Unraveling the transcriptional regulators of polyphenolic variation in Thymus daenensis Celak

Abstract

Due to its economic value and antioxidant phenolic compositions, there is a growing interest for Thymus daenensis in the food, cosmetic, and pharmaceutical industries. The current study was motivated by the paucity of studies on the molecular regulation of polyphenols and flavonoids in T. daenensis. From breeding materials, we selected and explored the transcriptome profiles of two chemotypes (‘Zagheh-11’ and ‘Malayer-21’). Tandem mass spectrometry identified 14 phenolic and flavonoid compounds in T. daenensis. Quantitative HPLC-PDA also revealed that ‘Zagheh-11’ contains higher amounts of flavonoids (luteolin, apigenin, kaempferol, quercetin, and catechin derivatives), while ‘Malayer-21’ was a rich source of rosmarinic acid. RNA-seq data mining indicated that 1840 unigenes have differential expression (DE) patterns between these chemotypes. Mapping of unigenes in flavonoids and phenylpropanoids pathways identified a total of 74% and 45% of structural genes, respectively. Four out of 15 DE unigenes in the aforementioned pathways played a key role in the metabolic divergence of these genotypes. RNA-seq and qRT-PCR indicated that the richness of flavonoids in ‘Zagheh-11’ was driven by higher expression of chalcone isomerase (CHI) and flavonoid 3′-hydroxlase (F3′H). In contrast, overexpression of phenylalanine ammonia lyase (PAL) and rosmarinic acid synthase (RAS) coincided with enhanced accumulation of rosmarinic acid in ‘Malayer-21’. To further understanding of these four key genes, we performed bioinformatic and structural analysis on their complete coding sequences. These findings should improve knowledge on how specialized metabolites are governed by transcriptional regulators and which are suitable for targeted metabolic engineering.