The taxonomy of the genus Colletotrichum has undergone tremendous changes over the last decade, with over 200 species being currently recognised and species complexes being informally used to cluster those species. Many of these species are important plant pathogens, some rather polyphagous and others host-specific, but several occur seldomly and some may in fact be ecologically endangered. Based mainly on literature from the past decade, in this work we review the occurrence, geographic distribution and host spectrum of currently recognised Colletotrichum species under phylogenetic, pathological/agronomic and ecological perspectives, providing a list arranged by Colletotrichum species and species complexes. A total of 257 species are listed and grouped into 15 species complexes. In this work we have recorded 1353 unique host species-Colletotrichum species association records from 720 hosts, with the Fabaceae as the family with higher number of hosts (52 host species) but with the Rosaceae as the family with the highest number of host species-Colletotrichum species association records (118 association records). According to occurrence data, 88 species are common in nature, 128 were considered as data deficient and 41 are threatened, some of which are likely extinct from nature and preserved only in culture collections. Several species are relevant plant pathogens, in some cases geographically confined and thus of potential quarantine relevance. Based on the major changes that occurred on Colletotrichum taxonomy over the last decade, this work provides a comprehensive overview of occurrence data of Colletotrichum species, compiling host range and geographical distribution, with relevance for plant pathology and conservation mycology. The current taxonomic framework in Colletotrichum is revealing numerous species but poses challenges to the employment of standard criteria for the evaluation of biological conservation of these fungi. We advocate that conservation mycology and taxonomy should find common routes simultaneously enabling the correct delimitation of species of Colletotrichum and the implementation of feasible criteria for the evaluation of conservation. The employment of new technologies, such whole genome sequencing (WGS), will help and support the description of new species and to gain a better understanding of the genetic bases of speciation processes.

Colletotrichum species and complexes: geographic distribution, host range and conservation status

The taxonomy of Colletotrichum has undergone profound changes over the past decade, with ca.340 species now recognised, and grouped into 20 species complexes (16 previously described and four proposed in this work).Over that period, the volatility of the taxonomic framework posed difficulties to the aetiology of anthracnose diseases along with uncertainty on cross-infection potential, quarantine rules, pesticide management and plant breeding strategies.Now that the Colletotrichum taxonomy is stabilising (still several new species being named, but no longer representing major pathogens), there is a point on reviewing the knowledge on the aetiology of anthracnose diseases in a global way, pointing out the relative importance of each Colletotrichum species for each host/crop and identifying areas/crops where information is missing (and there are several crops for which nothing is known regarding Colletotrichum species in modern terms).Based on 3400 host species-Colletotrichum species occurrence records (considering only records of Colletotrichum spp.identified in modern terms), we have listed over 760 host (plants) species and analysed the information available on the Colletotrichum species reported from them, the symptoms caused and the geographic distribution and pathological relevance.Whereas some of these hosts are wild plants, this work is mostly focused on cultivated plants and therefore on the aetiology of anthracnose diseases globally.In the context of Colletotrichum fungi, this compilation provides downstream users of Mycology, namely those in areas such as Plant Pathology, Plant Protection and Plant Breeding, with updated information on the main causal agents of anthracnose in each crop/plant species in each location, or alternatively with an alert on the lack of information on the identity of the species of Colletotrichum relevant for a given crop in a given location. 

Hosts of Colletotrichum

Phoma macdonaldii, the causal agent of sunflower black stem, severely affects sunflower yield and quality. A rapid and sensitive detection method is necessary for diagnosis of this disease. In this study, a loop-mediated isothermal amplification (LAMP) assay was developed for rapid detection of the pathogen from diseased sunflower tissues. The LAMP primers were designed to target the rDNA region of the fungus. The reaction condition was optimized to 60°C water baths for 45 min. The detection limit of the LAMP assay was 100 fg DNA or 10 conidia/g seeds. The LAMP assay was validated by detecting P. macdonaldii from infected sunflower tissue samples, including leaves, stems, and seeds, and applying to seed samples randomly collected from sunflower fields. This LAMP assay will be useful for estimating disease prevalence and implementing sustainable management of sunflower black stem. 

Loop-Mediated Isothermal Amplification Assay for Rapid Detection of Phoma macdonaldii, the Causal Agent of Sunflower Black Stem

First report of leaf anthracnose caused by Colletotrichum liriopes on Ophiopogon japonicus in China

Phoma macdonaldii (teleomorph Leptosphaeria lindquistii) is the causal agent of sunflower (Helianthus annuus L.) black stem. In order to investigate the molecular basis for the pathogenicity of P. ormacdonaldii, genomic and transcriptomic analyses were performed. The genome size was 38.24 Mb and assembled into 27 contigs with 11,094 putative predicted genes. These include 1133 genes for CAZymes specific for plant polysaccharide degradation, 2356 for the interaction between the pathogen and host, 2167 for virulence factors, and 37 secondary metabolites gene clusters. RNA-seq analysis was conducted at the early and late stages of the fungal spot formation in infected sunflower tissues. A total of 2506, 3035, and 2660 differentially expressed genes (DEGs) between CT and each treatment group (LEAF-2d, LEAF-6d, and STEM) were retrieved, respectively. The most significant pathways of DEGs from these diseased sunflower tissues were the metabolic pathways and biosynthesis of secondary metabolites. Overall, 371 up-regulated DEGs were shared among LEAF-2d, LEAF-6d, and STEM, including 82 mapped to DFVF, 63 mapped to PHI-base, 69 annotated as CAZymes, 33 annotated as transporters, 91 annotated as secretory proteins, and a carbon skeleton biosynthetic gene. The most important DEGs were further confirmed by RT-qPCR. This is the first report on the genome-scale assembly and annotation for P. macdonaldii. Our data provide a framework for further revealing the underlying mechanism of the pathogenesis of P. macdonaldii, and also suggest the potential targets for the diseases caused by this fungal pathogen.

Genomic and Transcriptomic Survey Provides Insights into Molecular Basis of Pathogenicity of the Sunflower Pathogen Phoma macdonaldii

First report of anthracnose on Hosta ventricosa caused by Colletotrichum spaethianum in China

Proteome of the fungus Phoma macdonaldii, the causal agent of black stem of sunflower.

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First report of anthracnose on Hosta ventricosa caused by Colletotrichum spaethianum in China

Proteome of the fungus Phoma macdonaldii, the causal agent of black stem of sunflower.