Table_1_Genome-Based Taxonomic Classification of the Phylum Actinobacteria.XLSX

The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.

系统发育分类学方法的应用推动了放线菌门（Actinobacteria）所属细菌的分类学修订，但即便如此，对于涵盖农业、生物技术、临床及生态领域重要物种的该类群，其内部类群间的演化关系仍有待进一步阐明。基于有限数量的分类特征对该大型门类中形态多样的细菌开展分类工作已被证实颇具难度，尤其是当分类学决策高度依赖分辨率欠佳的16S rRNA基因树的解读结果时。本研究利用大量放线菌模式菌株的草图基因组序列，基于系统发育系统学原理，从全基因组尺度的数据中推断得到系统发育树。研究发现，绝大多数类群均为单系（monophyletic）类群，但多个目、科、属，以及诸多物种和少量亚种均需要进行分类学修订。据此，本研究提出如下修订建议：新增2个目、10个科及17个属，并将超过100个物种转移至其他属中。此外，本研究还对诸多物种进行了修订描述，主要补充了基因组大小与DNA G+C含量（DNA G+C content）相关数据；其中基因组大小可被视为放线菌分类系统学中一项极具价值的分类标记。将本研究结果与现有分类系统进行比对时发现的诸多不一致之处，此前多可通过16S rRNA基因系统发育树得以发现，但全基因组系统发育树的分辨率显然更高。16S/23S rRNA系统发育树与全基因组系统发育树之间仅存的几处显著不一致，也凸显了基于单基因序列构建系统发育树所固有的缺陷。同样，表型性状的不连续分布与系统发育树中界定的类群之间也呈现出良好的一致性；不过诸多非单系（non-monophyletic）类群似乎是因将祖征性状状态（plesiomorphic character states）作为诊断特征而被错误界定的。