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

SIMPLE SUMMARY: Diaporthe eres is one of the most serious plant pathogenic fungi that affect many economically important plants. It can cause rootstock death, stem canker, stem necrosis, dead branch, shoot blight, fruit rot, leaf spot, leaf necrosis, and umbel browning. In general, morphological and molecular characterization using multiple loci sequences were performed for the identification of Diaporthe species. However, there are morphological differences due to culture conditions, and the taxonomy of species of Diaporthe is unclear because the phylogeny based on different genes gives different tree topologies. In this study, we evaluate the phylogenetic relationships and population diversity among D. eres and other Diaporthe species. Our results showed that phylogenetic analyses from concatenated multi-locus DNA sequence data could resolve the D. eres species. Furthermore, haplotype network analysis showed that no correlation existed between population diversity and distribution or hosts across China. These results could improve our understanding of the epidemiology of D. eres and provide useful information for effective disease management. ABSTRACT: Diaporthe eres 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 (EF1-α), beta-tubulin gene (TUB2), calmodulin gene (CAL), and histone-3 gene (HIS) 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 D. eres with closely related species. The results strongly support that the D. eres 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 EF1-α, whereas ITS showed an ineffective reconstruction and, thus, was unsuitable for speciating boundaries for Diaporthe species. A combined dataset of EF1-α, CAL, TUB2, and HIS showed strong resolution for Diaporthe species, providing insights for the D. eres complex. Accordingly, besides D. biguttusis, D. camptothecicola, D. castaneae-mollissimae, D. cotoneastri, D. ellipicola, D. longicicola, D. mahothocarpus, D. momicola, D. nobilis, and Phomopsis fukushii, which have already been previously considered the synonymous species of D. eres, another three species, D. henanensis, D. lonicerae and D. rosicola, were further revealed to be synonyms of D. eres in this study. In order to demonstrate the genetic diversity of D. eres species in China, 138 D. eres 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 D. eres. The haplotype networks were widely dispersed and not uniquely correlated to specific populations. Overall, our analyses evaluated the phylogenetic identification for D. eres species and demonstrated the population diversity of D. eres in China.