Transcriptomic analysis of blackberry plant (Rubus spp.) reveals a comprehensive metabolic network involved in fruit ripening process

Blackberry (Rubus spp.) fruit, contains high levels of anthocyanins in the pulp, is a good source of antioxidants. However, the molecular mechanisms underlying anthocyanin accumulation remains elusive. To improve our understanding of this process, we used RNA-seq to evaluate the transcriptional regulation of plant secondary metabolites, especially anthocyanin biosynthesis during fruit ripening. We constructed nine sequencing libraries, obtained 7.7 Gb clean bases and identified 50,563 annotated unigenes. Comparative transcriptome analysis revealed that 11,136, 33,268, and 31,913 genes were differentially expressed at Green vs. Red, Green vs. Black, and Red vs. Black, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment revealed that 35, 47, and 47 pathways were significantly enriched from these genes, respectively. We identified 58, 18, 24 and 48 differentially expressed genes (DEGs) involved in the anthocyanin biosynthesis, sucrose metabolism, abscisic acid (ABA), and ethylene (ETH) biosynthesis, respectively. Moreover, 66 DEGs of MYB were also identified in blackberry fruit. 24 DEGs from anthocyanin biosynthesis pathway and two DEGs of MYB were positively correlated with anthocyanin accumulation. Six DEGs of sucrose, six DEGs of ABA and seven DEGs of ETH were changed concomitantly with sucrose, ABA and ETH production. This study will provide an important information for understanding the molecular mechanism of anthocyanin accumulation during fruit ripening and a reference for related studies.