Abstract
BackgroundMagnaporthaceae, a family of ascomycetes, includes three fungi of great economic importance that cause disease in cereal and turf grasses: Magnaporthe oryzae (rice blast), Gaeumannomyces graminis var. tritici (take-all disease), and Magnaporthe poae (summer patch disease). Recently, the sequenced and assembled genomes for these three fungi were reported. Here, the genomes were compared for orthologous genes in order to identified genes that are unique to the Magnaporthaceae family of fungi. In addition, ortholog clustering was used to identify a core proteome for the Magnaporthaceae, which was examined for diversifying and purifying selection and evidence of two-speed genome evolution.ResultsA genome-scale comparative study was conducted across 74 fungal genomes to identify clusters of orthologous genes unique to the three Magnaporthaceae species as well as species specific genes. We found 1149 clusters that were unique to the Magnaporthaceae family of fungi with 295 of those containing genes from all three species. Gene clusters involved in metabolic and enzymatic activities were highly represented in the Magnaporthaceae specific clusters. Also highly represented in the Magnaporthaceae specific clusters as well as in the species specific genes were transcriptional regulators. In addition, we examined the relationship between gene evolution and distance to repetitive elements found in the genome. No correlations between diversifying or purifying selection and distance to repetitive elements or an increased rate of evolution in secreted and small secreted proteins were observed.ConclusionsTaken together, these data show that at the genome level, there is no evidence to suggest multi-speed genome evolution or that proximity to repetitive elements play a role in diversification of genes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2491-y) contains supplementary material, which is available to authorized users.
Highlights
IntroductionMagnaporthaceae, a family of ascomycetes, includes three fungi of great economic importance that cause disease in cereal and turf grasses: Magnaporthe oryzae (rice blast), Gaeumannomyces graminis var. tritici (takeall disease), and Magnaporthe poae (summer patch disease)
Magnaporthaceae, a family of ascomycetes, includes three fungi of great economic importance that cause disease in cereal and turf grasses: Magnaporthe oryzae, Gaeumannomyces graminis var. tritici, and Magnaporthe poae
We found that few carbohydrate active enzymes (CAzymes) were clustered by OrthoMCL, while a higher number were identified in the species specific genes
Summary
Magnaporthaceae, a family of ascomycetes, includes three fungi of great economic importance that cause disease in cereal and turf grasses: Magnaporthe oryzae (rice blast), Gaeumannomyces graminis var. tritici (takeall disease), and Magnaporthe poae (summer patch disease). Orthologs and paralogs can Okagaki et al BMC Genomics (2016) 17:135 be useful tools in genome comparison studies because they can highlight genes shared among species that are important to conserved biological processes or can reveal those genes that are unique to a particular subset of fungi, such as families of fungi or fungi with a specific lifestyle. Developed by Li et al [2], OrthoMCL uses multiple steps including BLASTp and Markov clustering in order to group genes into likely orthologous clusters. Using such algorithms, genes with similar functions as well as those genes unique to each species can be identified
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