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
Related Records:
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Species diversity and distribution of inland fishes in China
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Species diversity and distribution of inland fishes in China
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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
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
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
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
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
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
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
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
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
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: Cyprinidae)
Li, C., Chen, H., Zhao, Y., Chen, S. and Xiao, H. (2020)
Comparative transcriptomics reveals the molecular genetic basis of pigmentation loss in Sinocyclocheilus cavefishes
Li, C., Chen, H., Zhao, Y., Chen, S. and Xiao, H. (2020)
Comparative transcriptomics reveals the molecular genetic basis of pigmentation loss in Sinocyclocheilus cavefishes
Li, C., Chen, H., Zhao, Y., Chen, S. and Xiao, H. (2020)
Comparative transcriptomics reveals the molecular genetic basis of pigmentation loss in Sinocyclocheilus cavefishes
Zhao, Y., Zhang, C. and Proudlove, G.S. (2021)
Fishes of the Genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in China. Systematics, biology, biogeography and cave adaptation
Zhao, Y., Zhang, C. and Proudlove, G.S. (2021)
Fishes of the Genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in China. Systematics, biology, biogeography and cave adaptation
Zhao, Y., Zhang, C. and Proudlove, G.S. (2021)
Fishes of the Genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in China. Systematics, biology, biogeography and cave adaptation
Zhao, Y., Zhang, C. and Proudlove, G.S. (2021)
Fishes of the Genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in China. Systematics, biology, biogeography and cave adaptation
Zhao, Y., Zhang, C. and Proudlove, G.S. (2021)
Fishes of the Genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in China. Systematics, biology, biogeography and cave adaptation
Zhao, Y., Zhang, C. and Proudlove, G.S. (2021)
Fishes of the Genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in China. Systematics, biology, biogeography and cave adaptation
Yang, N., Li, Y., Liu, Z., Chen, Q. and Shen, Y. (2021)
Molecular phylogenetics and evolutionary history of Sinocyclocheilus (Cypriniformes: Cyprinidae) species within Barbinae in China
Yang, N., Li, Y., Liu, Z., Chen, Q. and Shen, Y. (2021)
Molecular phylogenetics and evolutionary history of Sinocyclocheilus (Cypriniformes: Cyprinidae) species within Barbinae in China
Yang, N., Li, Y., Liu, Z., Chen, Q. and Shen, Y. (2021)
Molecular phylogenetics and evolutionary history of Sinocyclocheilus (Cypriniformes: Cyprinidae) species within Barbinae in China
Li, R., Wang, X., Bian, C., Gao, Z., Zhang, Y., Jiang, W., Wang, M., You, X., Cheng, L., Pan, X., Yang, J. and Shi, Q. (2021)
Whole-genome sequencing of Sinocyclocheilus maitianheensis reveals phylogenetic evolution and immunological variances in various Sinocyclocheilus fishes
Li, R., Wang, X., Bian, C., Gao, Z., Zhang, Y., Jiang, W., Wang, M., You, X., Cheng, L., Pan, X., Yang, J. and Shi, Q. (2021)
Whole-genome sequencing of Sinocyclocheilus maitianheensis reveals phylogenetic evolution and immunological variances in various Sinocyclocheilus fishes
Yin, Y.H., Zhang, X.-H., Wang, X.-A.,Li, R.-H., Zhang, Y.-W., Shan, X.-X., You, X.-X., Huang, X.-D., Wu, A.-L., Wang, M., Pan, X.-F., Bian, C., Jiang, W.-S., Shi, Q., Yang, J.X. (2021)
Construction of a chromosome-level genome assembly for genome-wide identification of growth-related quantitative trait loci in Sinocyclocheilus grahami (Cypriniformes, Cyprinidae)
Luo, Q. and Zhang, R. (2021)
The complete mitochondrial genome and phylogenetic analysis of Sinocyclocheilus angularis (Cypriniformes: Cyprinidae)
Duan, Y.-F., Li, M., Xu, K.-W., Zhang, L. and Zhang, L.-B. (2021)
Protect China’s karst cave habitats
Zhao, Y., Huang, Z., Huang, J., Zhang, C. and Meng, F. (2021)
Phylogenetic analysis and expression differences of eye‐related genes in cavefish genus Sinocyclocheilus
Li, R., Wang, X., Bian, C., Gao, Z., Zhang, Y., Jiang, W., Wang, M., You, X., Cheng, L., Pan, X., Yang, J. and Shi, Q. (2021)
Whole-genome sequencing of Sinocyclocheilus maitianheensis reveals phylogenetic evolution and immunological variances in various Sinocyclocheilus fishes
Chen, B., Mao, T., Liu, Y., Dai, W., Li, X., Rajput, A.P., Yang, J., Gross, J.B. and Meegaskumbura, M. (2021)
Sensory convergence in the world’s largest cavefish diversification: patterns of neuromast evolution, distribution and associated behaviour in Sinocyclocheilus
Zhao, Y., Zhang, C. and Proudlove, G.S. (2021)
Fishes of the Genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in China. Systematics, biology, biogeography and cave adaptation
Zhou, S., Rajput, A.P., Liu, Y., Mao, T., Yang, J., Herath, J. and Meegaskumbura, M. (2021)
Adapting to novel environments together: evolutionary and ecological correlates of the bacterial microbiome of the world’s largest cavefish diversification
Zhao, Y., Zhang, C. and Proudlove, G.S. (2021)
Fishes of the Genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in China. Systematics, biology, biogeography and cave adaptation
Zhao, Y., Zhang, C. and Proudlove, G.S. (2021)
Fishes of the Genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in China. Systematics, biology, biogeography and cave adaptation
Zhao, Y., Zhang, C. and Proudlove, G.S. (2021)
Fishes of the Genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in China. Systematics, biology, biogeography and cave adaptation
Wang, Y., Xiao, N., Wang, S., Luo, T., Yang, X., Liu, T. and Zhou, J. (2021)
The complete mitochondrial genome of a cavedwelling loach Triplophysa baotianensis (Teleostei:Nemacheilidae)
Zhao, Y., Zhang, C. and Proudlove, G.S. (2021)
Fishes of the Genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in China. Systematics, biology, biogeography and cave adaptation
Lei, F., Xu, M., Ji, Z., Rose, K.A., Zakirov, V. and Bisset, M. (2022)
Swimming behavior and hydrodynamics of the Chinese cavefish Sinocyclocheilus rhinocerous and a possible role of its head horn structure
Wen, H., Luo., T., Wang, Y., Wang, S., Liu, T., Xiao, N. and Zhou, J. (2022)
Molecular phylogeny and historical biogeography of the cave fish genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in southwest China
Wen, H., Luo., T., Wang, Y., Wang, S., Liu, T., Xiao, N. and Zhou, J. (2022)
Molecular phylogeny and historical biogeography of the cave fish genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in southwest China
Wen, H., Luo., T., Wang, Y., Wang, S., Liu, T., Xiao, N. and Zhou, J. (2022)
Molecular phylogeny and historical biogeography of the cave fish genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in southwest China
Wen, H., Luo., T., Wang, Y., Wang, S., Liu, T., Xiao, N. and Zhou, J. (2022)
Molecular phylogeny and historical biogeography of the cave fish genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in southwest China
Yang, Z., Gong, Z., Jiang, Y., Cai, Y., Ma, Z., Xin Na, Dong, Z. and Zhang, D. (2022)
Maximized hydrodynamic stimulation strategy for placement of differential pressure and velocity sensors in artificial lateral line systems
Zhou, S., Rajput, A.P., Mao, T., Liu, Y., Ellepola, G., Herath, J., Yang, J. and Meegaskumbura, M. (2022)
Adapting to novel environments together: Evolutionary and ecological correlates of the bacterial microbiome of the world’s largest cavefish diversification (Cyprinidae, Sinocyclocheilus)
Zhou, S., Rajput, A.P., Mao, T., Liu, Y., Ellepola, G., Herath, J., Yang, J. and Meegaskumbura, M. (2022)
Adapting to novel environments together: Evolutionary and ecological correlates of the bacterial microbiome of the world’s largest cavefish diversification (Cyprinidae, Sinocyclocheilus)
Zhao, X., Lan, C., Yu, J., Zhou, J., Lu, X., Xiao, N., Dengban, H. and Zhou, J. (2023)
Mitochondrial genome of a typical cavefish ofSinocyclocheilus anatirostris
Huang, S., Zhao, M., Luo, X., Bedos, A., Wang, Y., Chocat, M., Tian, M. and Liu, W. (2023)
Feihu Dong, a new hotspot cave of subterranean biodiversity from China
Jiang, W.-S., Li, J., Xiang, H.-X., Sun, C., Chang, J.B. and Yang, J.X. (2023)
Comparative analysis and phylogenetic and evolutionary implications of mitogenomes of Chinese Sinocyclocheilus cavefish (Cypriniformes: Cyprinidae)
Jiang, W.-S., Li, J., Xiang, H.-X., Sun, C., Chang, J.B. and Yang, J.X. (2023)
Comparative analysis and phylogenetic and evolutionary implications of mitogenomes of Chinese Sinocyclocheilus cavefish (Cypriniformes: Cyprinidae)
Wen, H., Wang, Y., Yang, X., Yan, S., Luo, T., He, Y. and Zhou, J. (2023)
Variable eyes degeneration of the cave carp Sinocyclocheilus bicornutus (Cyprinidae) from Guizhou Province, southwest China
Tian, M., He, L. and Zhou, J. (2023)
New genera and new species of cavernicolous beetles from southwestern China (Coleoptera:Carabidae: Trechini, Platynini)
He, Y. and He, D.K. (2023)
X-ray microtomography study of cranium, pectoral fin and girdle, and Weberian Apparatus development in juvenile Triplophysa stewarti (Nemacheilidae)