De novo transcriptome sequencing of Rhododendron molle and identification of genes involved in the biosynthesis of secondary metabolites

Abstract

Background: Rhododendron molle (Ericaceae) is a traditional Chinese medicinal plant, its flower and root have been widely used to treat rheumatism and relieve pain for thousands of years in China. Chemical studies have revealed that R. molle contains abundant secondary metabolites such as terpenoinds, flavonoids and lignans, some of which have exhibited various bioactivities including antioxidant, hypotension and analgesic activity. In spite of immense pharmaceutical importance, the mechanism underlying the biosynthesis of secondary metabolites remains unknown and the genomic information is unavailable. Results: To gain molecular insight into this plant, especially on the pharmaceutically important secondary metabolic information, we conducted deep transcriptome sequencing for R. molle flower and root using the Illumina Hiseq platform. In total, 100,603 unigenes were generated through de novo assembly with mean length of 778 bp, 57.1% of these unigenes were annotated in public databases and 17,906 of those unigenes showed significant match in the KEGG database. Unigenes involved in the biosynthesis of secondary metabolites were annotated, including the TPSs and CYPs that were potentially responsible for the biosynthesis of grayanoids. Moreover, 3,376 transcription factors and 10,828 simple sequence repeats (SSRs) were also identified. Additionally, we further performed differential gene expression (DEG) analysis of the flower and root transcriptome libraries and identified numerous genes that were specifically expressed or up-regulated in flower.Conclusions: To the best of our knowledge, this is the first time to generate and thoroughly analyze the transcriptome data of both R. molle flower and root. This study provided an important genetic resource which will shed light on elucidating various secondary metabolite biosynthetic pathways in R. molle, especially for those with medicinal value and allow for drug development in this plant.

Integrative analysis of transcriptome and metabolome reveals flavonoid biosynthesis regulation in Rhododendron pulchrum petals

“…Flavanols and anthocyanins are the main pigments in Rhododendron [22], their quantities determine the petal color ranging from light pink to violet [23][24][25][26][27][28]. At present, several studies have been done on genes and transcription factors involved in the flavonoid biosynthesis pathway in Rhododendron [29][30][31]. Rhododendron pulchrum Sweet is a species of Rhododendron belonging to the Ericaceae family and is widely cultivated in temperate Europe, Asia and North America [32].…”

Chromosome-scale genome assembly of Rhododendron molle provides insights into its evolution and terpenoid biosynthesis

“…We ligated the BTS1-ERG20 construct into the high-copy yeast expression plasmid pESC-LEU, along with tHMG1, and the recombinant plasmid pESC-LEU-(BTS1-ERG20)-tHMG1 was introduced into yeast strain IN-0 to generate strain IN-1, which was used as chassis to examine enzymatic function of the diterpene synthase. In our previous transcriptome studies of R. molle, three diterpene synthases (ID in RNA-seq: c95076, c86861 and c92044) were identified [25], corresponding to RmTPS1, RmTPS2 and RmTPS5, respectively. The full-length cDNA sequences of these genes were obtained by 5′-and 3′-RACE and cloned into the yeast expression vector pESC-URA individually or in combination.…”