Differential Expression of Fungal Genes Determines the Lifestyle of Plectosphaerella Strains During Arabidopsis thaliana Colonization

The fungal genus Plectosphaerella comprises species and strains with different lifestyles on plants, such as P. cucumerina, which has served as model for the characterization of Arabidopsis thaliana basal and nonhost resistance to necrotrophic fungi. We have sequenced, annotated, and compared the genomes and transcriptomes of three Plectosphaerella strains with different lifestyles on A. thaliana, namely, PcBMM, a natural pathogen of wild-type plants (Col-0), Pc2127, a nonpathogenic strain on Col-0 but pathogenic on the immunocompromised cyp79B2 cyp79B3 mutant, and P0831, which was isolated from a natural population of A. thaliana and is shown here to be nonpathogenic and to grow epiphytically on Col-0 and cyp79B2 cyp79B3 plants. The genomes of these Plectosphaerella strains are very similar and do not differ in the number of genes with pathogenesis-related functions, with the exception of secreted carbohydrate-active enzymes (CAZymes), which are up to five times more abundant in the pathogenic strain PcBMM. Analysis of the fungal transcriptomes in inoculated Col-0 and cyp79B2 cyp79B3 plants at initial colonization stages confirm the key role of secreted CAZymes in the necrotrophic interaction, since PcBMM expresses more genes encoding secreted CAZymes than Pc2127 and P0831. We also show that P0831 epiphytic growth on A. thaliana involves the transcription of specific repertoires of fungal genes, which might be necessary for epiphytic growth adaptation. Overall, these results suggest that in-planta expression of specific sets of fungal genes at early stages of colonization determine the diverse lifestyles and pathogenicity of Plectosphaerella strains.

Inside Plectosphaerellaceae

The family Plectosphaerellaceae (Glomerellales, Sordariomycetes) includes numerous plant pathogenic genera and soil-borne fungal species. Ten genera are currently accepted, including several taxa that occupy an unresolved position within the family. To address this issue, a multilocus sequence analysis was carried out using partial gene sequences from the 28S large subunit nrRNA gene (LSU), the internal transcribed spacer (ITS) regions of the nrDNA region, including the 5.8S nrRNA gene, the translation elongation factor 1-alpha (TEF1-α), tryptophan synthase (TS), actin (ACT) and the RNA polymerase II second largest subunit (RPB2), based on a large set of isolates mainly from the CBS collection. Results of the molecular data combined with a detailed morphological study resolved 22 genera in the family, of which 12 are newly described. Additionally, 15 new species and 10 new combinations are proposed. An epitype and neotype are also introduced for Stachylidium bicolor and Plectosphaerella cucumerina, respectively.