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

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.

Using Genealogical Concordance and Coalescent-Based Species Delimitation to Assess Species Boundaries in the Diaporthe eres Complex

“…Given the lack of sequences available for some loci, these species could not be included in the analyses. Nevertheless, considering that these species fall into the D. eres complex, based in the individual genealogies performed, and knowing that Chasiri et al [ 25 ] synonymized D. rosicola as D. eres , which we also corroborate in the present study, we feel comfortable considering D. maritima and D. phragmitis as synonymous with D. eres .…”

“…Low nucleotide diversity values in addition to high haplotype diversity indices indicate a high number of closely related haplotypes [ 73 ]. Moreover, although TEF1-α locus showed the highest informative characters to resolve the D. eres complex, as also corroborated by previous studies [ 23 , 25 ], the Tajima’s D test gave negative values for TEF1-α locus and the remaining genes (except for the ITS locus), which is indicative of inbreeding events within the population occurring at these loci. Therefore, this suggests that D. eres complex is a population that may have undergone a recent expansion, producing a large number of offspring [ 73 , 74 ].…”

“…Therefore, this suggests that D. eres complex is a population that may have undergone a recent expansion, producing a large number of offspring [ 73 , 74 ]. In a recent study, Chaisiri et al [ 25 ] also showed high levels of haplotype diversity within the five loci among D. eres , thus reflecting high genetic diversity. The neutrality Tajima’s test run by these authors similarly showed negative values, which suggests a population expansion in D. eres isolates.…”

“…In several studies, many species have been demonstrated to be synonymous to the D. eres species, based on multi-locus analyses such us D. biguttusis , D. camptothecicola , D. castaneae-mollissimae , D. cotoneastri , D. ellipicola , D. longicicola , D. mahothocarpus , D. momicola and Phomopsis fukushii [ 18 , 23 , 24 ]. In a recent study, Chaisiri et al [ 25 ] found that D. henanensis , D. lonicerae and D. rosicola were also synonyms of D. eres , based on the GCPSR principle coupled with haplotype network analysis and population genetic diversity. Although D. eres has been regarded as a minor pathogen, it is also considered one of the main causal agents of cankers on grapevines [ 17 ], blueberries [ 26 ] and apple trees [ 27 ].…”

Investigations on Fungi Isolated from Apple Trees with Die-Back Symptoms from Basilicata Region (Southern Italy)

“…Moreover, D . eres , is among the most serious phytopathogenic fungi affecting many plant species all over the world [ 26 , 28 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 ]. The outcomes from this study, showing the frequent isolation from apple with die-back symptoms of D .…”