Natural selection on coding and noncoding DNA sequences is associated with virulence genes in a plant pathogenic fungus

Abstract

Natural selection leaves imprints on DNA, offering the opportunity to identify functionally important regions of the genome. Identifying the genomic regions affected by natural selection within pathogens can aid in the pursuit of effective strategies to control diseases. In this study, we analyzed genome-wide patterns of selection acting on different classes of sequences in a worldwide sample of eight strains of the model plant-pathogenic fungus Colletotrichum graminicola. We found evidence of selective sweeps, balancing selection, and positive selection affecting both protein-coding and noncoding DNA of pathogenicity-related sequences. Genes encoding putative effector proteins and secondary metabolite biosynthetic enzymes show evidence of positive selection acting on the coding sequence, consistent with an Arms Race model of evolution. The 5' untranslated regions (UTRs) of genes coding for effector proteins and genes upregulated during infection show an excess of high-frequency polymorphisms likely the consequence of balancing selection and consistent with the Red Queen hypothesis of evolution acting on these putative regulatory sequences. Based on the findings of this work, we propose that even though adaptive substitutions on coding sequences are important for proteins that interact directly with the host, polymorphisms in the regulatory sequences may confer flexibility of gene expression in the virulence processes of this important plant pathogen.

Keywords: Colletotrichum graminicola; PAML; arms race hypothesis; pathogenicity; positive selection.

Fig. 1.—

Distribution of Tajima’s D values for each class of sequences. (A) Typical eukaryotic protein-coding gene and sequence classes analyzed in the present study. (B) Boxplots showing the distribution of Tajima’s D values in each class of sequences. Values inside each box correspond to the middle 50% of the data (between the 25th [Q1] and 75th [Q3] percentiles) and the red line within the box represents the median. The ends of the vertical dotted lines (whiskers) at the top and bottom of each box indicate the maximum and minimum limits to consider outliers according to the inter quartile range (IQR = Q3-Q1). Whiskers lengths were calculated as Q3+3*IQR (upper) and Q1−3*IQR (lower). Values outside the lines (red crosses) are extreme outliers. Red stars and values at the top of the boxplots indicate mean Tajima’s D value for each class of sequence.

Fig. 2.—

Enrichment of putative nonneutrally evolving sequences in different functional gene categories related with pathogenicity. Table values represent the number of sequences for each class and gene category. Tests: D* (D < 5th percentile or D > 95th percentile), D* < 0 (D < 5th percentile), D* > 0 (D > 95th percentile), and PS (sequences under PS according to LRT tests). Background colors indicate significance of the Fisher’s exact test for enrichment after correction for multiple comparisons by the FDR. See supplementary table S2, Supplementary Material online for more details.