Molecular markers delimit cryptic species in Ceratocystis sensu stricto

Abstract

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 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 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 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.

A possible centre of diversity in South East Asia for the tree pathogen, Ceratocystis manginecans

“…When species concepts alternative to the genealogical concordance phylogenetic concept are considered, these isolates could be seen as different haplotypes of C. fimbriata (Oliveira et al, 2015). However, based on previous phylogenetic analyses including five gene regions (Fourie et al, 2014) we consider C. manginecans as a species distinct from the sweet potato black rot fungus which includes the type of C.…”

“…The sequences obtained were aligned to previously generated data sets of the ITS and βT 1 regions, respectively, of C. fimbriata sensu stricto (Fourie et al, 2014). Alignments were performed using MUSCLE in MEGA v. 5 (Tamura et al, 2011) and used to construct phylogenetic trees of ITS and βT 1 based on Maximum parsimony (MP).…”

“…manginecans (Fourie et al, 2014), all isolates in this study were considered to represent C. manginecans.…”

New Ceratocystis species from Eucalyptus and Cunninghamia in South China

“…There are only six previous reports of Ceratocystis species from China and all species reside in the South American Clade. These species include C. manginecans from recently harvested stumps of Eucalyptus in GuangDong Province (Chen et al 2013;Fourie et al 2015), and C. fimbriata s.l, causing a disease on Eucalyptus (Li et al 2014b), Ipomoea batatas (sweet potato; Sy 1956), Punica granatum (pomegranate; Huang et al 2003;Xu et al 2011), Colocasia esculenta (taro; Huang et al 2008) and Eriobotrya japonica (loquat; Li et al 2014a). Considering the number of Ceratocystis species found in other countries, and the small number of studies on species of Ceratocystis and other Ceratocystidaceae found in China, the discovery of C. cercfabiensis and C. collisensis suggests that many other species in the genus and family remain to be discovered in this geographic area.…”

“…For example, the delimitation of species in the South American Clade lack sufficient markers for their clear delimitation (Al Adawi et al 2013;Harrington et al 2014;Fourie et al 2015). The ITS region, which has been selected as the universal barcoding region for fungal species (Schoch et al 2012), has been shown to be present as multiple ITS types in single isolates of some Ceratocystis species (Al Adawi et al 2013;Naidoo et al 2013;Harrington et al 2014).…”