Rapid phylogenetic identification of members of the Pseudomonas syringae species complex using the rpoD locus
Rapid phylogenetic identification of members of the Pseudomonas syringae species complex using the rpoD locus
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DOI：
10.1111/j.1365-3059.2010.02366.x
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发表时间：
2011-04-01
期刊：
影响因子：
2.7
通讯作者：
Elphinstone, J.
中科院分区：
文献类型：
--
作者：
Parkinson, N.;Bryant, R.;Elphinstone, J.
基于四个位点的系统发育证实了所有9个有效公布的种型菌株内的假单胞菌种复合体的相关性。为了进一步建立复合物内的系统发育结构，使用578个核苷酸的rpoD基因座对所有67个致病变种型菌株（具有限定的宿主范围）进行测序。由于该位点涵盖了以前的7个位点研究中使用的位点，因此有可能将这些菌株与现有的基因组、基因种和二项式分类联系起来。所有种型菌株的区别在于所有四个位点的相对较长的分支长度，除了P. savastanoi，P. ficerectae，P. meliae，P. amygdali和P. tremae，它们被归属于第3组。将P. tremae与这些基因组种-2种分组是令人惊讶的，因为该种先前被指定为基因组种5的唯一代表。燕麦疫霉P. gravingae pv. coronafaciens的区别还在于所有四个基因座的相对长的分支长度。rpoD进化将所有致病变种类型菌株分为与先前定义的致病变种组相对应的主要进化枝，除了两个基因型种-7菌株和P. caricapapayae，其被鉴定为新的致病变种组（6）。除2个基因种8株（P. avellanae和P. eriningae pv.）茶）与P. lingae pvsmorsprunorum和Actiniocarcinoma沿着被发现为一个独特的进化枝。rpoD基因座将提供一个共同的参考框架，以改善这些重要病原体的监测和监视。
Phylogenies based on four loci confirmed the relatedness of all nine validly published species type strains within the Pseudomonas syringae species complex. To further establish the phylogenetic structure within the complex, all 67 pathovar type strains (with defined host ranges) were sequenced using a 578-nucleotide rpoD locus. Since this locus encompassed that used in a previous seven-locus study, it was possible to relate these strains to the existing phylogroup, genomospecies and binomial classifications. All species type strains were distinguished by relatively long branch lengths with all four loci, except for P. savastanoi, P. ficuserectae, P. meliae, P. amygdali and P. tremae, which were attributed to phylogroup 3. The grouping of P. tremae with these genomospecies-2 species was surprising since this species was previously designated as the sole representative of genomospecies 5. The oat pathogen P. syringae pv. coronafaciens was also distinguished by relatively long branch lengths with all four loci. The rpoD phylogeny grouped all the pathovar type strains into major clades that corresponded to previously defined phylogroups, except for two genomospecies-7 strains and P. caricapapayae, which were identified as a new phylogroup (6). There was good correlation between phylogroup and genomospecies classifications, except that two genomospecies-8 strains (P. avellanae and P. syringae pv. theae) were found as a distinct clade within phylogroup 1 along with P. syringae pvs morsprunorum and actinidiae. The rpoD locus will provide a common reference framework to improve monitoring and surveillance of these important pathogens.