Transcriptomic analysis of Salvia miltiorrhiza hairy roots in response to smoke-isolated karrikinolide (KAR1) using RNA-seq

Abstract

• KAR 1 might participated in the biosynthesis of phenylpropanoid by up-regulating genes involved in relative pathway in S. miltiorrhiza hairy roots. • The expression of 4CL, C4H, TAT, HPPR and RAS genes in S. miltiorrhiza hairy roots were up-regulated by treatment with KAR 1 , indicating that the salvianolic acids synthesis pathway was activated. • The genes related to the salvianolic acids biosynthesis were regulated by KAR 1 in S. miltiorrhiza hairy roots. The effect of karrikinolide (KAR 1 ) on the salvianolic acid biosynthesis in hairy roots of Salvia miltiorrhiza has been studied by applying transcriptomics technology. Application of Illumina RNA-seq provides insights into the transcriptome profiles 0, 24 and 48 h after treatment with KAR 1 . The transcriptome was assembled with Trinity software, producing 138,993 unigenes with an average length of 1711 bp and an N50 value of 2523 bp. These included generous secondary metabolite biosynthesis and genes defense-related. Our investigations indicated significant differences in the responses of S. miltiorrhiza to KAR 1 treatment. A total of 9411 and 9406 significant differentially expressed genes (DEGs) were respectively identified by treatment with KAR 1 at 24 and 48 h. Among these DEGs, 865 DEGs (24 h) and 596 DEGs (48 h) were respectively classified into KEGG pathways. The result indicated that a significant number of these DEGs were enriched in phenylpropanoid biosynthesis. The expression of most glycosylsis-, glycosyltransferase-related genes were largely induced by KAR 1 . Furthermore, the genes that participated in biosynthesis of salvianolic acids were up-regulated after KAR 1 treatment, including 4-coumaric acid CoA-ligase (4CL, 2 genes), phenylalanine ammonia-lyase (PAL, 3 genes), tyrosine aminotransferase (TAT, 5 genes), 4-hydroxyphenylpyruvate reductase (HPPR, 7 genes), rosmarinic acid synthase (RAS, 18 genes) and cinnamic acid 4-hydroxylase (C4H, 24 genes). The results revealed that genes related to the salvianolic acid biosynthesis were regulated by KAR 1 in S. miltiorrhiza hairy roots. The findings provide insights into the molecular mechanism of salvianolic acid biosynthesis and a reference for the genetics research of S. miltiorrhiza next.