Phylogenetic and Haplotype Network Analyses of Species in China Based on Sequences of Multiple Loci.

is considered one of the most important causal agents of many plant diseases, with a broad host range worldwide. In this study, multiple sequences of ribosomal internal transcribed spacer region (ITS), translation elongation factor 1-α gene (), beta-tubulin gene (), calmodulin gene (), and histone-3 gene () were used for multi-locus phylogenetic analysis. For phylogenetic analysis, maximum likelihood (ML), maximum parsimony (MP), and Bayesian inferred (BI) approaches were performed to investigate relationships of with closely related species. The results strongly support that the species falls into a monophyletic lineage, with the characteristics of a species complex. Phylogenetic informativeness (PI) analysis showed that clear boundaries could be proposed by using , whereas ITS showed an ineffective reconstruction and, thus, was unsuitable for speciating boundaries for species. A combined dataset of , , , and showed strong resolution for species, providing insights for the complex. Accordingly, besides , , , , , , , , , and , which have already been previously considered the synonymous species of , another three species, , and , were further revealed to be synonyms of in this study. In order to demonstrate the genetic diversity of species in China, 138 isolates were randomly selected from previous studies in 16 provinces. These isolates were obtained from different major plant species from 2006 to 2020. The genetic distance was estimated with phylogenetic analysis and haplotype networks, and it was revealed that two major haplotypes existed in the Chinese populations of . The haplotype networks were widely dispersed and not uniquely correlated to specific populations. Overall, our analyses evaluated the phylogenetic identification for species and demonstrated the population diversity of in China.