Song Shuang, Cao Jianhan, Xiang Hongmei, Liu Zhixiao, Jiang Wansheng
College of Biology and Environmental Sciences, Jishou University, Jishou, 416000, China.
National and Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia ulmoides, Jishou University, Zhangjiajie, 427000, China.
BMC Genomics. 2025 Mar 24;26(1):293. doi: 10.1186/s12864-025-11486-0.
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.
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.
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.
洞穴鱼表现出显著的形态变化，这导致在永久黑暗中代谢需求和能量利用方面的权衡。作为细胞的“动力源”，线粒体在能量代谢中发挥着关键作用，这表明线粒体基因在洞穴鱼进化过程中可能经历了选择压力。
本研究首次组装了中国典型洞穴鱼物种——杨氏高原鳅（Triplophysa yangi）的完整线粒体基因组。该线粒体基因组长度为17,068 bp，是高原鳅属中记录到的最长的，包括13个蛋白质编码基因（PCGs）、2个rRNA、25个tRNA和一个非编码控制区。在ND2和WANCY区域之间观察到一个约500 bp的插入片段，由一个大的完整串联重复单元（A'-N'-OL'-C'）组成，两侧是两个未注释的序列（U1/U2）。这个重复单元的进化起源可能涉及原位复制事件及随后的功能分化——其中新功能化、亚功能化或假基因化导致旁系同源物之间的差异突变率不同——或者是从外源遗传物质的水平获得，通过共选择机制在功能上整合到杨氏高原鳅祖先的线粒体基因组中。系统发育分析揭示了高原鳅属内的两个主要分支——地表分支和地下分支——与先前的分类一致，而局限于洞穴的物种在地下分支内表现出平行进化的迹象。选择压力分析表明，与地表分支（地表栖息群体，I）相比，地下分支（洞穴栖息群体，II和III）的非同义替换率与同义替换率之比（ω）显著增加，这表明洞穴栖息物种存在适应性选择和放松的功能限制。
杨氏高原鳅中tRNA的重复以及在高原鳅洞穴鱼中鉴定出的潜在正选择位点进一步表明线粒体PCGs在应对极端地下条件时的适应性进化。
