Phytopathology. 2014 Jun;104(6):650-9. doi: 10.1094/PHYTO-07-13-0180-R.
Verticillium wilts caused by the soilborne fungus Verticillium dahliae are among the most challenging diseases to control. Populations of this pathogen have been traditionally studied by means of vegetative compatibility groups (VCGs) under the assumption that VCGs comprise genetically related isolates that correlate with clonal lineages. We aimed to resolve the phylogenetic relationships among VCGs and their subgroups based on sequences of the intergenic spacer region (IGS) of the ribosomal DNA and six anonymous polymorphic sequences containing single-nucleotide polymorphisms (VdSNPs). A collection of 68 V. dahliae isolates representing the main VCGs and subgroups (VCGs 1A, 1B, 2A, 2B, 3, 4A, 4B, and 6) from different geographic origins and hosts was analyzed using the seven DNA regions. Maximum parsimony (MP) phylogenies inferred from IGS and VdSNP sequences showed five and six distinct clades, respectively. Phylogenetic analyses of individual and combined data sets indicated that certain VCG subgroups (e.g., VCGs 1A and 1B) are closely related and share a common ancestor; however, other subgroups (e.g., VCG 4B) are more closely related to members of a different VCG (e.g., VCG 2A) than to subgroups of the same VCG (VCG 4B). Furthermore, MP analyses indicated that VCG 2B is polyphyletic, with isolates placed in at least three distinct phylogenetic lineages based on IGS sequences and two lineages based on VdSNP sequences. Results from our study suggest the existence of main VCG lineages that contain VCGs 1A and 1B; VCGs 2A and 4B; and VCG 4A, for which both phylogenies agree; and the existence of other VCGs or VCG subgroups that seem to be genetically heterogeneous or show discrepancies in their phylogenetic placement: VCG 2B, VCG 3, and VCG 6. These results raise important caveats regarding the interpretation of VCG analyses: genetic homogeneity and close evolutionary relationship between members of a VCG should not be assumed.
由土壤真菌黄萎轮枝菌引起的黄萎病是最难控制的病害之一。传统上，人们通过营养体亲和群（VCG）来研究这种病原体，假设 VCG 由与克隆谱系相关的遗传上相关的分离株组成。我们旨在根据核糖体 DNA 的基因间 spacer 区（IGS）和包含单核苷酸多态性（VdSNP）的六个匿名多态性序列的序列来解决 VCG 及其亚群之间的系统发育关系。使用七个 DNA 区域分析了来自不同地理来源和宿主的 68 个代表主要 VCG 和亚群（VCG 1A、1B、2A、2B、3、4A、4B 和 6）的黄萎轮枝菌分离株。从 IGS 和 VdSNP 序列推断的最大简约（MP）系统发育树分别显示了五个和六个不同的分支。个体和组合数据集的系统发育分析表明，某些 VCG 亚群（例如 VCG 1A 和 1B）密切相关，具有共同的祖先；然而，其他亚群（例如 VCG 4B）与不同 VCG（例如 VCG 2A）的成员比同一 VCG（VCG 4B）的亚群更密切相关。此外，MP 分析表明，VCG 2B 是多系的，根据 IGS 序列，分离株位于至少三个不同的系统发育谱系中，根据 VdSNP 序列则位于两个谱系中。我们的研究结果表明，存在主要的 VCG 谱系，其中包含 VCG 1A 和 1B；VCG 2A 和 4B；以及 VCG 4A，两者的系统发育都一致；以及其他 VCG 或 VCG 亚群的存在，这些亚群似乎在遗传上是异质的，或者在其系统发育位置上存在差异：VCG 2B、VCG 3 和 VCG 6。这些结果对 VCG 分析的解释提出了重要的警告：不应假设 VCG 成员之间具有遗传同质性和密切的进化关系。
