Berge Odile, Monteil Caroline L, Bartoli Claudia, Chandeysson Charlotte, Guilbaud Caroline, Sands David C, Morris Cindy E
INRA, UR0407 Pathologie Végétale, Montfavet, France.
INRA, UR0407 Pathologie Végétale, Montfavet, France; Department of Science and Technology for Agriculture, Forestry, Nature and Energy (DAFNE), Tuscia University, Viterbo, Italy.
PLoS One. 2014 Sep 3;9(9):e105547. doi: 10.1371/journal.pone.0105547. eCollection 2014.
The Pseudomonas syringae complex is composed of numerous genetic lineages of strains from both agricultural and environmental habitats including habitats closely linked to the water cycle. The new insights from the discovery of this bacterial species in habitats outside of agricultural contexts per se have led to the revelation of a wide diversity of strains in this complex beyond what was known from agricultural contexts. Here, through Multi Locus Sequence Typing (MLST) of 216 strains, we identified 23 clades within 13 phylogroups among which the seven previously described P. syringae phylogroups were included. The phylogeny of the core genome of 29 strains representing nine phylogroups was similar to the phylogeny obtained with MLST thereby confirming the robustness of MLST-phylogroups. We show that phenotypic traits rarely provide a satisfactory means for classification of strains even if some combinations are highly probable in some phylogroups. We demonstrate that the citrate synthase (cts) housekeeping gene can accurately predict the phylogenetic affiliation for more than 97% of strains tested. We propose a list of cts sequences to be used as a simple tool for quickly and precisely classifying new strains. Finally, our analysis leads to predictions about the diversity of P. syringae that is yet to be discovered. We present here an expandable framework mainly based on cts genetic analysis into which more diversity can be integrated.
丁香假单胞菌复合体由来自农业和环境栖息地（包括与水循环密切相关的栖息地）的众多菌株遗传谱系组成。在农业环境本身之外的栖息地中发现这种细菌物种所带来的新见解，揭示了该复合体中菌株的广泛多样性，超出了农业环境中已知的范围。在这里，通过对216株菌株进行多位点序列分型（MLST），我们在13个系统发育组中鉴定出23个进化枝，其中包括先前描述的7个丁香假单胞菌系统发育组。代表9个系统发育组的29株菌株的核心基因组系统发育与通过MLST获得的系统发育相似，从而证实了MLST系统发育组的稳健性。我们表明，即使某些组合在某些系统发育组中极有可能出现，表型特征也很少能为菌株分类提供令人满意的方法。我们证明，柠檬酸合酶（cts）管家基因可以准确预测超过97%测试菌株的系统发育归属。我们提出了一份cts序列清单，用作快速准确分类新菌株的简单工具。最后，我们的分析对尚未发现的丁香假单胞菌多样性进行了预测。我们在此提出一个主要基于cts基因分析的可扩展框架，可将更多的多样性整合其中。
