J., R (2016)Qiu, Y., Yang, J.X.,, Jiang, W.S., Chen, X., Bian, C. and Shi, Q. (2016)Zhang, C. G. and Zhou, YH (2016)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., Chen, J., R (2016)Zhang, C. G. and Zhou, YH (2016)Zhang, C. G. and Zhou, YH (2016)Peng, S, Lu, J, Yang, J and al., et (2017)Li, J.X. Wang, Y., Jina H.F.,Li, W.J., Yan, C.C., Yan, P.F., Zhang, X.Y., He, S.P. and Song, Z.B. (2017)Zhang, YH, Wang, Z, Zhang, Z, Wu, MS and Chen, JY (2017)Wang, X., Liang,C. and Zhang, E. (2017)Li, C.Q., Huang, H.T., Yang, S., He, H., Fu, Q.Y., Chen, S.Y. and Xiao, H. (2018)Li, C.Q., Huang, H.T., Yang, S., He, H., Fu, Q.Y., Chen, S.Y. and Xiao, H. (2018)Li, C.Q., Huang, H.T., Yang, S., He, H., Fu, Q.Y., Chen, S.Y. and Xiao, H. (2018)Li, C.Q., Huang, H.T., Yang, S., He, H., Fu, Q.Y., Chen, S.Y. and Xiao, H. (2018)Zhang, Y., Wang, Z., Zhang, Z., Wu, M.. Chen, J. and Zhao, Y. (2018)