Directed indels, insertions or deletions within paralogous genes, have the potential to root the tree of life. Here we apply the top-down rooting algorithm to indels found in PyrD (dihydroorotate dehydrogenase), a key enzyme involved in the de novo biosynthesis of pyrimidines, and HisA (P-ribosylformimino-AICAR-P-isomerase), an essential enzyme in the histidine biosynthesis pathway. Through the comparison of each indel with its two paralogous outgroups, we exclude the root of the tree of life from the clade that encompasses the Actinobacteria, the double-membrane prokaryotes, and their last common ancestor. In combination with previous indel rooting studies excluding the root from a clade consisting of the Firmicutes, the Archaea, and their last common ancestor, this provides evidence for a unique eubacterial root for the tree of life located between the actinobacterial-double-membrane clade and the archaeal-firmicute clade. Mapping the phylogenetic distributions of genes involved in peptidoglycan and lipid synthesis onto this rooted tree parsimoniously implies that the cenancestral prokaryotic population consisted of organisms enclosed by a single, ester-linked lipid membrane, covered by a peptidoglycan layer.

中文翻译：

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生命之树新根的证据

旁系同源基因中的定向插入缺失、插入或缺失有可能成为生命之树的根源。在这里，我们将自上而下的生根算法应用于 PyrD（二氢乳清酸脱氢酶）中的插入缺失，这是一种参与嘧啶从头生物合成的关键酶，以及 HisA（P-核糖基甲亚氨基-AICAR-P-异构酶），一种必需的酶组氨酸生物合成途径。通过将每个 indel 与其两个旁系同源外群进行比较，我们从包含放线菌、双膜原核生物及其最后一个共同祖先的进化枝中排除了生命之树的根。结合先前的 indel 生根研究，将根从由厚壁菌门、古细菌和它们最后一个共同祖先组成的进化枝中排除，这为位于放线菌-双膜进化枝和古菌-厚壁菌进化枝之间的生命之树的独特真细菌根提供了证据。将参与肽聚糖和脂质合成的基因的系统发育分布映射到这棵有根的树上，这意味着先祖原核种群由被单个酯连接的脂质膜包围的生物组成，并被肽聚糖层覆盖。