Gene expression profiling analysis reveals a crucial gene regulating metabolism in adventitious roots of neem (Azadirachta indica)

Abstract

Neem is a widely used traditional plant containing bioactive secondary metabolites, especially azadirachtin. Neem adventitious roots (ARs) were induced on young leaf explants in Murashige and Skoog (MS) medium supplemented with 0.5 mg L⁻¹ indolyl-3-butyric (IBA). Next generation sequencing technique was used to characterize and assemble the AR and leaf explant transcriptomes. A total of 31 607 224 and 31 541 094 clean reads were obtained from ARs and leaves, respectively. Then 30 236 unigenes were clustered with an average length of 962.34 bp. Digital gene profiling revealed 1459 unigenes showing differential expression patterns compared to leaves. Additionally, we identified 112 transcripts encoding enzymes involved in terpenoid biosynthesis pathways and 552 transcripts involved in signal transduction. This report explores the characteristics of gene expression and provides new insights into the fundamental transcriptome in development and secondary metabolite biosynthesis in ARs of neem.