Comparative transcriptome analysis of lingonberry (Vaccinium vitis-idaea) provides insights into genes associated with flavonoids metabolism during fruit development

Because the genomic information of lingonberry (Vaccinium vitis-idaea L.) is not available, the mechanism underlying the flavonoid metabolism in the fruits of this species is still unknown. The objective of this study was to obtain a comprehensive transcriptome assembly during lingonberry fruit development and characterize the key genes associated with the flavonoid metabolism in lingonberry. Our transcriptome data of lingonberry was obtained with next-generation sequencing technology. The expression patterns of key genes were analysed by quantitative reverse transcription polymerase chain reaction (qRT-PCR). The results showed that the total flavonoid content and the total anthocyanin content gradually increased during the lingonberry fruit development process. In total, about 169 million sequencing raw reads were obtained and de novo assembled into 67,836 unigenes, and 38,460 unigenes had been annotated from public databases. The average size of unigenes was 1040 nt, and the N50 value was 1718 nt. Among the unigenes mapped to KEGG pathways, 2697 (10.95%) were assigned to the category of ‘Biosynthesis of secondary metabolites’, 1533 unigenes were predicted to be associated with flavonoid biosynthesis, transport and regulation. We also found 10,022 candidate genes expressed differentially between green and white fruits, with 5335 differentially expressed genes uncovered between white and red fruits and 14,364 ones between green and red fruits. A comprehensive transcriptome assembly of lingonberry was generated, with data representing gene expression profiles throughout fruit development and ripening processes in lingonberry. Our results provide further insights into the molecular mechanisms of flavonoid metabolism.