Journal Article

Comparative mitogenomic analysis of Chinese cavefish Triplophysa (Cypriniformes: Nemacheilidae): novel gene tandem duplication and evolutionary implications

Song, S., Cao, J., Xiang, H., Liu, Z. and Jiang, W.

Record Number:
6952
Year:
2025
Journal:
BMC Genomics
Pages:
1-16
Volume:
26:293
Notes:
© The Author(s) 2025. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credi
PMCID:
https://doi.org/10.1186/s12864-025-11486-0
Abstract:
Cavefish exhibit significant morphological changes that result in trade-offs in metabolic requirements and energy utilization in perpetual darkness. As cellular “powerhouses”, mitochondria play crucial roles in energy metabolism, suggesting that mitochondrial genes have likely experienced selective pressures during cavefish evolution. Results This study presents the first assembly of the complete mitogenome of Triplophysa yangi, a typical cavefish species in China. The mitogenome is 17,068 bp long, marking the longest recorded for the genus Triplophysa, and includes 13 protein-coding genes (PCGs), 2 rRNAs, 25 tRNAs, and a noncoding control region. An ~ 500 bp insertion between ND2 and WANCY regions was observed, comprising a large intact tandem repeat unit (A’-N’-OL’-C’) flanked by two unannotated sequences (U1/U2). The evolutionary origin of this repeat unit may involve either in situ duplication events with subsequent functional divergence—where neofunctionalization, subfunctionalization, or pseudogenization drove differential mutation rates between paralogs—or alternatively, horizontal acquisition from exogenous genetic material that became functionally integrated into the ancestral T. yangi mitogenome through co-option mechanisms. Phylogenetic analyses revealed two major clades within Triplophysa—epigean and hypogean lineages—consistent with previous classifications, while cave-restricted species exhibited signs of parallel evolution within the hypogean lineage. Selective pressure analysis indicated that the hypogean lineage (cave-dwelling groups, II & III) have a significantly increased ratio of nonsynonymous to synonymous substitution rates (ω) compared to the epigean lineage (surface-dwelling group, I), suggesting a combination of adaptive selection and relaxed functional constraints in cave-dwelling species. Conclusions The duplication of tRNAs in T. yangi and the potential positive selection sites identified in Triplophysa cavefish further indicated adaptive evolution in mitochondrial PCGs in response to extreme subterranean conditions. Keywords Cave fish, Mitogenome, Phylogeny, Positive selection, Karst, China
Times Cited:
28
Relevent Species:
Triplophysa langpingensis Yang in Lan, Gan, Wu and Yang 2013Triplophysa fengshanensis Lan in Lan, Gan, Wu and Yang 2013Triplophysa tianlinensis Li, Li, Lan and Du 2016Triplophysa xichouensis Liu, Pan, Yang and Chen 2017Triplophysa nandanensis Lan, Yang and Chen 1995Triplophysa aluensis Li and Zhu 2000Triplophysa qiubeiensis Li, Yang, Chen, Tao, Qi and Han 2008Triplophysa tianeensis Chen, Cui and Yang 2004Triplophysa xiangshuingensis Li 2004Triplophysa yunnanensis Yang in Wu 1990Triplophysa gejiuensis (Chu and Chen 1979) Chen, Yang and Xu 1992Triplophysa xiangxiensis (Yang, Yuan and Liao 1986) Chen, Yang and Xu 1992Triplophysa shilinensis Chen and Yang 1992Triplophysa tianxingensis Yang, Li and Chen 2016Triplophysa rosa Chen and Yang 2005Triplophysa microphthalma (Liao and Wang in Liao, Wang and Luo 1997) Kottelat 2012Triplophysa macrocephala Yang, Wu and Yang 2012Triplophysa anshuiensis Wu, Wei, Lan and Du 2018Triplophysa baotianensis Li, Li, Liu and Li in Li, Liu, Li and Li 2018Triplophysa erythraea Liu and Huang in Huang, Zhang, Huang, Wu, Gong, Zhang, Peng and Liu 2019Triplophysa qini Deng, Wang and Zhang 2022Triplophysa cehengensis Luo, Mao, Xiao and Zhou 2023Triplophysa luochengensis Li, Lan, Chen and Du 2017Triplophysa xuanweiensis Lu, Li, Mao and Zhao 2022Triplophysa wudangensis Liu, Zheng and Gong 2022Triplophysa qingzhenensis Liu, Zeng and Gong 2022Triplophysa yangi Cao, Song, Yi, Xiang, Yang, Li and Jiang 2025Triplophysa wenshanensis Cao, Song, Yi, Xiang, Yang, Li and Jiang 2025