Genomic-wide identification and expression analysis of AP2/ERF transcription factors related to andrographolide biosynthesis in Andrographis paniculata

Abstract

Andrographolide, produced by Andrographis paniculata, is a popular “naturale antibiotics” with strong anti-inflammatory and antiviral biological activities. Knowledge of its biosynthesis has rapidly advanced since the genome sequence of Andrographis paniculata was released. However, the transcription factors (TFs) involved in andrographolide biosynthesis have rarely been investigated. Here, a genome-wide analysis of the APETALA2 (AP2)/ ethylene-responsive factor (ERF) transcription factor (TF) gene family of Andrographis paniculata was performed, including phylogenic analysis, chromosomal distribution, gene structure, conserved motifs, synteny analysis, alternative splicing events, Gene Ontology annotation, miRNA target prediction and differential gene expression analysis. In total, 111 APETALA2 (AP2)/ethylene-responsive factor (ERF) genes were identified, and phylogenetically classified into four subfamilies: APETALA2 (24 genes), Dehydration-Responsive Element Binding Proteins (34 genes), Ethylene-Responsive Factor (51 genes), and Related to ABI3/VP1 (2 genes). Genes associated with andrographolide biosynthesis were then screened according to RNA-seq data. Based on the quantitative real-time PCR (qRT-PCR) detection, coexpression analysis and binding site prediction, five AP2/ERF transcription factors were proposed to regulate andrographolide biosynthesis. These candidates belong to the Ethylene-Responsive Factor-B3 subgroup, sharing a high sequence similarity with the functional transcription factors (TFs) from other plant species. These results will be useful for the functional characterization of AP2/ERF genes in Andrographis paniculata and lay the foundation to increase andrographolide production via manipulation of the regulatory elements.