Transcriptome profiling reveals metabolic alteration in Andrographis paniculata in response to continuous cropping

Abstract Andrographis paniculata (Burm. f.) Nees is one of the most important economic crops for its various medicinal properties, which has been widely used as medicinal herb in several folk medicine systems all over the world. A. paniculata suffers from continuous cropping problem in cultivation; however, effects of continuous cropping on A. paniculata and the underlying mechanism at molecular level are rarely understood. In this study, Illumina paired-end RNA-seq was performed for de novo transcriptome construction of A. paniculata leaf with or without 2-years continuous cropping, to identify gene expression in response to continuous cropping stress. A total of 43,683 Unigenes were obtained by de novo assembly of 231.53 million paired-end clean reads. RNA-seq based gene expression profiling showed a total of 6193 Unigenes was significantly up-/down-regulated after continuous cropping. Integrating the GO and KEGG enrichment analysis of differentially expressed genes (DEGs) revealed that A. paniculata could alter enzyme genes expression to adjust the complicated metabolic pathways to tolerate the continuous cropping stress. Specially, accorded with the downtrend of active component contents in A. paniculata , majority of genes involved in the terpenoids biosynthesis, phenylpropanoid biosynthesis and flavonoids biosynthesis pathways were down-regulated, indicating that continuous cropping led to a declined synthesis of active ingredients through repressing the expression levels of genes involved in these metabolites’ biosynthesis pathways. The transcriptome profiling will deepen the understanding of A. paniculata under continuous cropping stress at transcriptional level, and provide useful genomic resource for further interpretation on the regulation mechanism.