视紫红质基因在早期硬骨鱼类中的进化。
Rhodopsin gene evolution in early teleost fishes.
机构信息
Institute of Oceanography, National Taiwan University, Taipei, Taiwan.
Institute de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle-CNRS, Sorbonne Université, EPHE, Paris, France.
出版信息
PLoS One. 2018 Nov 5;13(11):e0206918. doi: 10.1371/journal.pone.0206918. eCollection 2018.
Rhodopsin mediates an essential step in image capture and is tightly associated with visual adaptations of aquatic organisms, especially species that live in dim light environments (e.g., the deep sea). The rh1 gene encoding rhodopsin was formerly considered a single-copy gene in genomes of vertebrates, but increasing exceptional cases have been found in teleost fish species. The main objective of this study was to determine to what extent the visual adaptation of teleosts might have been shaped by the duplication and loss of rh1 genes. For that purpose, homologous rh1/rh1-like sequences in genomes of ray-finned fishes from a wide taxonomic range were explored using a PCR-based method, data mining of public genetic/genomic databases, and subsequent phylogenomic analyses of the retrieved sequences. We show that a second copy of the fish-specific intron-less rh1 is present in the genomes of most anguillids (Elopomorpha), Hiodon alosoides (Osteoglossomorpha), and several clupeocephalan lineages. The phylogenetic analysis and comparisons of alternative scenarios for putative events of gene duplication and loss suggested that fish rh1 was likely duplicated twice during the early evolutionary history of teleosts, with one event coinciding with the hypothesized fish-specific genome duplication and the other in the common ancestor of the Clupeocephala. After these gene duplication events, duplicated genes were maintained in several teleost lineages, whereas some were secondarily lost in specific lineages. Alternative evolutionary schemes of rh1 and comparison with previous studies of gene evolution are also reviewed.
视紫红质介导了图像捕获的一个基本步骤,与水生生物的视觉适应密切相关,尤其是那些生活在弱光环境中的物种(例如深海)。编码视紫红质的 rh1 基因以前被认为是脊椎动物基因组中的单拷贝基因,但在硬骨鱼类中发现了越来越多的特殊情况。本研究的主要目的是确定视紫红质基因的重复和丢失在多大程度上塑造了硬骨鱼类的视觉适应。为此,我们使用基于 PCR 的方法、公共遗传/基因组数据库的数据挖掘以及随后对检索到的序列进行系统基因组分析,探索了来自广泛分类范围的硬骨鱼类基因组中 rh1/rh1 同源序列。我们表明,大多数鳗鲡目鱼类(鳗鲡目)、弓鳍鱼(骨舌鱼目)和几个鲱形目鱼类谱系的基因组中存在第二个无内含子的鱼类特异性 rh1 拷贝。对可能发生基因重复和丢失的替代事件的系统发育分析和比较表明,鱼类 rh1 可能在硬骨鱼类的早期进化历史中重复了两次,其中一次与假设的鱼类特异性基因组重复事件同时发生,另一次发生在 Clupeocephala 的共同祖先中。在这些基因重复事件之后,重复的基因在几个硬骨鱼类谱系中得以保留,而在某些谱系中则被二次丢失。还对 rh1 的替代进化方案以及与之前基因进化研究进行了比较。