Molecular markers delimit cryptic species in Ceratocystis sensu stricto

Ceratocystis sensu stricto is a genus of closely related fungi that are mostly plant pathogens. Morphological variation between species in this genus is limited, and species delineation is strongly reliant on phylogenetic inference. Primary support for many of the species is based on the ITS region which, on its own, can be used to delineate all species described in the genus. However, the recent discovery of two ITS types in a single isolate of Ceratocystis questions the use of this marker in taxonomic studies. The aim of this study was to consider the potential use of alternative gene regions to support the species boundaries in this genus. The phylogenetic value of the beta T 1 and EF 1-alpha gene regions, generally used in combination with ITS, were re-evaluated and compared to five single-copy protein coding genes (CAL, RPBII, MS204, FG1093 and Mcm7). As an alternative approach, genome-wide single nucleotide polymorphisms (SNPs) were identified and evaluated as diagnostic markers to distinguish among the species. Fifteen species residing in Ceratocystis were used in this study. None of the protein-coding genes could be used to distinguish all species, but a combination of the beta T 1, MS204 and RPBII gene regions resolved 11 of the 15 described species. Unique SNP markers were identified for 13 of the species, and these provided significant additional support for most of the established taxon boundaries. Other than ITS, none of the markers tested could distinguish between C. acaciivora and C. manginecans, and therefore these species are reduced to synonymy, with the name C. manginecans being retained. Results of this study also revealed the likely existence of additional species in Ceratocystis.