Comparative transcripome data for commercial maturity and physiological maturity of 'Royal Gala' apple fruit under room temperature storage condition

- RNA-Seq analysis of “Royal Gala” apple fruits during postharvest ripening at room temperature.
- Transcriptomic differences between samples provide an overview into the molecular mechanisms underlying the postharvest ripening.
- Novel identified genes and/or transcription factors provide new clues to illuminate the complicated ripening process.

'Royal Gala' apple fruit (Malus domestica) is one of the popular apple fruit consumed world-wide. A great amount literature was accumulated for this classical apple variety about the molecular mechanisms of individual gene or gene family transcript changes during ripening, yet few of them on the large scale at transcriptomic levels. The present study was designed to use RNA-Seq to compare expression profiles between commercial ripening and physiological ripening stages of apple fruit in order to provide a deeper whole view for understanding the molecular control of 'Royal Gala' fruit ripening on transcript level. 13.78 G and 12.28 G clean reads were obtained for the commercial ripening and physiological ripening stages apple fruit, respectively acquired and were blasted against the apple genome. 78,553 genes were expressed in ripening apple fruit and among them 860 genes were differentially expressed between the two maturity stages, with 199 up-regulated and 661 down-regulated. The enrichment of differentially expressed genes (DEGs) in gene ontology (GO) pathways revealed that genes in 8 GO terms were more activated at physiological maturity stage. Meanwhile, KEGG enrichment showed that secondary metabolism contained more up-regulated DEGs at physiological maturity stage than at commercial maturity stage. Furthermore, genes working on ripening-related processes were examined. For transcription factors regulating ethylene biosynthesis such as ERFs and HBs, the expression levels were significantly different between the two samples. Regarding fruit firmness decline, expression variation happened to genes encoding enzymes involving in cell wall metabolism, such as polygalacturonase PG1, xyloglucan endotransglucosylase XTHs and EXP3, as well as cell wall structure protein gene FLA. In conclusion, the RNA-Seq data presents the global expression changes of ripening related transcripts in 'Royal Gala' apple and novel identified genes and/or transcription factors may provide new clues to illuminate this complicated event.