AUTHOR=Du Zhaokui , You Shixian , Zhao Xin , Xiong Lihu , Li Junmin 

TITLE=Genome-Wide Identification of WRKY Genes and Their Responses to Chilling Stress in Kandelia obovata

JOURNAL=Frontiers in Genetics

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2022.875316

DOI=10.3389/fgene.2022.875316

ISSN=1664-8021

ABSTRACT=<p><bold>Background:</bold><italic>Kandelia obovata</italic>, a dominant mangrove species, is widely distributed in tropical and subtropical areas. Low temperature is the major abiotic stress that seriously limits the survival and growth of mangroves. WRKY transcription factors (TFs) play vital roles in responses to biotic and abiotic stresses. However, genome-wide analysis of <italic>WRKY</italic> genes in <italic>K. obovata</italic> and their responses to chilling stress have not been reported.</p><p><bold>Methods:</bold> Bioinformatic analysis was used to identify and characterize the <italic>K. obovata WRKY</italic> (<italic>KoWRKY</italic>) gene family, RNA-seq and qRT–PCR analyses were employed to screen <italic>KoWRKYs</italic> that respond to chilling stress.</p><p><bold>Results:</bold> Sixty-four <italic>KoWRKYs</italic> were identified and they were unevenly distributed across all 18 <italic>K. obovata</italic> chromosomes. Many orthologous <italic>WRKY</italic> gene pairs were identified between <italic>Arabidopsis thaliana</italic> and <italic>K. obovata</italic>, showing high synteny between the two genomes. Segmental duplication events were found to be the major force driving the expansion for the <italic>KoWRKY</italic> gene family. Most of the <italic>KoWRKY</italic> genes contained several kinds of hormone- and stress-responsive <italic>cis</italic>-elements in their promoter. KoWRKY proteins belonged to three groups (I, II, III) according to their conserved WRKY domains and zinc-finger structure. Expression patterns derived from the RNA-seq and qRT–PCR analyses revealed that 9 <italic>KoWRKY</italic>s were significantly upregulated during chilling acclimation in the leaves. KEGG pathway enrichment analysis showed that the target genes of KoWRKYs were significantly involved in 11 pathways, and coexpression network analysis showed that 315 coexpressed pairs (<italic>KoWRKYs</italic> and mRNAs) were positively correlated.</p><p><bold>Conclusion:</bold> Sixty-four <italic>KoWRKYs</italic> from the <italic>K. obovata</italic> genome were identified, 9 of which exhibited chilling stress-induced expression patterns. These genes represent candidates for future functional analysis of <italic>KoWRKYs</italic> involved in chilling stress related signaling pathways in <italic>K. obovata</italic>. Our results provide a basis for further analysis of <italic>KoWRKY</italic> genes to determine their functions and molecular mechanisms in <italic>K. obovata</italic> in response to chilling stress.</p>