Phylogenomics and Molecular Signatures for Species from the Plant Pathogen-Containing Order Xanthomonadales

The species from the order Xanthomonadales, which harbors many important plant pathogens and some human pathogens, are currently distinguished primarily on the basis of their branching in the 16S rRNA tree. No molecular or biochemical characteristic is known that is specific for these bacteria. Phylogenetic and comparative analyses were conducted on 26 sequenced Xanthomonadales genomes to delineate their branching order and to identify molecular signatures consisting of conserved signature indels (CSIs) in protein sequences that are specific for these bacteria. In a phylogenetic tree based upon sequences for 28 proteins, Xanthomonadales species formed a strongly supported clade with Rhodanobacter sp. 2APBS1 as its deepest branch. Comparative analyses of protein sequences have identified 13 CSIs in widely distributed proteins such as GlnRS, TypA, MscL, LysRS, LipA, Tgt, LpxA, TolQ, ParE, PolA and TyrB that are unique to all species/strains from this order, but not found in any other bacteria. Fifteen additional CSIs in proteins (viz. CoxD, DnaE, PolA, SucA, AsnB, RecA, PyrG, LigA, MutS and TrmD) are uniquely shared by different Xanthomonadales except Rhodanobacter and in a few cases by Pseudoxanthomonas species, providing further support for the deep branching of these two genera. Five other CSIs are commonly shared by Xanthomonadales and 1–3 species from the orders Chromatiales, Methylococcales and Cardiobacteriales suggesting that these deep branching orders of Gammaproteobacteria might be specifically related. Lastly, 7 CSIs in ValRS, CarB, PyrE, GlyS, RnhB, MinD and X001065 are commonly shared by Xanthomonadales and a limited number of Beta- or Gamma-proteobacteria. Our analysis indicates that these CSIs have likely originated independently and they are not due to lateral gene transfers. The Xanthomonadales-specific CSIs reported here provide novel molecular markers for the identification of these important plant and human pathogens and also as potential targets for development of drugs/agents that specifically target these bacteria.目前，黄单胞菌目（Xanthomonadales）包含诸多重要植物病原菌与部分人类病原菌，该目物种的分类界定主要依据其在16S rRNA系统发育树中的分支结构，暂未发现针对这类细菌的特异性分子或生化特征。本研究对26株已完成全基因组测序的黄单胞菌目菌株进行了系统发育与比较基因组分析，旨在明确其分支演化关系，并鉴定这类细菌特有的蛋白质序列保守特征插入缺失（CSIs, conserved signature indels）作为分子标记。基于28种蛋白质序列构建的系统发育树显示，黄单胞菌目物种形成了一个高支持度的演化支，其中红杆菌属（Rhodanobacter）菌株2APBS1为该演化支的最深分支节点。蛋白质序列比较分析共鉴定出13处保守特征插入缺失，它们分布于GlnRS、TypA、MscL、LysRS、LipA、Tgt、LpxA、TolQ、ParE、PolA及TyrB等广泛存在的蛋白质中，仅为该目所有物种/菌株所特有，未在其他细菌中发现。另有15处保守特征插入缺失分布于CoxD、DnaE、PolA、SucA、AsnB、RecA、PyrG、LigA、MutS及TrmD等蛋白质中，仅为不同黄单胞菌目物种所共有，但红杆菌属与假单胞菌属（Pseudoxanthomonas）的部分菌株除外，这一结果进一步支持了这两个属的深层分支演化地位。另有5处保守特征插入缺失为黄单胞菌目与着色菌目（Chromatiales）、甲基球菌目（Methylococcales）及心杆菌目（Cardiobacteriales）的1~3个物种所共有，提示γ-变形菌纲（Gammaproteobacteria）的这些深层分支类群可能存在特异性演化关联。最后，在ValRS、CarB、PyrE、GlyS、RnhB、MinD及X001065等蛋白质中发现的7处保守特征插入缺失，仅为黄单胞菌目与少量β-变形菌纲或γ-变形菌纲物种所共有。本研究分析表明，这些保守特征插入缺失大概率独立起源，并非由侧向基因转移导致。本研究鉴定的黄单胞菌目特异性保守特征插入缺失，为这类重要植物及人类病原菌的鉴定提供了新型分子标记，同时也可为开发特异性靶向这类细菌的药物或制剂提供潜在靶点。