Insights into the genus Diaporthe: phylogenetic species delimitation in the D. eres species complex.
The genus Diaporthe comprises pathogenic, endophytic and saprobic species with both temperate and tropical distributions. Cryptic diversification, phenotypic plasticity and extensive host associations have long complicated accurate identifications of species in this genus. The delimitation of the generic type species Diaporthe eres has been uncertain due to the lack of ex-type cultures. Species limits of D. eres and closely related species were evaluated using molecular phylogenetic analysis of eight genes including nuclear ribosomal internal transcribed spacer (ITS), partial sequences of actin (ACT), DNA-lyase (Apn2), translation elongation factor 1-α (EF1-α), beta-tubulin (TUB), calmodulin (CAL), 60s ribosomal protein L37 (FG1093) and histone-3 (HIS). The occurrence of sequence heterogeneity of ITS within D. eres is observed, which complicates the analysis and may lead to overestimation of the species diversity. The strict criteria of Genealogical Concordance Phylogenetic Species Recognition (GCPSR) were applied to resolve species boundaries based on individual and combined analyses of other seven genes except the ITS. We accept nine distinct phylogenetic species including Diaporthe alleghaniensis, D. alnea, D. bicincta, D. celastrina, D. eres, D. helicis, D. neilliae, D. pulla and D. vaccinii. Epitypes are designated for D. alnea, D. bicincta, D. celastrina, D. eres, D. helicis and D. pulla. Modern descriptions and illustrations are provided for these species. Newly designed primers are introduced to amplify and sequence the Apn2 (DNA-lyase) gene in Diaporthe. Based on phylogenetic informativeness profiles, EF1-α, Apn2 and HIS genes are recognised as the best markers for defining species in the D. eres complex.