Intraspecific and intragenomic variability of ITS rDNA sequences reveals taxonomic problems in Ceratocystis fimbriata sensu stricto

Abstract

Fourteen new species in the Latin American Clade (LAC) of the Ceratocystis fimbriata complex recently were distinguished from C. fimbriata sensu stricto largely based on variation in ITS rDNA sequences. Among the 116 isolates representing the LAC, there were 41 ITS haplotypes. Maximum parsimony (MP) analysis of ITS sequences produced poorly resolved trees. In contrast, analyses of mating-type genes (MAT1-1-2 and MAT1-2-1) resolved a single MP tree with branches of high bootstrap and posterior probability support. Four isolates showed intragenomic variation in ITS sequences. Cloning and sequencing of PCR products from a single haploid strain identified two or more ITS sequences differing at up to 16 base positions and representing two described species. Isolates from introduced populations that appeared to be clonal based on microsatellite markers varied at up to 14 bp in ITS sequence. Strains of seven Brazilian ITS haplotypes and an isolate from Ipomoea batatas (on which the species name C. fimbriata was based) were fully interfertile in sexual crosses. These analyses support three phylogenetic species that differ in pathogenicity: C. platani, C. cacaofunesta and C. colombiana. Five ITS species (C. manginecans, C. mangicola, C. mangivora, C. acaciivora, C. eucalypticola) appear to be ITS haplotypes that have been moved from or within Brazil on nursery stock. The taxonomic status of other species delineated primarily by ITS sequences (C. diversiconidia, C. papillata, C. neglecta, C. ecuadoriana, C. fimbriatomima, C. curvata) needs further study, but they are considered doubtful species.

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

“…This species has also been reported on the widely planted A. mangium in South East Asian countries, including Indonesia (Tarigan et al, 2011) and Malaysia (Brawner et al, 2015), and on Eucalyptus species in South China (Chen et al, 2013). Isolates of Ceratocystis spp, which could represent the same species, have also been reported from Eucalyptus trees in Brazil and Punica granatum (pomegranate) in India (Harrington et al, 2014).…”

“…The data showed that the isolates from M. indica and H. mangiferae represent a single clonal population, suggesting that the fungus is an introduced pathogen in these countries. This introduction could have come from South East Asia where the fungus occurs on A. mangium (Tarigan et al, 2011), or from South-America, as suggested by Harrington et al (2014). The rapid distribution of the pathogen in Oman and Pakistan was most likely facilitated by H. mangiferae (Al Adawi et al, 2013a;Al Adawi et al, 2013b;Masood et al, 2010).…”

Real-Time PCR for Ceratocystis platani detection: in-depth validation to assess the diagnostic potential and include additional technical options

“…Of these isolates, six reside in the Latin American Clade (LAC) of the complex with C. platani (Harrington 2013). There are numerous short regions of insertions and deletions in the ITS sequences of Ceratocystis, and these indels are not phylogenetically informative (Harrington et al 2014). However, they likely influence the specificity of the assays.…”

New Ceratocystis species from Eucalyptus and Cunninghamia in South China

“…However, in this study, we used cloning to provide direct evidence for the occurrence of multiple ITS types in C. cercfabiensis. Our results revealed that more than one ITS haplotype can occur in a single isolate, which has also been reported previously for Ceratocystis species in the South American Clade (Naidoo et al 2013;Harrington et al 2014;Fourie et al 2015). The ITS region should, thus, be used with caution for species delineation in Ceratocystis.…”

“…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). It is hoped that with full genome sequences of representatives of each of these species (Wilken et al 2013), and in some cases multiple species, robust and reliable taxonomic markers will be found to define species in the genus.…”