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

IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Shuang Song, Jianhan Cao, Hongmei Xiang, Zhixiao Liu, Wansheng Jiang
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Abstract

Background: 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.

中国穴居鱼三重体的比较有丝分裂基因组分析:新的基因串联复制及其进化意义。
背景:洞穴鱼表现出显著的形态变化,导致代谢需求和能量利用在永久黑暗中的权衡。作为细胞的“发电站”,线粒体在能量代谢中起着至关重要的作用,这表明线粒体基因在洞穴鱼的进化过程中可能经历了选择压力。结果:首次完成了中国典型穴居鱼类杨氏三物理(Triplophysa yangi)有丝分裂全基因组的组装。有丝分裂基因组全长17068 bp,是记录到的最长的三瘤属植物,包括13个蛋白质编码基因(PCGs)、2个rnas、25个trna和一个非编码控制区。在ND2和WANCY区域之间观察到约500 bp的插入,包括一个大的完整串联重复单元(a '-N'-OL'-C'),两侧是两个未注释的序列(U1/U2)。该重复单元的进化起源可能涉及原位复制事件和随后的功能分化——其中新功能化、亚功能化或假原化驱动了近亲之间的差异突变率——或者另一种选择是,通过共同选择机制,从外源遗传物质水平获取,在功能上整合到祖先杨氏T.有丝分裂基因组中。系统发育分析显示,在上第三纪和下第三纪谱系中存在两个主要分支,这与之前的分类一致,而洞穴限制物种在下第三纪谱系中表现出平行进化的迹象。选择压力分析表明,与上古系(表层居群,I)相比,下古系(穴居群,II和III)的非同义取代率与同义取代率(ω)显著增加,表明穴居物种存在适应选择和放松功能约束的双重作用。结论:在三物理洞穴鱼中发现的trna复制和潜在的阳性选择位点进一步表明线粒体PCGs在极端地下条件下的适应性进化。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
BMC Genomics
BMC Genomics 生物-生物工程与应用微生物
CiteScore
7.40
自引率
4.50%
发文量
769
审稿时长
6.4 months
期刊介绍: BMC Genomics is an open access, peer-reviewed journal that considers articles on all aspects of genome-scale analysis, functional genomics, and proteomics. BMC Genomics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work.
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