A user's guide to a data base of the diversity of Pseudomonas syringae and its application to classifying strains in this phylogenetic complex.
A user's guide to a data base of the diversity of Pseudomonas syringae and its application to classifying strains in this phylogenetic complex.
复制标题
DOI：
10.1371/journal.pone.0105547
复制
发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Morris CE
中科院分区：
文献类型：
--
作者：
Berge O;Monteil CL;Bartoli C;Chandeysson C;Guilbaud C;Sands DC;Morris CE
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）的菌株的许多遗传谱系组成。在农业环境本身之外的栖息地发现这种细菌物种的新见解，揭示了这种复杂的菌株的广泛多样性，超出了农业环境的已知范围。通过对216株菌的多位点序列分型（MLST），我们在13个群中鉴定出23个进化枝，其中包括7个先前描述的P.代表9个突变群的29个菌株的核心基因组的突变发生与用MLST获得的突变发生相似，从而证实了MLST-突变群的稳健性。我们表明，表型性状很少提供一个令人满意的手段，即使一些组合是非常可能的，在某些群体的菌株分类。我们证明了柠檬酸合酶（cts）管家基因可以准确地预测超过97%的测试菌株的系统发育关系。我们提出了一个cts序列的列表，作为一个简单的工具，用于快速，准确地分类新菌株。最后，我们的分析导致了对尚未发现的P. palingae多样性的预测。我们在这里提出了一个可扩展的框架，主要是基于cts遗传分析，其中更多的多样性可以集成。
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.
登录
查看更多内容
影响因子：
2.8
作者：
Bodilis, J;Barray, S
通讯作者：
Barray, S
影响因子：
6.7
作者：
Baltrus DA;Nishimura MT;Romanchuk A;Chang JH;Mukhtar MS;Cherkis K;Roach J;Grant SR;Jones CD;Dangl JL
通讯作者：
Dangl JL
影响因子：
4.9
作者：
Baltrus, David A.;Dougherty, Kevin;Foster, Jeffrey T.
通讯作者：
Foster, Jeffrey T.
影响因子：
5
作者：
Joly, Muriel;Attard, Eleonore;Delort, Anne-Marie
通讯作者：
Delort, Anne-Marie
影响因子：
1.8
作者：
Marchi, G;Viti, C;Surico, G
通讯作者：
Surico, G