De novo transcriptome sequencing in Pueraria lobata to identify putative genes involved in isoflavones biosynthesis.

KEY MESSAGE: Using Illumina sequencing technology, we have generated the large-scale transcriptome sequencing data and indentified many putative genes involved in isoflavones biosynthesis in Pueraria lobata. Pueraria lobata, a member of the Leguminosae family, is a traditional Chinese herb which has been used since ancient times. P. lobata root has extensive clinical usages, because it contains a rich source of isoflavones, including daidzin and puerarin. However, the knowledge of isoflavone metabolism and the characterization of corresponding genes in such a pathway remain largely unknown. In this study, de novo transcriptome of P. lobata root and leaf was sequenced using the Solexa sequencing platform. Over 140 million high-quality reads were assembled into 163,625 unigenes, of which about 43.1% were aligned to the Nr protein database. Using the RPKM (reads per kilo bases per million reads) method, 3,148 unigenes were found to be upregulated, and 2,011 genes were downregulated in the leaf as compared to those in the root. Towards a further understanding of these differentially expressed genes, Gene ontology enrichment and metabolic pathway enrichment analyses were performed. Based on these results, 47 novel structural genes were identified in the biosynthesis of isoflavones. Also, 22 putative UDP glycosyltransferases and 45 O-methyltransferases unigenes were identified as the candidates most likely to be involved in the tailoring processes of isoflavonoid downstream pathway. Moreover, MYB transcription factors were analyzed, and 133 of them were found to have higher expression levels in the roots than in the leaves. In conclusion, the de novo transcriptome investigation of these unique transcripts provided an invaluable resource for the global discovery of functional genes related to isoflavones biosynthesis in P. lobata.