Wei Wei, Davis Robert E, Lee Ing-Ming, Zhao Yan
Molecular Plant Pathology Laboratory, USDA-Agricultural Research Service, Beltsville, MD 20705, USA.
Int J Syst Evol Microbiol. 2007 Aug;57(Pt 8):1855-1867. doi: 10.1099/ijs.0.65000-0.
Phytoplasmas are cell wall-less bacteria that cause numerous plant diseases. As no phytoplasma has been cultured in cell-free medium, phytoplasmas cannot be differentiated and classified by the traditional methods which are applied to culturable prokaryotes. Over the past decade, the establishment of a phytoplasma classification scheme based on 16S rRNA restriction fragment length polymorphism (RFLP) patterns has enabled the accurate and reliable identification and classification of a wide range of phytoplasmas. In the present study, we expanded this classification scheme through the use of computer-simulated RFLP analysis, achieving rapid differentiation and classification of phytoplasmas. Over 800 publicly available phytoplasma 16S rRNA gene sequences were aligned using the CLUSTAL_X program and the aligned 1.25 kb fragments were exported to pDRAW32 software for in silico restriction digestion and virtual gel plotting. Based on distinctive virtual RFLP patterns and calculated similarity coefficients, phytoplasma strains were classified into 28 groups. The results included the classification of hundreds of previously unclassified phytoplasmas and the delineation of 10 new phytoplasma groups representing three recently described and seven novel putative 'Candidatus Phytoplasma' taxa.
植原体是一类无细胞壁的细菌，可引发多种植物病害。由于尚未在无细胞培养基中培养出任何植原体，因此无法用适用于可培养原核生物的传统方法对植原体进行区分和分类。在过去十年中，基于16S rRNA限制性片段长度多态性（RFLP）模式建立的植原体分类方案，使得广泛的植原体能够得到准确可靠的鉴定和分类。在本研究中，我们通过使用计算机模拟RFLP分析扩展了该分类方案，实现了植原体的快速区分和分类。使用CLUSTAL_X程序对800多个公开可用的植原体16S rRNA基因序列进行比对，并将比对后的1.25 kb片段导出到pDRAW32软件中进行电子限制性消化和虚拟凝胶电泳图绘制。基于独特的虚拟RFLP模式和计算出的相似系数，将植原体菌株分为28组。结果包括对数百种先前未分类的植原体进行分类，以及划分出10个新的植原体组，它们代表了最近描述的3个和7个新的假定“候选植原体”分类单元。
