A genome phylogeny for mitochondria among α-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes
A genome phylogeny for mitochondria among α-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes
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DOI：
10.1093/molbev/msh160
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发表时间：
2004-09-01
影响因子：
10.7
通讯作者：
Martin, W
中科院分区：
文献类型：
--
作者：
Esser, C;Ahmadinejad, N;Martin, W
55个单独的和31个串联的蛋白质数据集编码的美洲Reclinomonasamericana和地钱线粒体基因组的分析表明，目前的方法构建系统发育树是不够敏感（或人为因素不敏感），以确定目前的样品中的8个α-变形菌基因组使用的蛋白质编码的线粒体的姐妹。然而，Rhododocellum rubrum与研究的任何α-变形杆菌一样接近线粒体。这促使人们寻找直接比较真核生物基因组与原核生物基因组的方法，以从核基因的角度研究寄生虫及其宿主的起源。我们检查了成对的氨基酸序列的同一性比较6,214核蛋白编码基因的酿酒酵母的177,117蛋白质编码的测序基因组中的45个真细菌和15个古细菌。结果表明，在目前的原核样品中，有相似于75%的酵母基因具有同源性，与真细菌的同源性比与古细菌的同源性更大。在高严格性比较中，仅酵母基因组的真细菌组分是可检测的。我们的研究结果表明，在整体氨基酸序列的同一性和基因含量的水平，酵母股的姐妹组关系与真细菌，而不是与古细菌，在目前的系统发育的基础上核糖体RNA的范例。在真细菌和古细菌中，变形菌和产甲烷菌基因组分别与酵母基因组比其他原核生物基因组具有更多的相似性。
Analyses of 55 individual and 31 concatenated protein data sets encoded in Reclinomonas americana and Marchantia polymorpha mitochondrial genomes revealed that current methods for constructing phylogenetic trees are insufficiently sensitive (or artifact-insensitive) to ascertain the sister of mitochondria among the current sample of eight alpha-proteobacterial genomes using mitochondrially-encoded proteins. However, Rhodospirillum rubrum came as close to mitochondria as any alpha-proteobacterium investigated. This prompted a search for methods to directly compare eukaryotic genomes to their prokaryotic counterparts to investigate the origin of the mitochondrion and its host from the standpoint of nuclear genes. We examined pairwise amino acid sequence identity in comparisons of 6,214 nuclear protein-coding genes from Saccharomyces cerevisiae to 177,117 proteins encoded in sequenced genomes from 45 eubacteria and 15 archaebacteria. The results reveal that similar to75% of yeast genes having homologues among the present prokaryotic sample share greater amino acid sequence identity to eubacterial than to archaebacterial homologues. At high stringency comparisons, only the eubacterial component of the yeast genome is detectable. Our findings indicate that at the levels of overall amino acid sequence identity and gene content, yeast shares a sister-group relationship with eubacteria, not with archaebacteria, in contrast to the current phylogenetic paradigm based on ribosomal RNA. Among eubacteria and archaebacteria, proteobacterial and methanogen genomes, respectively, shared more similarity with the yeast genome than other prokaryotic genomes surveyed.