Journal Article
The complete mitochondrial genome of a rare cavefish (Sinocyclocheilus cyphotergous) and comparative genomic analyses in Sinocyclocheilus
Gao, X., Li, Y., Zhang, R., Lv, Y., Wang, Y., Shi, J., Xie, J., Kong, C. and Li, L.
Record Number:
6806
Year:
2024
Journal:
Pakistan Journal of Zoology
Pages:
2245-2254
Volume:
56(5)
Notes:
Copyright 2022 by the authors. Licensee Zoological Society of Pakistan.
This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/)
Abstract:
The Sinocyclocheilus cyphotergous, belonging to the family Cyprinidae, is endemic to the Karst area of the Yunnan-Guizhou Plateau. Here, we determined the complete mitogenome of S. cyphotergous using an Illumina Hiseq X Ten sequencer. This mitogenome’s structure is typical circular with 16,611 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region. The overall base composition of S. cyphotergous is 31.33% A, 25.89% T, 26.49% C, and 16.29% G with a
slight AT bias of 57.22%. Most mitochondrial genes except ND6 and eight tRNAs were encoded on the heavy strand. All tRNA genes fold into the typical cloverleaf secondary structures, except for tRNA-Ser (AGY) that lacked the dihydrouracil arm. 15 of 22 tRNA genes were found to have 29 G-U mismatches in their secondary structures, which formed a weak bond. In addition, mismatches of A-C, C-C, U-U, and A-A were also found
in their tRNA secondary structures. Result of substitution rate estimation among the mitochondrial protein coding genes (PCGs) showed ATP8 had the largest average Ka and Ka/Ks, while COI had the lowest, which implied that ATP8 might evolve more quickly than the other mitochondrial protein coding genes. Phylogenetic analyses based on Bayesian inference (BI) and maximum likelihood (ML) revealed all Sinocyclocheilus species in this research formed a solid monophyletic group and grouped into two major clades with strong
support excluded S. jii. Additionally, S. cyphotergous in this study was closely related to S. multipunctatus and S. punctatus. In summary, this study provided novel insights into the phylogeny of the Sinocyclocheilus fishes, conducive to the conservation genetics and cave adaptation for S. cyphotergous.
Times Cited:
1
Relevent Species:
Related Records:
Dai, D. Y. (1988)
Un nouveau poisson cavernicole
Wang, D, Huang, Y, Liao, J and Zheng, J (1995)Taxonomic revision of the genus Gibbibarbus Dai
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)
Kottelat, M. and Brehier, F. (1999)Troglocyclocheilus khammouanensis, a new genus and species of cave fish from the Khammouan karst, Laos (Teleostei: Cyprinidae)
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
Huang, J.Q., Gluesenkamp, A., Fenolio, D.B., Wu, Z.Q. and Zhao, Y.H. (2017)Neotype designation and redescription of Sinocyclocheilus cyphotergous (Dai) 1988, a rare and bizarre cavefish species distributed in China (Cypriniformes: Cyprinidae)
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
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
Zhao, Y., Zhang, C. and Proudlove, G.S. (2021)Fishes of the Genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in China. Systematics, biology, biogeography and cave adaptation
Gao, X., Li, Y., Zhang, R., Lv, Y., Wang, Y., Shi, J., Xie, J., Kong, C. and Li, L. (2024)The complete mitochondrial genome of a rare cavefish (Sinocyclocheilus cyphotergous)
and comparative genomic analyses in Sinocyclocheilus