Parkinson Neil, Cowie Claire, Heeney John, Stead David
Central Science Laboratory, Sand Hutton, York YO41 1LZ, UK.
Int J Syst Evol Microbiol. 2009 Feb;59(Pt 2):264-74. doi: 10.1099/ijs.0.65825-0.
Previously, we have produced a phylogeny of species type strains from the plant-pathogenic genus Xanthomonas based on gyrB sequences. To evaluate this locus further for species and infraspecies identification, we sequenced an additional 203 strains comprising all the pathovar reference strains (which have defined plant hosts), 67 poorly characterized pathovars, currently classified as Xanthomonas campestris, and 59 unidentified xanthomonads. The well-characterized pathovars grouped either in clades containing their respective species type strain or in clades containing species related to Xanthomonas axonopodis. The Xanthomonas euvesicatoria, Xanthomonas perforans and Xanthomonas alfalfae species complex, Xanthomonas fuscans and Xanthomonas citri were discriminated as X. axonopodis-related clades and comprised a large proportion of unidentified strains as well as 80 pathovars representing all the X. axonopodis pathovars and many poorly characterized pathovars, greatly increasing the plant host ranges of the constituent species. Most xanthomonads from these three large clades were isolated from a taxonomically diverse range of plant hosts, including many weed species, from field systems in India, suggesting that these lineages became established and diversified in agricultural areas in this region. The majority of these xanthomonads had minimal sequence diversity, consistent with rapid and highly extensive pathovar diversification that has occurred in relatively recent times. Low-intensity farming practices may have provided conditions conducive to pathovar development, and evidence for pathovar diversification within other regional angiosperm floras is discussed. The gyrB locus was sufficiently discriminating to identify diversity within many species. Seven branches or clades were sufficiently distinct to be considered as potential novel species. This study has provided a comprehensive xanthomonad classification framework and has firmly established gyrB sequencing as a rapid and efficient identification tool.
此前，我们基于gyrB序列构建了植物致病黄单胞菌属物种模式菌株的系统发育树。为了进一步评估该基因座在物种和种下分类鉴定中的作用，我们对另外203株菌株进行了测序，这些菌株包括所有致病变种参考菌株（已明确植物寄主）、67个特征描述较少的致病变种（目前归类为野油菜黄单胞菌）以及59株未鉴定的黄单胞菌。特征明确的致病变种要么聚集在包含其各自物种模式菌株的分支中，要么聚集在包含与柑桔黄单胞菌相关物种的分支中。番茄溃疡病菌、穿孔黄单胞菌和苜蓿黄单胞菌复合种、变黑黄单胞菌和柑桔黄单胞菌被区分为与柑桔黄单胞菌相关的分支，其中包含大量未鉴定菌株以及80个致病变种，代表了所有柑桔黄单胞菌致病变种和许多特征描述较少的致病变种，极大地扩大了组成物种的植物寄主范围。来自这三个大分支的大多数黄单胞菌分离自印度田间系统中分类学上多样的植物寄主，包括许多杂草物种，这表明这些谱系在该地区的农业区域中得以建立并多样化。这些黄单胞菌中的大多数序列多样性极小，这与相对近期发生的快速且高度广泛的致病变种多样化一致。低强度农业实践可能提供了有利于致病变种发展的条件，并讨论了其他区域被子植物区系中致病变种多样化的证据。gyrB基因座具有足够的鉴别力来识别许多物种内的多样性。七个分支或进化枝足够独特，可被视为潜在的新物种。本研究提供了一个全面的黄单胞菌分类框架，并牢固确立了gyrB测序作为一种快速有效的鉴定工具。
