Parras-Moltó Marcos, Aguirre de Cárcer Daniel
Departamento de Biología, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
Sci Rep. 2021 Apr 15;11(1):8299. doi: 10.1038/s41598-021-87909-1.
In this report we use available curated phylogenies, taxonomy, and genome annotations to assess the phylogenetic and gene content similarity associated with each different taxon and taxonomic rank. Subsequently, we employ the same data to assess the frontiers of functional coherence along the bacterial phylogeny. Our results show that within-group phylogenetic and gene content similarity of taxa in the same rank are not homogenous, and that these values show extensive overlap between ranks. Functional coherence along the 16S rRNA gene-based phylogeny was limited to 44 particular nodes presenting large variations in phylogenetic depth. For instance, the deep subtree affiliated to class Actinobacteria presented functional coherence, while the shallower family Enterobacteriaceae-affiliated subtree did not. On the other hand, functional coherence along the genome-based phylogeny delimited deep subtrees affiliated to phyla Actinobacteriota, Deinococcota, Chloroflexota, Firmicutes, and a subtree containing the rest of the bacterial phyla. The results presented here can be used to guide the exploration of results in many microbial ecology and evolution research scenarios. Moreover, we provide dedicated scripts and files that can be used to continue the exploration of functional coherence along the bacterial phylogeny employing different parameters or input data ( https://git.io/Jec5U ).
在本报告中，我们使用现有的经过整理的系统发育树、分类法和基因组注释，来评估与每个不同分类单元和分类等级相关的系统发育和基因内容相似性。随后，我们利用相同的数据来评估沿细菌系统发育的功能连贯性前沿。我们的结果表明，同一等级分类单元的组内系统发育和基因内容相似性并非均匀一致，并且这些值在不同等级之间存在广泛重叠。沿基于16S rRNA基因的系统发育的功能连贯性仅限于44个在系统发育深度上呈现出较大差异的特定节点。例如，隶属于放线菌纲的深层子树呈现出功能连贯性，而隶属于肠杆菌科的较浅子树则没有。另一方面，沿基于基因组的系统发育的功能连贯性划定了隶属于放线菌门、异常球菌门、绿弯菌门、厚壁菌门的深层子树，以及包含其余细菌门的一个子树。此处呈现的结果可用于指导许多微生物生态学和进化研究场景中的结果探索。此外，我们提供了专用脚本和文件，可用于使用不同参数或输入数据继续探索沿细菌系统发育的功能连贯性（https://git.io/Jec5U）。
