A unifying feature of the bacterial Candidate Phyla Radiation (CPR) is a limited and highly variable repertoire of biosynthetic capabilities. However, the distribution of metabolic traits across the CPR and the evolutionary processes underlying them are incompletely resolved. Here, we selected ~ 1000 genomes of CPR bacteria from diverse environments to construct a robust internal phylogeny that was consistent across two unlinked marker sets. Mapping of glycolysis, the pentose phosphate pathway, and pyruvate metabolism onto the tree showed that some components of these pathways are sparsely distributed and that similarity between metabolic platforms is only partially predicted by phylogenetic relationships. To evaluate the extent to which gene loss and lateral gene transfer have shaped trait distribution, we analyzed the patchiness of gene presence in a phylogenetic context, examined the phylogenetic depth of clades with shared traits, and compared the reference tree topology with those of specific metabolic proteins. While the central glycolytic pathway in CPR is widely conserved and has likely been shaped primarily by vertical transmission, there is evidence for both gene loss and transfer especially in steps that convert glucose into fructose 1,6-bisphosphate and glycerate 3P into pyruvate. Additionally, the distribution of Group 3 and Group 4-related NiFe hydrogenases is patchy and suggests multiple events of ancient gene transfer. We infer that patterns of gene gain and loss in CPR, including acquisition of accessory traits in independent transfer events, could have been driven by shifts in host-derived resources and led to sparse but varied genetic inventories.

中文翻译：

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整个候选Phyla辐射中新陈代谢平台的多样性上升。

细菌菌斑辐射（CPR）的一个统一特征是生物合成功能有限且变化很大。但是，整个CPR的代谢特征分布及其背后的进化过程尚未完全解决。在这里，我们从不同的环境中选择了约1000个CPR细菌基因组，以构建一个稳健的内部系统发育，该系统发育在两个未链接的标记集之间保持一致。将糖酵解，磷酸戊糖途径和丙酮酸代谢映射到树上表明，这些途径的某些成分稀疏分布，并且代谢平台之间的相似性仅通过系统发育关系部分预测。为了评估基因丧失和基因横向转移对性状分布的影响程度，我们分析了系统发育中基因存在的不连续性，检查了具有共同特征的进化枝的系统发育深度，并将参考树的拓扑结构与特定代谢蛋白质的拓扑结构进行了比较。虽然CPR中的中央糖酵解途径被广泛保存，并且可能主要由垂直传播形成，但有证据表明基因丢失和转移都存在，尤其是在将葡萄糖转化为果糖1,6-双磷酸酯和将甘油3P转化为丙酮酸的步骤中。此外，第3组和第4组相关的NiFe氢化酶的分布是零散的，并暗示了古代基因转移的多个事件。我们推断出CPR中的基因增减模式，包括在独立转移事件中获得辅助性状，