Figure 3

Differential gene expression and over-represented GO terms between the gametophyte and the sporophyte transcriptomes. (a) Quantification of gametophytic-gametophytic, gametophytic-sporophytic and sporophytic-sporophytic overlaps of transcriptome profiles. Four-way Venn diagram showing all 15 possible overlaps between four independent transcriptome datasets. For each sample, the total number of expressed genes is given in parentheses, together with the total number of unique probes harboured on the array (Whole array). The 9,174 probes were not reliably expressed in any tissue. (b) Volcano plot showing pairwise analysis of differentially expressed genes computed through statistical t-test of the normalized data. The plot shows differences between the means of the two analysed samples on the x-axis and -log₁₀ p-values on the y-axis. Probe sets that passed the set criteria (see Materials and Methods section) are highlighted in red (differentially expressed genes), and blue spots represent total probe population. (c) Summary of differentially expressed genes following two-way comparison. (d) Relative percentage of genes of selected GO categories that were significantly over-represented between the sporophyte and gametophyte transcriptomes. (e) Over-represented GO terms of MPG- and PT4-enriched genes not expressed in any sporophytic tissue analyzed. Asterisks indicate GO categories that were significantly different (p < 0.05).