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
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
Related Records:
Yijing, Jie (1541)
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The Sinocyclocheilus cavefish genome provides insights into cave adaptation
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The Sinocyclocheilus cavefish genome provides insights into cave adaptation
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The Sinocyclocheilus cavefish genome provides insights into cave adaptation
Zhang, C.G. and Zhou, Y.H. (2016)
Species diversity and distribution of inland fishes in China
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The Sinocyclocheilus cavefish genome provides insights into cave adaptation
Xing, Y.C., Zhang, C.G., Fan, E.Y. and Zhao, Y.H. (2016)
Freshwater fishes of China: species richness, endemism, threatened species and conservation
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. (2016)
The Sinocyclocheilus cavefish genome provides insights into cave adaptation
Zhang, C.G. and Zhou, Y.H. (2016)
Species diversity and distribution of inland fishes in China
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. (2016)
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. (2016)
The Sinocyclocheilus cavefish genome provides insights into cave adaptation
Xing, Y.C., Zhang, C.G., Fan, E.Y. and Zhao, Y.H. (2016)
Freshwater fishes of China: species richness, endemism, threatened species and conservation
Zhang, C.G. and Zhou, Y.H. (2016)
Species diversity and distribution of inland fishes in China
Zhang, C.G. and Zhou, Y.H. (2016)
Species diversity and distribution of inland fishes in China
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. (2016)
The Sinocyclocheilus cavefish genome provides insights into cave adaptation
Zhang, C.G. and Zhou, Y.H. (2016)
Species diversity and distribution of inland fishes in China
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. (2016)
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. (2016)
The Sinocyclocheilus cavefish genome provides insights into cave adaptation
Xing, Y.C., Zhang, C.G., Fan, E.Y. and Zhao, Y.H. (2016)
Freshwater fishes of China: species richness, endemism, threatened species and conservation
Zhang, C.G. and Zhou, Y.H. (2016)
Species diversity and distribution of inland fishes in China
Zhang, C.G. and Zhou, Y.H. (2016)
Species diversity and distribution of inland fishes in China
Zhang, C.G. and Zhou, Y.H. (2016)
Species diversity and distribution of inland fishes in China
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. (2016)
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A metagenomic study of intestinal microbial diversity in relation to feeding habits of surface and cave-dwelling Sinocyclocheilus species
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A metagenomic study of intestinal microbial diversity in relation to feeding habits of surface and cave-dwelling Sinocyclocheilus species
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A metagenomic study of intestinal microbial diversity in relation to feeding habits of surface and cave-dwelling Sinocyclocheilus species
Chen, H., Li, C., Liu, T., Chen, S. and Xiao, H. (2019)
A metagenomic study of intestinal microbial diversity in relation to feeding habits of surface and cave-dwelling Sinocyclocheilus species
Chen, H., Li, C., Liu, T., Chen, S. and Xiao, H. (2019)
A metagenomic study of intestinal microbial diversity in relation to feeding habits of surface and cave-dwelling Sinocyclocheilus species
Yang, X., Liu, H., Ma, Z., Zou, Y., Zou, M., Mao, Y., Li, X., Wang, H., Chen, T.,Wang, W. and Yang, R. (2019)
Chromosome‐level genome assembly of Triplophysa tibetana, a fish adapted to the harsh high‐altitude environment of the Tibetan Plateau
Lunghi, E., Zhao, Y., Sun, X. and Zhao, Y. (2019)
Morphometrics of eight Chinese cavefish species
Lunghi, E., Zhao, Y., Sun, X. and Zhao, Y. (2019)
Morphometrics of eight Chinese cavefish species
Lunghi, E., Zhao, Y., Sun, X. and Zhao, Y. (2019)
Morphometrics of eight Chinese cavefish species
Lunghi, E., Zhao, Y., Sun, X. and Zhao, Y. (2019)
Morphometrics of eight Chinese cavefish species
Lunghi, E., Zhao, Y., Sun, X. and Zhao, Y. (2019)
Morphometrics of eight Chinese cavefish species
Lunghi, E., Zhao, Y., Sun, X. and Zhao, Y. (2019)
Morphometrics of eight Chinese cavefish species
Lunghi, E., Zhao, Y., Sun, X. and Zhao, Y. (2019)
Morphometrics of eight Chinese cavefish species
Lunghi, E., Zhao, Y., Sun, X. and Zhao, Y. (2019)
Morphometrics of eight Chinese cavefish species
Lunghi, E., Zhao, Y., Sun, X. and Zhao, Y. (2019)
Morphometrics of eight Chinese cavefish species
Lunghi, E., Zhao, Y., Sun, X. and Zhao, Y. (2019)
Morphometrics of eight Chinese cavefish species
Lunghi, E., Zhao, Y., Sun, X. and Zhao, Y. (2019)
Morphometrics of eight Chinese cavefish species
Sgouros, K., Page, L.M., Orlofske, S.A. and Jadin, R.C. (2019)
A revised molecular phylogeny reveals polyphyly in Schistura (Teleostei: Cypriniformes: Nemacheilidae)
Soares, D., Pluviose, M. and Zhao, Y. (2019)
Ontogenetic development of the horn and hump of the Chinese cavefish Sinocyclocheilus furcodorsalis (Cypriniformes: Cyprinidae)
Policarpo, M., Fumey, J., Lafargeas, P., Legendre, L., Naquin, D., Thermes, C., Møller, P.R., Bernatchez, L., García-Machado, E., Rétaux, S. and Casane, D. (2019)
Molecular decay of light-processing genes in cavefishes: assessing the effects of time, genome architecture and gene flow
Mao, T.-R., Liu, Y.-W., Meegaskumbura, M., Yang, J., Ellepola, G., Senevirathne, G., Fu, C.-H., Gross, J.B. and Pie, M.R. (2020)
Evolution in Sinocyclocheilus cavefish is marked by rate shifts, reversals and origin of novel traits
Mao, T.-R., Liu, Y.-W., Meegaskumbura, M., Yang, J., Ellepola, G., Senevirathne, G., Fu, C.-H., Gross, J.B. and Pie, M.R. (2020)
Evolution in Sinocyclocheilus cavefish is marked by rate shifts, reversals and origin of novel traits
Mao, T.-R., Liu, Y.-W., Meegaskumbura, M., Yang, J., Ellepola, G., Senevirathne, G., Fu, C.-H., Gross, J.B. and Pie, M.R. (2020)
Evolution in Sinocyclocheilus cavefish is marked by rate shifts, reversals and origin of novel traits
Policarpo, M., Fumey, J., Lafargeas, P., Naquin, D., Thermes, C., Naville, M., Dechaud, C., Volff, J.-M., Cabau, C., Klopp, C., Rask Møller, P., Bernatchez, L., García-Machado, E., Rétaux, S. and Casane, D. (2020)
Contrasted gene decay in subterranean vertebrates: insights from cavefishes and fossorial mammals
Policarpo, M., Fumey, J., Lafargeas, P., Naquin, D., Thermes, C., Naville, M., Dechaud, C., Volff, J.-M., Cabau, C., Klopp, C., Rask Møller, P., Bernatchez, L., García-Machado, E., Rétaux, S. and Casane, D. (2020)
Contrasted gene decay in subterranean vertebrates: insights from cavefishes and fossorial mammals
Policarpo, M., Fumey, J., Lafargeas, P., Naquin, D., Thermes, C., Naville, M., Dechaud, C., Volff, J.-M., Cabau, C., Klopp, C., Rask Møller, P., Bernatchez, L., García-Machado, E., Rétaux, S. and Casane, D. (2020)
Contrasted gene decay in subterranean vertebrates: insights from cavefishes and fossorial mammals
Policarpo, M., Fumey, J., Lafargeas, P., Naquin, D., Thermes, C., Naville, M., Dechaud, C., Volff, J.-M., Cabau, C., Klopp, C., Rask Møller, P., Bernatchez, L., García-Machado, E., Rétaux, S. and Casane, D. (2020)
Contrasted gene decay in subterranean vertebrates: insights from cavefishes and fossorial mammals
Ma, Z., Herzog, H., Jiang, Y., Zhao, Y. and Zhang, D. (2020)
Exquisite structure of the lateral line system in eyeless cavefish Sinocyclocheilus tianlinensis contrast to eyed Sinocyclocheilus macrophthalmus (Cypriniformes
Mao, T.-R., Liu, Y.-W., Meegaskumbura, M., Yang, J., Ellepola, G., Senevirathne, G., Fu, C.-H., Gross, J.B. and Pie, M.R. (2020)
Evolution in Sinocyclocheilus cavefish is marked by rate shifts, reversals and origin of novel traits
Mao, T.-R., Liu, Y.-W., Meegaskumbura, M., Yang, J., Ellepola, G., Senevirathne, G., Fu, C.-H., Gross, J.B. and Pie, M.R. (2020)
Evolution in Sinocyclocheilus cavefish is marked by rate shifts, reversals and origin of novel traits
Mao, T.-R., Liu, Y.-W., Meegaskumbura, M., Yang, J., Ellepola, G., Senevirathne, G., Fu, C.-H., Gross, J.B. and Pie, M.R. (2020)
Evolution in Sinocyclocheilus cavefish is marked by rate shifts, reversals and origin of novel traits
Mao, T.-R., Liu, Y.-W., Meegaskumbura, M., Yang, J., Ellepola, G., Senevirathne, G., Fu, C.-H., Gross, J.B. and Pie, M.R. (2020)
Evolution in Sinocyclocheilus cavefish is marked by rate shifts, reversals and origin of novel traits
Mao, T.-R., Liu, Y.-W., Meegaskumbura, M., Yang, J., Ellepola, G., Senevirathne, G., Fu, C.-H., Gross, J.B. and Pie, M.R. (2020)
Evolution in Sinocyclocheilus cavefish is marked by rate shifts, reversals and origin of novel traits