Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México.
Genome Biol Evol. 2019 Sep 1;11(9):2531-2541. doi: 10.1093/gbe/evz178.
The Gram-negative Acinetobacter genus has several species of clear medical relevance. Many fully sequenced genomes belonging to the genus have been published in recent years; however, there has not been a recent attempt to infer the evolutionary history of Acinetobacter with that vast amount of information. Here, through a phylogenomic approach, we established the most up-to-date view of the evolutionary relationships within this genus and highlighted several cases of poor classification, especially for the very closely related species within the Acinetobacter calcoaceticus-Acinetobacter baumannii complex (Acb complex). Furthermore, we determined appropriate phylogenetic markers for this genus and showed that concatenation of the top 13 gives a very decent reflection of the evolutionary relationships for the genus Acinetobacter. The intersection between our top markers and previously defined universal markers is very small. In general, our study shows that, although there seems to be hardly any universal markers, bespoke phylogenomic approaches can be used to infer the phylogeny of different bacterial genera. We expect that ad hoc phylogenomic approaches will be the standard in the years to come and will provide enough information to resolve intricate evolutionary relationships like those observed in the Acb complex.
革兰氏阴性不动杆菌属有几个具有明显医学相关性的种。近年来，已经有许多完全测序的该属基因组被发表；然而，尚未有最近的尝试利用这些大量的信息推断不动杆菌属的进化历史。在这里，我们通过系统发生基因组学方法，建立了该属内进化关系的最新视图，并突出了几个分类不当的情况，特别是在密切相关的 Acinetobacter calcoaceticus-Acinetobacter baumannii 复合体（Acb 复合体）内的种。此外，我们确定了该属的适当系统发生标记，并表明前 13 个标记的串联很好地反映了不动杆菌属的进化关系。我们的顶级标记与之前定义的通用标记的交点很小。总的来说，我们的研究表明，尽管似乎几乎没有通用标记，但定制的系统发生基因组学方法可用于推断不同细菌属的系统发育。我们预计，在未来几年内，特定的系统发生基因组学方法将成为标准，并将提供足够的信息来解决像 Acb 复合体中观察到的复杂进化关系。
