A comparative genomic analysis of putative pathogenicity genes in the host-specific sibling species Colletotrichum graminicola and Colletotrichum sublineola

Abstract

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.

Comparative genome analysis indicates rapid evolution of pathogenicity genes inColletotrichum tanaceti

“…However, the drop in orthology was less dramatic, emphasizing the contribution of non-coding regions in generating diversity within the genus. The extent of synteny between C. tanaceti and C. higginsianum was high and very similar to the percentage synteny previously reported for the two graminicola complex species, C. sublineola and C. graminicola [150]. This suggested that even though there was high diversity within the genus, the species in the same species complex tend to share more synteny than the between species complexes.…”

Genetic map‐guided genome assembly reveals a virulence‐governing minichromosome in the lentil anthracnose pathogen Colletotrichum lentis

“…Several draft and optical map-based genomes of species in the genus Colletotrichum have been published in past years, addressing and comparing the molecular mechanisms governing the pathogenic life of the species (O'Connell et al, 2012;Baroncelli et al, 2014;Crouch et al, 2014;Gan et al, 2016;Zampounis et al, 2016;Buiate et al, 2017). Although an increasingly more comprehensive understanding of the pathogenesis of these pathogens is thus emerging, the key genes determining compatibility and virulence in the host have not been identified, with the exception of the C. lindemuthianum-Phaseolus vulgaris pathosystem, which follows a gene-for-gene concept as described by Flor in 1946(Luna-Mart ınez et al, 2007.…”

Comparative Genome Analysis of Rathayibacter tritici NCPPB 1953 with Rathayibacter toxicus Strains Can Facilitate Studies on Mechanisms of Nematode Association and Host Infection

“…CRISPRFinder was used to identify the CRISPR ( Grissa et al, 2007 ). Predicted genes were compared with the Pathogen-Host Interaction (PHI) database ( Urban et al, 2015 ) using the BLASTp method and an e -value cutoff of 1.0 × 10 −5 ( Buiate et al, 2017 ). The annotation results were verified using the Artemis ( Rutherford et al, 2000 ).…”