Background Colletotrichum graminicola and C. sublineola cause anthracnose leaf and stalk diseases of maize and sorghum, respectively. In spite of their close evolutionary relationship, the two species are completely host-specific. Host specificity is often attributed to pathogen virulence factors, including specialized secondary metabolites (SSM), and small-secreted protein (SSP) effectors. Genes relevant to these categories were manually annotated in two co-occurring, contemporaneous strains of C. graminicola and C. sublineola. A comparative genomic and phylogenetic analysis was performed to address the evolutionary relationships among these and other divergent gene families in the two strains.ResultsInoculation of maize with C. sublineola, or of sorghum with C. graminicola, resulted in rapid plant cell death at, or just after, the point of penetration. The two fungal genomes were very similar. More than 50% of the assemblies could be directly aligned, and more than 80% of the gene models were syntenous. More than 90% of the predicted proteins had orthologs in both species. Genes lacking orthologs in the other species (non-conserved genes) included many predicted to encode SSM-associated proteins and SSPs. Other common groups of non-conserved proteins included transporters, transcription factors, and CAZymes. Only 32 SSP genes appeared to be specific to C. graminicola, and 21 to C. sublineola. None of the SSM-associated genes were lineage-specific. Two different strains of C. graminicola, and three strains of C. sublineola, differed in no more than 1% percent of gene sequences from one another.ConclusionsEfficient non-host recognition of C. sublineola by maize, and of C. graminicola by sorghum, was observed in epidermal cells as a rapid deployment of visible resistance responses and plant cell death. Numerous non-conserved SSP and SSM-associated predicted proteins that could play a role in this non-host recognition were identified. Additional categories of genes that were also highly divergent suggested an important role for co-evolutionary adaptation to specific host environmental factors, in addition to aspects of initial recognition, in host specificity. This work provides a foundation for future functional studies aimed at clarifying the roles of these proteins, and the possibility of manipulating them to improve management of these two economically important diseases.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3457-9) contains supplementary material, which is available to authorized users.

Two Florida populations of foliar nematodes were collected from strawberries originating from Cashiers, North Carolina (USA) located west from Willard, the type locality of Aphelenchoides besseyi. Both nematodes were cultured on Monilinia fructicola and identified using morphological characteristics and molecular assays as Aphelenchoides besseyi and Aphelenchoides pseudogoodeyi sp. n., a herein described new species related to Aphelenchoides goodeyi belonging to the Group of Aphelenchoides exhibiting stellate tails. The morphological and biological characters of Florida A. besseyi fit those of the original description of this species. A. pseudogoodeyi sp. n., which was initially misidentified as Aphelenchoides fujianensis, differed from the type population of the latter species from China because it was without males, and females lacked a functional spermatheca, whereas type A. fujianensis is an amphimictic species. Phylogenetic analyses using near full-length 18S ribosomal RNA (rRNA), the D2-D3 expansion fragments of 28S rRNA, and partial COI gene sequences indicated that A. besseyi is a species complex. A. pseudogoodeyi sp. n. grouped in different clades from those of the type A. fujianensis, instead merging with populations identified of ‘A. fujianensis’ from Brazil and other countries, suggesting that the latter are conspecific and incorrectly identified. The Florida A. besseyi infected strawberry and gerbera daisy, but not soybean and alfalfa. A. pseudogoodeyi sp. n. is mainly mycetophagous. Localized inoculation of 300 specimens applied with filter paper adhering to the blade of the soybean leaves resulted in nematode penetration into the mesophyll with subsequent development of lesions limited to the inoculated area of the blade.

Anthracnose caused by Colletotrichum sublineola is an important disease of cultivated sorghum (Sorghum bicolor) worldwide. Anthracnose is also common on the ubiquitous wild sorghum relative Johnsongrass (S. halepense). Analysis of repetitive molecular fingerprinting markers revealed that isolates of C. sublineola from both hosts in the southeastern United States were genotypically diverse, with relatively few haplotypes found in more than one location. With few exceptions, isolates recovered from S. bicolor belonged to a population that was genetically distinct from the population recovered from S. halepense. Twenty-three isolates from cultivated sorghum were all pathogenic to at least one of 13 heritage inbred lines of S. bicolor. In all, 4 of 10 isolates from S. halepense were also pathogenic to one or more of the lines, while the rest caused no disease in greenhouse assays. The four pathogenic isolates from S. halepense were less aggressive, on average, than isolates from S. bicolor, although the ranges overlapped. Pathogenicity tests involving 15 representative pathogenic isolates from S. bicolor and S. halepense on eight heritage inbred lines of S. bicolor identified 12 races. The combined results of this study demonstrated that C. sublineola comprises two separate host-associated subpopulations in the field, even though some isolates from S. halepense were able to cause disease on S. bicolor under ideal greenhouse conditions. Nonetheless, the apparent existence of infrequent cross-infection events in the field, indicated by molecular fingerprinting, suggests that Johnsongrass has the potential to serve as a refuge and an incubator for genetic diversity in C. sublineola, which can complicate efforts to develop and deploy resistant sweet sorghum varieties in the region.