The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.

中文翻译：

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对 1,000 多个菌株基因组的分析显着改进了 Alphaproteobacteria 的分类学分类。

α变形菌纲由多种革兰氏阴性菌组成，其中包括具有不同形态、生理学和栖息地偏好的生物体，其中许多具有临床和生态重要性。α-变形菌分类已被证明是困难的，尤其是当分类学决策很大程度上依赖于有限数量的表型特征和解析不佳的 16S rRNA 基因树的解释时。尽管近年来在细菌分类方面取得了进展，但仍然需要进一步澄清分类学关系。在这里，使用系统发育系统学得出的原理，使用 1000 多种 Alphaproteobacteria 和外群类型菌株的基因组集合的基因组草图序列，从基因组规模的数据推断系统发育树。大多数分类单元被发现是单系的，但有几个目、科和属，包括很久以前就被认为有问题的分类单元，但也包括最近的分类单元，以及一些物种被证明需要修订。据此，提出了承认新目、科和属，以及将多种物种转移到其他属以及将多种属转移到其他科的建议。此外，对许多物种进行了修正描述，主要涉及DNA G+C含量和（近似）基因组大小信息，这两者都被确认为有价值的分类标记。同样，基因内容的分析被证明可以在课堂上提供有价值的分类学见解。班级中未发现16S rRNA基因与全基因组树之间存在显着不一致。将本研究的结果与现有分类进行比较时，明显的不一致似乎主要是由于 16S rRNA 基因树解析不充分或分类单元采样不完整造成的。过去错误分类的另一个可能原因是表型特征与基于序列的树的整体拟合度较低。尽管在所有研究的性状中都检测到了显着程度的系统发育保守性，但与树的整体拟合度差异很大。