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Background   Lycium barbarum  and  L. ruthenicum  have been used as traditional medicinal plants in China and other Asian counties for centuries. However, the molecular mechanisms underlying fruit development and ripening, as well as the associated production of medicinal and nutritional components, have been little explored in these two species.    Results  A competitive transcriptome analysis was performed to identify the regulators and pathways involved in the fruit ripening of red wolfberry ( L. barbarum ) and black wolfberry ( L. ruthenicum ) using an Illumina sequencing platform. In total, 155,606 genes and 194,385 genes were detected in red wolfberry (RF) and black wolfberry (BF), respectively. Of them, 20,335, 24,469, and 21,056 genes were differentially expressed at three different developmental stages in BF and RF. Functional categorization of the differentially expressed genes revealed that phenylpropanoid biosynthesis, flavonoid biosynthesis, anthocyanin biosynthesis, and sugar metabolism were the most differentially regulated processes during fruit development and ripening in the RF and BF. Furthermore, we also identified 38 MYB transcription factor-encoding genes that were differentially expressed during black wolfberry fruit development. Overexpression of  LrMYB1  resulted in the activation of structural genes for flavonoid biosynthesis and led to an increase in flavonoid content, suggesting that the candidate genes identified in this RNA-seq analysis are credible and might offer important utility.    Conclusion  This study provides novel insights into the molecular mechanism of  Lycium  fruit development and ripening and will be of value to novel gene discovery and functional genomic studies.

bmc genomics

Comparative transcriptome analysis of two contrasting wolfberry genotypes during fruit development and ripening and characterization of the LrMYB1 transcription factor that regulates flavonoid biosynthesis