Colletotrichum – current status and future directions

Abstract

A review is provided of the current state of understanding of Colletotrichum systematics, focusing on species-level data and the major clades. The taxonomic placement of the genus is discussed, and the evolution of our approach to species concepts and anamorph-teleomorph relationships is described. The application of multilocus technologies to phylogenetic analysis of Colletotrichum is reviewed, and selection of potential genes/loci for barcoding purposes is discussed. Host specificity and its relation to speciation and taxonomy is briefly addressed. A short review is presented of the current status of classification of the species clusters that are currently without comprehensive multilocus analyses, emphasising the orbiculare and destructivum aggregates. The future for Colletotrichum biology will be reliant on consensus classification and robust identification tools. In support of these goals, a Subcommission on Colletotrichum has been formed under the auspices of the International Commission on Taxonomy of Fungi, which will administer a carefully curated barcode database for sequence-based identification of species within the BioloMICS web environment.

The CD1/CD2 marker for specific detection of Colletotrichum lindemuthianum is an iron transporter pseudogene

“…From this result it was also evident that a new forward primer, analogous to CD1, can be designed to specifically identify C. orbiculare, adding up a new marker to identify this species to the sequence analysis of 900-bp intron of the glutamine synthetase gene used by Liu et al (2007). Furthermore, each of the species in the Orbiculare clade (sensu Cannon et al, 2012) presented distinct host specificity: isolates of C. orbiculare, C. lindemuthianum, and C. trifolii being pathogenic only on cucurbits, common bean, and alfalfa, respectively, while de other species (C. malvarum, C. bidentis, C. sidae, C. spinosum and C. tebeestii) were found on different weeds . FTR1 proteins, together with iron transport multicopper oxidases (fet3), are part of a conserved binary permease-oxidase complex involved in a highaffinity iron uptake in fungi (Philpott, 2006;Sutak et al, 2008).…”

“…In fact, C. lindemuthianum is a member of a clade of closely related species that originally included C. orbiculare, C. trifolii, and C. malvarum (Liu et al, 2007;Cannon et al, 2012). Based on spore morphology, appressorium development, and rDNA sequence similarities, it was proposed that these species should be regarded as a single species (Sherriff et al, 1994).…”

“…In this study, by sequencing the CD1/CD2 amplicon and 454 pyrosequencing of one C. lindemuthianum isolate, we demonstrate that the CD1/CD2 marker corresponds to a portion of an iron permease (Ftr1) pseudogene. The potential of using this genomic region for phylogenetic analysis of the Orbiculare clade sensu Cannon et al (2012) and for the detection of their related species is discussed.…”

“…Certification of disease-free donor plants and seeds depends on the availability of accurate, sensitive and timeeffective diagnostic tools such as conventional and realtime PCR (qPCR), which has been proposed to detect C. lindemuthianum quickly and reliably using species-specific primers and or probes (Chen et al, 2007;2013;Wang et al, 2008). DNA sequencing has also been used to differentiate closely related species within the main Colletotrichum clades Cannon et al, 2012;Damm et al, 2013). The partial annotated genomes of C. higginsianum and C. graminicola, pathogens of maize (O'Connell et al, 2012) and of C. orbiculare and C. gloeosporioides isolated from strawberry (Gan et al, 2013) have identified pathogenicity-related genes.…”

“…Cox1) and some protein genes such as actin (ACT), beta-tubulin (TUB2), calmodulin (CAL), chitin synthase I (CHS-1), manganese superoxide dismutase (SOD2) and the translation elongation factor 1-α (EF1α) Cannon et al, 2012;. In Colletotrichum, species definition based on ITS sequence has proved unsatisfactory in some species-complexes, so a multilocus genotyping approach combining ITS with several other genes or their introns, such as the 900-bp intron of the glutamine synthetase gene and the 200-bp intron of the glyceraldehyde-3-phosphate dehydrogenase gene, is used (Liu et al, 2007;Cannon et al, 2012).…”