Accumulation mechanism of indigo and indirubin in Polygonum tinctorium revealed by metabolite and transcriptome analysis

The harvest time of a plant usually affects the yield of its metabolites. Polygonum tinctorium ( Polygonum tinctorium Ait., P. tinctorium ) is an important cultivated plant that produces the natural blue dye indigo and the medicinal metabolite indirubin. To explore the mechanism of indigo and indirubin accumulation, the leaves of P. tinctorium at different harvest times, namely July, August, and October, were investigated by metabolite and de novo transcriptome analyses. The results revealed that the indigo and indirubin content varied at different harvest times. Moreover, their contents were significantly higher (p < 0.05) in August than in either July or October. Transcriptome analysis showed different gene expression patterns of P. tinctorium leaves in August. Almost all the identified differentially expressed genes (DEGs) that were responsible for the biosynthesis of indigo and indirubin, including four anthranilate synthase (AS) genes, two indole-3-glycerolphosphate synthase (IGPS) genes, three tryptophan synthase (TS) genes and seven cytochrome P450 (CYP450) genes were expressed at significantly higher levels in August ( p  <  0.05), which correlated with the increase of the two compounds. Overall, the results of this study provide useful information for understanding the accumulation mechanism of indigo and indirubin in P. tinctorium , which may promote the development of agricultural breeding and industrial production of P. tinctorium. Moreover, sequence data obtained by de novo transcriptome sequencing of P. tinctorium provides a platform for future molecular biological studies.