RNA-Seq analysis of gene expression changes during berry fruit development and ripening. (A) Photographs of berries exemplifying five stages of berry fruit development and ripening and the number of differentially expressed (DE) genes between adjacent stages. (B) Multi-dimensional scaling (MDS) plot of expression values from five sample types and three plants (P1-P3). Samples that are near each other in the two-dimensional space are more similar with respect to gene expression. (C) Gene expression profiles detected by clustering program Short Time-series Expression Minor (STEM). The x-axes represent stage (earlier to the left) and the y-axes represent expression level. Clusters 0 through 9 are listed in order of statistical significance, with clusters 1, 6, 2, and 0 being the most significant. (D-G) Cufflinks-predicted genes from clusters 1, 6, 2, and 0 encoding proteins similar to (D) leucoanthocyanidin reductase, (E) MYB-like transcription factor up-regulated in ripening fruit, (F) tryptophan synthase (indole-salvaging), and (G) abscisic acid signaling transcription factor ABI3, respectively. In (D-G), graphs represent the number of reads overlapping genomic positions indicated on the ‘coordinates’ axis. RNA-Seq coverage graphs from P3 (plant 3-33) are shown.