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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phytogeny and thousands of cyanobacterial genes in the nucleus
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Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phytogeny and thousands of cyanobacterial genes in the nucleus

机译：拟南芥，蓝细菌和叶绿体基因组的进化分析揭示了质体植物遗传学和核中成千上万的蓝细菌基因

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摘要

Chloroplasts were once free-living cyanobacteria that became endosymbionts, but the genomes of contemporary plastids encode only ≈5-10% as many genes as those of their free-living cousins, indicating that many genes were either lost from plastids or transferred to the nucleus during the course of plant evolution. Previous estimates have suggested that between 800 and perhaps as many as 2,000 genes in the Arabidopsis genome might come from cyanobacteria, but genome-wide phylogenetic surveys that could provide direct estimates of this number are lacking. We compared 24,990 proteins encoded in the Arabidopsis genome to the proteins from three cyanobacterial genomes, 16 other prokaryotic reference genomes, and yeast. Of 9,368 Arabidopsis proteins sufficiently conserved for primary sequence comparison, 866 detected homologues only among cyanobacteria and 834 other branched with cyanobacterial homologues in phylogenetic trees. Extrapolating from these conserved proteins to the whole genome, the data suggest that≈4,500 of Arabidopsis protein-coding genes (≈18% of the total) were acquired from the cyanobacterial ancestor of plastids. These proteins encompass all functional classes, and the majority of them are targeted to cell compartments other than the chloroplast. Analysis of 15 sequenced chloroplast genomes revealed 117 nuclear-encoded proteins that are also still present in at least one chloroplast genome. A phylogeny of chloroplast genomes inferred from 41 proteins and 8,303 amino acids sites indicates that at least two independent secondary endosymbi-otic events have occurred involving red algae and that amino acid composition bias in chloroplast proteins strongly affects plastid genome phylogeny.
机译：叶绿体曾经是自由生存的蓝细菌，后来变成了共生菌，但现代质体的基因组编码的基因数量仅为其自由生表亲的约5-10％，这表明许多基因要么从质体中丢失，要么转移到细胞核中。在植物进化过程中。先前的估计表明，拟南芥基因组中可能有800至2,000个基因来自蓝细菌，但是尚缺乏可以直接估计该数目的全基因组系统发育调查。我们将拟南芥基因组中编码的24,990种蛋白质与三个蓝藻基因组，其他16个原核参考基因组和酵母中的蛋白质进行了比较。在9,368个足够保守的用于一级序列比较的拟南芥蛋白中，只有866个检测到的同源物在蓝细菌中，而834个其他的与蓝细菌同源物在系统发生树中分支。从这些保守蛋白推算到整个基因组，数据表明≈4,500个拟南芥蛋白编码基因（占总数的≈18％）是从质体的蓝细菌祖先获得的。这些蛋白质涵盖所有功能类别，并且大多数针对叶绿体以外的细胞区室。对15个测序的叶绿体基因组的分析显示了117种核编码蛋白，它们仍至少存在于一个叶绿体基因组中。从41个蛋白和8,303个氨基酸位点推断出的叶绿体基因组系统发育表明，至少发生了两个独立的次生内共生事件，涉及红藻，并且叶绿体蛋白中的氨基酸组成偏倚强烈影响质体基因组系统发育。

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