Journal Article

Genome-wide identification and analysis of the WRKY gene family and low-temperature stress response in Prunus sibirica

Sun, Yongqiang, Wang, Shipeng, Liu, Quangang, Wen, Jiaxing, Chen, Jianhua, Dong, Shengjun

2023

Overview

Background WRKY transcription factors are a prominent gene family in plants, playing a crucial role in various biological processes including development, metabolism, defense, differentiation, and stress response. Although the WRKY gene family has been extensively studied and analysed in numerous plant species, research on Prunus sibirica ’s WRKY genes ( PsWRKY ) remains lacking. Results This study analysed the basic physicochemical properties, phylogeny, gene structure, cis-acting elements, and Gene ontology (GO) annotation of PsWRKY gene family members using bioinformatics methods based on the whole-genome data of P. sibirica . In total, 55 WRKYs were identified in P. sibirica and were heterogeneously distributed on eight chromosomes. Based on the phylogenetic analysis, these WRKYs were classified into three major groups: Group I, Group II (II-a, II-b, II-c, II-d, II-e), and Group III. Members of different subfamilies have different cis-acting elements, conserved motifs, and intron-exon structures, indicating functional heterogeneity of the WRKY family. Prediction of subcellular localisation indicated that PsWRKYs were mainly located in the nucleus. Twenty pairs of duplicated genes were identified, and segmental duplication events may play an important role in PsWRKY gene family expansion. Analysis of the Ka/Ks ratio showed that the PsWRKY family’s homologous genes were primarily purified by selection. Additionally, GO annotation analysis showed that the WRKY gene family was mainly involved in responses to stimuli, immune system processes, and reproductive processes. Furthermore, quantitative real-time PCR (qRT-PCR) analysis showed that 23 PsWRKYs were highly expressed in one or more tissues (pistils and roots) and PsWRKYs showed specific expression patterns under different low-temperature stress conditions. Conclusions Our results provide a scientific basis for the further exploration and functional validation of WRKYs in P. sibirica .

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Abiotic stress / Agricultural research / Amino acids / Animal Genetics and Genomics / Annotations / Bioinformatics / Biological activity / Biomedical and Life Sciences / Cellular stress response / Chromosomes / Cold / Environmental aspects / Evolution / Expression patterns / Gene duplication / Gene expression / Genes / Genetic aspects / Genome-wide identification / Genomes / Genomics / Hardiness / Heterogeneity / Identification and classification / Immune system / Life Sciences / Low temperature / Low-temperature stress / Methods / Microarrays / Microbial Genetics and Genomics / Mutation / Phylogenetics / Phylogeny / Physicochemical properties / Physiological aspects / Pistils / Plant Genetics and Genomics / Plant species / Plants / Proteins / Proteomics / Prunus / Prunus sibirica / Transcription factors / Water conservation / WRKY transcription factor