Figure 1.
Variation in gene clustering, GD, and HGT across the fungal phylogeny.
From top to bottom, the four box-and-whisker plots correspond to number of ECgenes per genome, percentage of clustered ECgenes per genome, percentage of horizontally transferred ECgenes per genome, and percentage of duplicated ECgenes per genome. The bottom and top of each box first and third quartiles (the 25th and 75th percentiles), respectively. The lower whisker extends from the box bottom to the lowest value within 1.5 * IQR (Inter-Quartile Range, defined as the distance between the first and third quartiles) of the first quartile. The upper whisker extends from the box top to the highest value that is within 1.5 * IQR of the third quartile. Data beyond the end of the whiskers are outliers and plotted as points. Numbers in parentheses after the lineages' names indicate numbers of genomes in each lineage; the numbers of genomes used from each lineage are also reflected by the widths of their branch triangles on the fungal species phylogeny shown at the bottom of the figure.
Figure 2.
Over/underrepresentation of KEGG metabolic categories across three major fungal lineages.
From top to bottom, the box-and-whisker plots correspond to number ECgenes per genome, number of clustered ECgenes per genome, number of transferred ECgenes per genome, and number of duplicated genes per genome. Agaricomycetes boxes are colored blue, Saccharomycotina boxes are colored red, and Pezizomycotina boxes green. Box-and-whisker convention is as described in Figure 1. Up arrows under boxes indicate overrepresentation, and down arrows indicate underrepresentation of the corresponding metabolic category in the corresponding lineage. Significance of differential representation was estimated using a two-tailed Fisher's exact test using a Benjamini & Hochberg adjusted P value≤0.05 to account for multiple testing (Table S4).
Figure 3.
The episodic occurrence of HGT across the fungal species phylogeny.
Numbers in parentheses indicate the number of HGT events and the number of genomes downstream of the collapsed nodes, respectively. Some clades have been collapsed for clarity; see Figure S2 for a depiction of the entire species phylogeny. The thickness and color of each branch corresponds to number of ECgenes transferred to each branch, adjusted by the number of genomes in the case of collapsed clades.
Figure 4.
The association between gene innovation and gene clustering across three major fungal lineages.
Percentage of non-clustered (blue bars) and clustered ECgenes (red bars) inferred to have undergone GD (top) and HGT (bottom). Asterisks (*) indicate statistically significant differences determined using a Benjamini & Hochberg adjusted P value≤0.05 in a two-tailed Fisher's exact test (Table S6).
Figure 5.
The fungal metabolic network of interactions between gene clustering and two major sources of gene innovation (GD and HGT).
Nodes of the metabolic network correspond to KEGG compounds. Thick edges of the metabolic network correspond to EC numbers from clustered ECgenes in one or more fungal species, whereas thin edges to EC numbers whose genes show no history of gene clustering. Colored edges correspond to EC numbers whose ECgenes have undergone HGT and GD (red), GD (blue), or show no history of GD or HGT (black). Note that none of the EC numbers in our dataset were affected by HGT alone. Pathway map created using iPATH2.0 [95].