Phytoplasma phylogenetics based on analysis of secA and 23S rRNA gene sequences for improved resolution of candidate species of 'Candidatus Phytoplasma'
Phytoplasma phylogenetics based on analysis of secA and 23S rRNA gene sequences for improved resolution of candidate species of 'Candidatus Phytoplasma'
复制标题
DOI：
10.1099/ijs.0.65668-0
复制
发表时间：
2008-08-01
影响因子：
2.8
通讯作者：
Dickinson, Matthew
中科院分区：
文献类型：
--
作者：
Hodgetts, Jennifer;Boonham, Neil;Dickinson, Matthew
植原体遗传学主要集中在非编码16 S rRNA基因和16 S-23 S rRNA基因间间隔区（16- 23 S ISR）的序列上，并且已经很好地建立了能够通过PCR从所有植原体扩增这些区域的引物。在这项研究中，引物的secA基因的基础上已经发展成一个半巢式PCR检测，结果在预期的大小（约480 bp）的序列，从所有34植原体检查，包括代表12个16 Sr组的菌株。与通过16- 23 S ISR-23 S rRNA基因重叠群或单独16 S rRNA基因的类似序列分析解析的簇相比，secA基因序列的系统发育分析显示植原体的相似簇。树之间的主要差异在于分支长度，与16 S rRNA基因树相比，16- 23 S ISR-23 S rRNA基因树中的分支长度延长，而secA基因树中的分支长度更长，尽管secA基因树的序列更短。在secA基因衍生的系统发育树的分辨率提高导致16 SrII组分裂成两个不同的集群，而植原体与椰子致命黄化型疾病分裂成三个不同的群体，从而支持过去的建议，他们代表不同的候选物种内的“Escheridatus植原体”。通过对secA基因序列的虚拟RFLP分析来区分16 Sr组和亚组的能力表明，该基因可以为植原体疾病的病原体鉴定和诊断提供信息的替代分子标记。
Phytoplasma phylogenetics has focused primarily on sequences of the non-coding 16S rRNA gene and the 16S-23S rRNA intergenic spacer region (16-23S ISR), and primers that enable amplification of these regions from all phytoplasmas by PCR are well established. In this study, primers based on the secA gene have been developed into a semi-nested PCR assay that results in a sequence of the expected size (about 480 bp) from all 34 phytoplasmas examined, including strains representative of 12 16Sr groups. Phylogenetic analysis of secA gene sequences showed similar clustering of phytoplasmas when compared with clusters resolved by similar sequence analyses of a 16-23S ISR-23S rRNA gene contig or of the 16S rRNA gene alone. The main differences between trees were in the branch lengths, which were elongated in the 16-23S ISR-23S rRNA gene tree when compared with the 16S rRNA gene tree and elongated still further in the secA gene tree, despite this being a shorter sequence. The improved resolution in the secA gene-derived phylogenetic tree resulted in the 16SrII group splitting into two distinct clusters, while phytoplasmas associated with coconut lethal yellowing-type diseases split into three distinct groups, thereby supporting past proposals that they represent different candidate species within 'Candidatus Phytoplasma'. The ability to differentiate 16Sr groups and subgroups by virtual RFLP analysis of secA gene sequences suggests that this gene may provide an informative alternative molecular marker for pathogen identification and diagnosis of phytoplasma diseases.