Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe

Background. Species identification is essential for controlling disease, understanding epidemiology, and to guide the implementation of phytosanitary measures against fungi from the genus Diaporthe. Accurate Diaporthe species separation requires using multi-loci phylogenies. However, defining the optimal set of loci that can be used for species identification is still an open problem. Methods. Here, we addressed that problem by identifying five loci that have been sequenced in 142 Diaporthe isolates representing 96 species: TEF1, TUB, CAL, HIS and ITS. We then used every possible combination of those loci to build, analyse, and compare phylogenetic trees. Results. As expected, species separation is better when all five loci are simultaneously used to build the phylogeny of the isolates. However, removing the ITS locus has little effect on reconstructed phylogenies, identifying the TEF1-TUB-CAL-HIS four loci tree as almost equivalent to the five loci tree. We further identify the best 3-loci, 2-loci, and 1-locus trees that should be used for species separation in the genus. Discussion. Our results question the current use of the ITS locus for DNA barcoding in the genus Diaporthe and suggest that TEF1 might be a better choice if one locus barcoding needs to be done.