Department of Computer Science, University of Sherbrooke, Quebec, Canada.
Programa Interunidades de Pós-graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
Genome Biol Evol. 2020 Apr 1;12(4):381-395. doi: 10.1093/gbe/evaa058.
Horizontal gene transfer is a common mechanism in Bacteria that has contributed to the genomic content of existing organisms. Traditional methods for estimating bacterial phylogeny, however, assume only vertical inheritance in the evolution of homologous genes, which may result in errors in the estimated phylogenies. We present a new method for estimating bacterial phylogeny that accounts for the presence of genes acquired by horizontal gene transfer between genomes. The method identifies and corrects putative transferred genes in gene families, before applying a gene tree-based summary method to estimate bacterial species trees. The method was applied to estimate the phylogeny of the order Corynebacteriales, which is the largest clade in the phylum Actinobacteria. We report a collection of 14 phylogenetic trees on 360 Corynebacteriales genomes. All estimated trees display each genus as a monophyletic clade. The trees also display several relationships proposed by past studies, as well as new relevant relationships between and within the main genera of Corynebacteriales: Corynebacterium, Mycobacterium, Nocardia, Rhodococcus, and Gordonia. An implementation of the method in Python is available on GitHub at https://github.com/UdeS-CoBIUS/EXECT (last accessed April 2, 2020).
水平基因转移是细菌中一种常见的机制，它促成了现有生物的基因组内容。然而，传统的估计细菌系统发育的方法假设同源基因在进化过程中只有垂直遗传，这可能导致估计的系统发育树出现错误。我们提出了一种新的方法来估计细菌系统发育，该方法考虑了基因组之间水平基因转移获得的基因的存在。该方法首先在应用基于基因树的汇总方法估计细菌种系树之前，识别和纠正基因家族中可能转移的基因。该方法被应用于估计放线菌门中最大的目棒状杆菌目（Corynebacteriales）的系统发育。我们报告了 360 个棒状杆菌目基因组的 14 个系统发育树。所有估计的树都显示每个属为单系分支。这些树还显示了过去研究提出的一些关系，以及棒状杆菌目主要属之间和内部的新的相关关系：棒状杆菌属（Corynebacterium）、分枝杆菌属（Mycobacterium）、诺卡氏菌属（Nocardia）、红球菌属（Rhodococcus）和戈登氏菌属（ Gordonia）。该方法的 Python 实现可在 GitHub 上获得，网址为 https://github.com/UdeS-CoBIUS/EXECT（最后访问日期：2020 年 4 月 2 日）。
