Genome-wide analysis of AP2/ERF superfamily in Isatis indigotica.
10.1016/j.joim.2022.09.003
- Author:
Liang XIAO
1
,
2
;
Jun-Ze REN
3
;
Qing LI
4
;
Bin YANG
5
;
Zhen-Jiang LIU
5
;
Rui-Bing CHEN
6
;
Lei ZHANG
1
,
7
Author Information
1. Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai 200433, China
2. Medical School of Nantong University, Nantong 226001, Jiangsu Province, China.
3. Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai 200433, China.
4. Department of Pharmacy, Changzheng Hospital, Naval Medical University, Shanghai 200433, China.
5. School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China.
6. Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai 200433, China. Electronic address: rbchenstar@163.com.
7. Medical School of Nantong University, Nantong 226001, Jiangsu Province, China. Electronic address: nmu_dpb@aliyun.com.
- Publication Type:Research Support, Non-U.S. Gov't
- Keywords:
AP2/ERF;
Expression pattern;
Genome analysis;
Isatis indigotica;
Lignan biosynthesis
- MeSH:
Abscisic Acid;
Isatis/genetics*;
Multigene Family;
Phylogeny;
Homeodomain Proteins/genetics*;
Genome, Plant
- From:
Journal of Integrative Medicine
2023;21(1):77-88
- CountryChina
- Language:English
-
Abstract:
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 superfamily 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. indigotica 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 network. 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 analysis 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. indigotica, providing valuable information for further functional characterization of IiAP2/ERF genes and discovery of genetic targets for metabolic engineering.
