Genome-wide analysis of AP2/ERF superfamily in Isatis indigotica

Objective: AP2/ERF (APETALA2/ethylene-responsive factor) superfamily is one of the largest gene families in plants and has been reported to participate in various biological processes, such as the regulation of biosynthesis of active lignan. However, few studies have investigated the genome-wide role of the AP2/ERF superfamily in Isatis indigotica. This study establishes a complete picture of the AP2/ERF super-family in I. indigotica and contributes valuable information for further functional characterization of IiAP2/ERF genes and supports further metabolic engineering.Methods: To identify the IiAP2/ERF superfamily genes, the AP2/ERF sequences from Arabidopsis thaliana and Brassica rapa were used as query sequences in the basic local alignment search tool. Bioinformatic analyses were conducted to investigate the protein structure, motif composition, chromosome location, phylogenetic relationship, and interaction network of the IiAP2/ERF superfamily genes. The accuracy of omics data was verified by quantitative polymerase chain reaction and heatmap analyses.Results: One hundred and twenty-six putative IiAP2/ERF genes in total were identified from the I. indig-otica genome database in this study. By sequence alignment and phylogenetic analysis, the IiAP2/ERF genes were classified into 5 groups including AP2, ERF, DREB (dehydration-responsive element-binding factor), Soloist and RAV (related to abscisic acid insensitive 3/viviparous 1) subfamilies. Among which, 122 members were unevenly distributed across seven chromosomes. Sequence alignment showed that I. indigotica and A. thaliana had 30 pairs of orthologous genes, and we constructed their interaction net-work. The comprehensive analysis of gene expression pattern in different tissues suggested that these genes may play a significant role in organ growth and development of I. indigotica. Members that may regulate lignan biosynthesis in roots were also preliminarily identified. Ribonucleic acid sequencing anal-ysis revealed that the expression of 76 IiAP2/ERF genes were up-or down-regulated under salt or drought treatment, among which, 33 IiAP2/ERF genes were regulated by both stresses.Conclusion: This study undertook a genome-wide characterization of the AP2/ERF superfamily in I. indig-otica, providing valuable information for further functional characterization of IiAP2/ERF genes and dis-covery of genetic targets for metabolic engineering. Please cite this article as: Xiao L, Ren JZ, Li Q, Yang B, Liu ZJ, Chen RB, Zhang L. Genome-wide analysis of AP2/ERF superfamily in Isatis indigotica. J Integr Med. 2023; 21(1): 77-88. (c) 2022 Shanghai Yueyang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine. All rights reserved.

Automated summary

This study conducted a genome-wide analysis of the AP2/ERF superfamily in Isatis indigotica, identifying 126 related genes and analyzing their functional characteristics and expression regulation. The findings provide valuable information for further understanding the function of these genes and for metabolic engineering.