Impact of Transposable Elements in introns on the functional annotation of C. sempervirens genes. GO term enrichment analysis.

We investigated the impact of TE in genes by comparing their functional annotation with those of the whole Cupressus genome. Among the 42,980 C. sempervirens genes, 18,257 genes are associated with at least one GO term. Among the 18,224 genes with TE in introns, a total of 8,339 genes were associated with at least one GO term. We performed a GO terms enrichment analysis using the topGO R package 2.58.0 with R 4.3.3. We considered the Molecular Function (MF) section of the GO graph structure and we used Fisher's exact statistical test based on gene count to identify the most significant GO terms. GO terms associated with at least 10 genes were kept for the analysis. In total, 210 GO terms were found significantly more frequent in genes containing TE (pvalue < 0.01). The same analysis was performed comparing GO terms identified for 4,300 genes with hAT transposable elements in their introns with those belonging to the whole genome genes set. We found 215 GO terms significantly more frequent in genes with hAT (pvalue < 0.01).