The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, China.
The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China.
Comp Biochem Physiol Part D Genomics Proteomics. 2018 Dec;28:27-36. doi: 10.1016/j.cbd.2018.06.002. Epub 2018 Jun 18.
Recent studies have shown that mitochondria play a crucial role in cellular energy production through the oxidative phosphorylation (OXPHOS) system. Complex I (NADH:ubiquinone oxidoreductase), the first and largest enzyme complex of the OXPHOS system, includes both nuclear- and mitochondrial-encoded proteins. However, the patterns of natural selection and phylogenetic implications of complex I in birds still remain unclear. In this study, we combined transcriptomic and phylogenetic analyses to comprehensively determine the evolution of avian complex I. The transcriptomes of three Passerida species (Leiothrix lutea, Spodiopsar sericeus, and Passer montanus) were obtained using the Illumina HiSeq™ 2500 system. More than 192,000,000 clean reads were assembled in a total of 828,267 transcripts. Evolutionary selection analysis suggested that six genes of the core subunits in avian complex I may have undergone putative positive selection. Notably, we found that the mean dN/dS (ω) ratio for mitochondrial genes of core subunits was significantly lower than that for nuclear genes of non-core subunits within complex I. The constructed maximum-parsimony, maximum-likelihood, and Bayesian inference phylogenetic trees were based on 44 complex I genes. We verified that the family Paridae (represented by Parus major and Pseudopodoces humilis) was clustered with Musicicapoidea. Our results provide new insights into the evolution of avian mitochondrial complex I.
最近的研究表明，线粒体通过氧化磷酸化（OXPHOS）系统在细胞能量产生中起着至关重要的作用。复合物 I（NADH：泛醌氧化还原酶）是 OXPHOS 系统的第一个也是最大的酶复合物，包含核编码和线粒体编码的蛋白质。然而，鸟类复合物 I 的自然选择模式和系统发育意义仍然不清楚。在这项研究中，我们结合转录组学和系统发育分析，全面确定了鸟类复合物 I 的进化。使用 Illumina HiSeq™ 2500 系统获得了三种雀形目物种（黄腰柳莺、白腰文鸟和麻雀）的转录组。总共组装了超过 192000000 条清洁读数，总计 828267 个转录本。进化选择分析表明，鸟类复合物 I 的核心亚基中的六个基因可能经历了假定的正选择。值得注意的是，我们发现核心亚基线粒体基因的平均 dN/dS（ω）比值明显低于复合物 I 中非核心亚基的核基因。构建的最大简约法、最大似然法和贝叶斯推断系统发育树是基于 44 个复合物 I 基因。我们验证了山雀科（以大山雀和燕雀属代表）与鹟科一起聚类。我们的结果为鸟类线粒体复合物 I 的进化提供了新的见解。
