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 βT 1 and EF 1-α 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 between 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 βT 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 these species are, therefore, reduced to synonymy with the name C.
manginecans being retained. Results of this study also revealed the likely existence of
additional species in Ceratocystis.