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The Genome and Development-Dependent Transcriptomes of Pyronema confluens: A Window into Fungal Evolution

Figure 6

Lineage-specific peptide lengths and gene expression.

Peptide lengths and expression of P. confluens genes from groups of genes with different levels of evolutionary conservation as indicated. A. Boxplot showing the distribution of peptide lengths (outliers left out for better visibility) with the median value as a horizontal line in the box between the first and third quartiles. Peptide length of predicted P. confluens orphan genes are smaller than those for the other groups, and from groups a to d, median peptide lengths increase with increasing conservation of genes. B. The number of genes in each group are indicated on the logarithmic y-axis to the right, and percentage of genes that are differentially regulated under any condition, and up- or down-regulated during sexual development (up or down in sex/DD and sex/vegmix, data shown for stringent expression analysis) are indicated on the y-axis to the left. The orphan genes have the highest percentage of differentially expressed genes, most of which are upregulated during sexual development. In the other groups, the portion of differentially regulated genes is smaller, and the percentage of genes upregulated during sexual development is similar or smaller than that of downregulated genes. C. Overall expression levels given in RPKM (reads per kilobase per million counted reads). For each group, RPKM values were calculated for samples sexual development (S), DD (D), and vegmix (V) as mean RPKM values of the two independent experiments. The boxplot shows the distribution with the median value as a horizontal line in the box between the first and third quartiles (outliers left out for better visibility). The small inlet shows a magnification of the RPKM values for group a (orphan genes). In this group, overall expression is lower, but the distribution of RPKM values for S is significantly different from D and V samples (p<0.01 in Kolmogorov-Smirnov-test). Within the other groups, no significantly different distribution between S, V, and D can be observed.

Figure 6

doi: https://doi.org/10.1371/journal.pgen.1003820.g006