Fig. 2

Analysis of global patterns in the proteomics dataset and comparison with related transcriptomic data. a Gene Ontology analysis of the 1163 proteins assessed indicated that this set was enriched in carboxylic acid metabolism, intracellular transport, and to a lesser extent in protein folding. b Expression levels from 18,074 genes from the “Fantasia” variety were assessed at 41, 54, 69, 83, 111 and 125 (ripe fruit) days after full bloom (DAFB). The analysis indicated that 31.7% of the genes did not display any change when comparing each developmental stage against ripe fruit, 14.6% displayed its highest level and 14.1% its lowest level at ripe fruit stage (black bars, first, second and third lane, respectively). When assessing the protein-coding genes detected in mature + ripe fruit (present study), it was estimated that 5.9% did not display any change when comparing each developmental stage against ripe fruit, 25.8% displayed its highest level and 17.6% displayed its lowest level at ripe fruit stage (grey bars, first, second and third lane, respectively). The last two analyses in ripe fruit yielded statistically significant results. c Expression levels from 20,149 genes of the “Babygold” variety were assessed in leaves, immature and ripe fruit. Genes that were more expressed in leaves compared to immature and ripe fruit tissues using the full transcriptome dataset accounted for 35.4% of the genes (black bars). This number dropped to 16.8% when using the proteomics dataset (grey bars). The same kind of comparison performed on the genes that were more expressed in the immature and ripe fruit yielded percentages of 38.3% vs 29.6 and 26.2% vs 53.7%, being the difference found in ripe fruit statistically significant