Using an updated GrapeGen Affymetrix GeneChip® annotation based on grapevine 12×v1 gene predictions, 2188 differentially accumulated transcripts between flesh and skin and 2839 transcripts differentially accumulated throughout ripening in the same manner in both tissues were identified. Purple, transcripts positively determining the PC1 (PC1 score >10) green, transcripts negatively determining the PC1 (PC1 score 10) red, transcripts negatively determining the PC2 (PC2 score 10) orange, transcripts negatively determining the PC3 (PC3 score <−10).

P, pre-veraison (>15 mm) V1, 50% veraison V2, 100% veraison R1, ripe 1 R2, ripe 2.

F, Expression profile of transcripts with |PC3 loading score| >10. Transcripts most contributing to the distribution in the PC3 (|PC3 loading score| >10) are highlighted. D, Expression profile of transcripts with |PC2 loading score| >10. Transcripts most contributing to the distribution in the PC2 (|PC2 loading score| >10) are highlighted. B, Expression profile of transcripts with |PC1 loading score| >10. Transcripts most contributing to the distribution in the PC1 (|PC1 loading score| >10) are highlighted. Figure S2: PCA plot of the unique transcripts according to their expression in flesh and skin throughout ripening.