A comparison between ITS, D1/D2 LSU rDNA, tub2, and rpb2 regions to delimit Allophoma, Didymella, and Neodidymelliopsis species from the family Didymellaceae

In this study, 12 native strains and 80 strains from the known species of Allophoma, Didymella, and Neodidymelliopsis were selected. The ITS, D1/D2 LSU rDNA, tub2 and rpb2 regions of the mentioned strains were compared for species delimitation using phylogenetic analysis. The genomic regions of the native strains were amplified using DNA extracted from freeze-dried mycelia and sequenced. The phylogenetic analysis was performed using the maximum likelihood algorithm. The regions of the D1/D2 LSU rDNA, ITS, tub2, and rpb2 delimited 0, 20, 43, and 46 out of 61 species studied, respectively. In the phylogenetic analysis based on combined regions, all datasets (ITS-tub2, ITS-rpb2, tub2-rpb2, ITS-tub2-rpb2, and ITS-28S-tub2-rpb2) could delimit 49 out of the 61 species under survey.Results showed that the sequencing and phylogenetic analysis of the ITS, tub2, and rpb2 regions in combination with morphological studies are necessary for species delimitation of the Allophoma, Didymella and Neodidymelliopsis genera. In a single-locus phylogeny, tub2 or rpb2 genes are the best markers among the genomic regions used.