Journal Article
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.
Record Number:
5515
Year:
2021
Journal:
Frontiers in Genetics
Pages:
1-9
Volume:
12:736500
Abstract:
An adult Sinocyclocheilus maitianheensis, a surface-dwelling golden-line barbel fish, was
collected from Maitian river (Kunming City, Yunnan Province, China) for whole-genome
sequencing, assembly, and annotation. We obtained a genome assembly of 1.7 Gb with a
scaffoldN50 of 1.4Mb and a contig N50 of 24.7 kb. A total of 39,977 protein-coding geneswere
annotated. Based on a comparative phylogenetic analysis of five Sinocyclocheilus species and
other five representative vertebrates with published genome sequences, we found that S.
maitianheensis is close to Sinocyclocheilus anophthalmus (a cave-restricted species with similar
locality).Moreover, the assembled genomes of S. maitianheensis and other four Sinocyclocheilus
counterparts were used for a fourfold degenerative third-codon transversion (4dTv) analysis. The
recent whole-genome duplication (WGD) event was therefore estimated to occur about 18.1
million years ago. Our results also revealed a decreased tendency of copy number in many
important genes related to immunity and apoptosis in cave-restricted Sinocyclocheilus species.
In summary, we report the first genome assembly of S.maitianheensis,which provides a valuable
genetic resource for comparative studies on cavefish biology, species protection, and practical
aquaculture of this potentially economical fish.
Keywords: Sinocyclocheilus maitianheensis, whole genome sequencing, assembly, annotation, phylogeny,
immunity, cave adaptation
Times Cited:
4
Relevent Species:
Related Records:
Chen, Y. R., Chu, X. L., Luo, Z. and Wu, J. (1988)
A new blind cyprinid fish from Yunnan, China with a reference to the evolution of its characters
Zheng, J. Z. and Wang, J. (1990)Description of a new species of the genus Sinocyclocheilus from China (Cypriniformes: Cyprinidae)
Chen, Y.R. and Yang, J.X. (1993)Species and origin of cave dwelling Sinocyclocheilus fishes
Chen, Y.R. and Yang, J.X. (1993)A synopsis of cavefishes from China
Chen, Y.R. and Yang, J.X. (1993)Species and origin of cave dwelling Sinocyclocheilus fishes
Chen, Y.R. and Yang, J.X. (1993)A synopsis of cavefishes from China
Yang, J. X. and Chen, Y. R. (1993)The cavefishes from Jiuxiang Limestone Cave of Yunnan, China with reference to character evolutions
Li, W.X and Tao, J.N. (1994)A new species of Cyprinidae from Yunnan, Sinocyclocheilus rhinocerous sp. nov.
Li, W., Wu, D., Chen, A. and Tao, J. (1997)Histological study on the horn-like projection on the head of Sinocyclocheilus rhinocerous
Wang, D. and Chen, Y.Y. (1998)On the diagnosis of Sinocyclocheilus and the taxonomic position of its closely related genus Anchicyclocheilus (Cypriniformes: Cyprinidae: Barbinae)
Wang, D. and Chen, Y.Y. (1998)On the diagnosis of Sinocyclocheilus and the taxonomic position of its closely related genus Anchicyclocheilus (Cypriniformes: Cyprinidae: Barbinae)
Wang, D. and Chen, Y.Y. (1998)On the diagnosis of Sinocyclocheilus and the taxonomic position of its closely related genus Anchicyclocheilus (Cypriniformes: Cyprinidae: Barbinae)
Yue, P. and Chen, Y. (1998)China Red Data Book of Endangered Animals. Pisces
Li, W., Wu, D., Chen, A. and Tao, J. (2000)The preliminary investigation of geographical distribution and elcological adaptation for cave environment of Sinocyclocheilus rhinocerous - a cyprinid fish
Li, W.X. and Tao, J.N. (2002)Local dissection of body of the fishes Sinocyclocheilus rhinocerous
Xiao, H, Zhang, R, Feng, J, Ou, Y., M, Li, W, Chen, S and Zan, R (2002)Nuclear DNA content and ploidy of seventeen species of fishes in Sinocyclocheilus
Xiao, H, Zhang, R, Feng, J, Ou, Y., M, Li, W, Chen, S and Zan, R (2002)Nuclear DNA content and ploidy of seventeen species of fishes in Sinocyclocheilus
Xiao, H, Zhang, R, Feng, J, Ou, Y., M, Li, W, Chen, S and Zan, R (2002)Nuclear DNA content and ploidy of seventeen species of fishes in Sinocyclocheilus
Li, W.X. and Tao, J.N. (2002)Partial anatomy of the Sinocyclocheilus rhinocerous
Romero, A., Zhao, Y.H. and Chen, X.Y. (2009)The hypogean fishes of China
Zhao, Y.H. and Zhang, C.G. (2009)Endemic fishes of Sinocyclocheilus (Cypriniformes: Cyprinidae) in China - Species diversity, cave adaptation, systematics and zoogeography
Romero, A., Zhao, Y.H. and Chen, X.Y. (2009)The hypogean fishes of China
Zhao, Y.H. and Zhang, C.G. (2009)Threatened fishes of the world: Sinocyclocheilus anophthalmus (Chen and Chu, 1988) (Cyprinidae)
Zhao, Y.H. and Zhang, C.G. (2009)Endemic fishes of Sinocyclocheilus (Cypriniformes: Cyprinidae) in China - Species diversity, cave adaptation, systematics and zoogeography
Romero, A., Zhao, Y.H. and Chen, X.Y. (2009)The hypogean fishes of China
Zhao, Y.H. and Zhang, C.G. (2009)Endemic fishes of Sinocyclocheilus (Cypriniformes: Cyprinidae) in China - Species diversity, cave adaptation, systematics and zoogeography
Zhao, Y.H., Gozlan, R.E. and Zhang, C.G. (2011)Out of sight out of mind: current knowledge of Chinese cave fishes
Zhao, Y.H., Gozlan, R.E. and Zhang, C.G. (2011)Out of sight out of mind: current knowledge of Chinese cave fishes
Zhao, Y.H., Gozlan, R.E. and Zhang, C.G. (2011)Out of sight out of mind: current knowledge of Chinese cave fishes
Gan, X., Wu, T.J., Wei, M.L. and Yang, J. (2013)A new blind barbine species, Sinocyclocheilus anshuiensis sp. nov. (Cypriniformes: Cyprinidae) from Guangxi, China
Meng, F.W., Braasch, I., Phillips, J.B., Lin, X.W., Titus, T., Zhang, C.G. and Postlethwait, J.H. (2013)Evolution of the eye transcriptome under constant darkness in Sinocyclocheilus cavefish
Meng, F.W., Zhao, Y.H., Postlethwait, J.H. and Zhang, C.G. (2013)Differentially-expressed opsin genes identified in Sinocyclocheilus cavefish endemic to China
Lan, J.H., Gan, X., Wu, T.J. and Yang, J. (2013)Cave fishes of Guangxi, China
Wang, X, Pan, X, Jiang, W., Yang, K, Liu, Q and Yang, J (2015)Establishment and cryopreservation of a cell line from cavefish Sinocyclocheilus anshuiensis
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
Qiu, Y., Yang, J.X.,, Jiang, W.S., Chen, X., Bian, C. and Shi, Q. (2016)A genomic survey on the immune differences among Sinocyclocheilus fishes
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
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
Hao, Z., Zhang, Q. and Qu, B. (2016)Complete mitochondrial genome of a cavefish, Sinocyclocheilus anophthalmus (Cypriniformes: Cyprinidae)
He, S., Lu, J., Jiang, W., Yang, S., Yang, J. and Shi, Q. (2016)The complete mitochondrial genome sequence of a cavefish Sinocyclocheilus anshuiensis (Cypriniformes: Cyprinidae)
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
Peng, S, Lu, J, Yang, J and al., et (2017)The complete mitochondrial genome of horned Golden-line barbell, Sinocyclocheilus rhinocerous (Cypriniformes, Cyprinidae)
Meng, F., Zhao, Y.H., Titus, T., Zhang, C.G. and Postlethwait, J.H. (2018)Brain of the blind: transcriptomics of the golden-line cavefish brain
Li, C.Q., Huang, H.T., Yang, S., He, H., Fu, Q.Y., Chen, S.Y. and Xiao, H. (2018)Complete mitochondrial genome and phylogenetic analysis of Sinocyclocheilus oxycephalus
(Cypriniformes: Cyprinidae)
Li, C.Q., Huang, H.T., Yang, S., He, H., Fu, Q.Y., Chen, S.Y. and Xiao, H. (2018)Complete mitochondrial genome and phylogenetic analysis of Sinocyclocheilus oxycephalus
(Cypriniformes: Cyprinidae)
Zhang, X.-Y., Huang, Z.-Q., Ning, T., Xiang, X.H. Li, C.-Q. Chen, S.-Y. and Xiao, H. (2018)Microscopic and submicroscopic gradient variation of olfactory systems among six Sinocyclocheilus species living in different environments
Niu, C., Luo, J., Yang, J. and Zhao, Y. (2018)Length–weight relationships of four cavefish species from China
Niu, C., Luo, J., Yang, J. and Zhao, Y. (2018)Length–weight relationships of four cavefish species from China
Li, C.Q., Huang, H.T., Yang, S., He, H., Fu, Q.Y., Chen, S.Y. and Xiao, H. (2018)Complete mitochondrial genome and phylogenetic analysis of Sinocyclocheilus oxycephalus
(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
Huang, Z., Titus, T., Postlethwait, J.H. and Meng, F. (2019)Eye degeneration and loss of otx5b expression in the cavefish Sinocyclocheilus tileihornes
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
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
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
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
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
Lam, S.M., Li, J., Sun, H., Mao, W., Liu, Z., Zhao, Q., Han, C., Gong, X., Jiang, B., Chua, G.H., Zhao, Z., Meng, F. and Shui, G. (2022)Quantitative lipidomics and spatial MS-Imaging uncovered neurological and systemic lipid metabolic pathways underlying troglomorphic adaptations in cave-dwelling fish
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
Tian, M., He, L. and Zhou, J. (2023)New genera and new species of cavernicolous beetles from southwestern China (Coleoptera:Carabidae: Trechini, Platynini)