US Department of Agriculture, Agricultural Research Service, Horticultural Crops Research Laboratory, Corvallis, OR, USA.
US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA.
Environ Microbiol. 2018 Jun;20(6):2142-2159. doi: 10.1111/1462-2920.14130. Epub 2018 Jul 22.
Pseudomonas is a large and diverse genus of Gammaproteobacteria. To provide a framework for discovery of evolutionary and taxonomic relationships of these bacteria, we compared the genomes of type strains of 163 species and 3 additional subspecies of Pseudomonas, including 118 genomes sequenced herein. A maximum likelihood phylogeny of the 166 type strains based on protein sequences of 100 single-copy orthologous genes revealed thirteen groups of Pseudomonas, composed of two to sixty three species each. Pairwise average nucleotide identities and alignment fractions were calculated for the data set of the 166 type strains and 1224 genomes of Pseudomonas available in public databases. Results revealed that 394 of the 1224 genomes were distinct from any type strain, suggesting that the type strains represent only a fraction of the genomic diversity of the genus. The core genome of Pseudomonas was determined to contain 794 genes conferring primarily housekeeping functions. The results of this study provide a phylogenetic framework for future studies aiming to resolve the classification and phylogenetic relationships, identify new gene functions and phenotypes, and explore the ecological and metabolic potential of the Pseudomonas spp.
假单胞菌是一种广泛存在且多样化的γ变形菌属。为了提供一个发现这些细菌进化和分类关系的框架，我们比较了 163 种假单胞菌的模式菌株和 3 种其他亚种的基因组，包括 118 种在此文中测序的基因组。基于 100 个单拷贝直系同源基因的蛋白质序列对 166 个模式菌株进行最大似然系统发育分析，揭示了假单胞菌的 13 个群，每个群由 2 到 63 个种组成。计算了 166 个模式菌株和公共数据库中 1224 个假单胞菌基因组数据集的成对平均核苷酸同一性和比对分数。结果表明，1224 个基因组中有 394 个与任何模式菌株都不同，这表明模式菌株仅代表该属基因组多样性的一部分。假单胞菌的核心基因组被确定包含 794 个基因，主要赋予其管家功能。这项研究的结果为未来的研究提供了一个分类和系统发育关系的框架，旨在解决分类和系统发育关系、识别新的基因功能和表型、以及探索假单胞菌属的生态和代谢潜力。
