Analysis of WRKY Resistance Gene Family in Boehmeria nivea (L.) Gaudich: Crosstalk Mechanisms of Secondary Cell Wall Thickening and Cadmium Stress

Abstract

A total of 60 WRKY family genes of ramie were identified in the ramie. The genes were unevenly distributed across 14 chromosomes in the specie and highly concentrated (72%) in the distal telomeric region. Phylogenetic analysis placed these genes into seven distinct subfamilies groups: I, II (a, b, c, d, e), and III, with group IIc containing only the variant of heptapetide sequence (WRKYGKK). Segmental duplication events (41.7%) was found to be the main driver of BnGWRKY evolution. Thirty eight from among the genes showed collinear relationships with WRKY genes from Arabidopsis thaliana, Cannabis sativa, Oryza sativa, and Zea mays. The number and density of stress and hormone responsives cis-acting elements were comparably higher than other elements, with abundant ARE and rare LTR cis-acting elements indicating the long-standing adaptability of ramie to its natural environment. GO and KEGG enrichment analysis of the WRKY target genes revealed their involvement in response to stimuli, immune system processes, transporter protein activity and antioxidant activity. Expression analysis show that most WRKYs were activated by the cadmium stress, more especially the BnGWRKY2, BnGWRKY15, BnGWRKY20, BnGWRKY50 and BnGWRKY58. Combining transcriptome, orthologous gene relationships and qPCR result, we established the possible involvement of BnGWRKY50 and BnGWRKY58 in crosstalk mechanism between secondary cell wall thickening and Cd2+ stress. This provided information into the role of BnGWRKY proteins in ramie secondary wall development and cadmium stress response to, and could serve as basis for improvement of the ramie.

Genome-wide identification and expression analysis of WRKY gene family members in red clover (Trifolium pratense L.)

“…Investigating the expression patterns of genes in various tissues is of paramount importance for mining functional genes ( Dutta et al., 2018 ). Research has demonstrated that WRKY genes exhibit expression in one or more tissues, and they are crucial for plant growth and development ( Feng et al., 2022 ; Zhang et al., 2022b ). The evolutionary relationship between CsWRKY7 and AtWRKY7 in Camellia sinensis is closely related, and root elongation was higher in CsWRKY7 than in wild type ( Chen et al., 2019 ).…”

Comparative transcriptome analysis of major lodging resistant factors in hulless barley

“…WRKY genes play an important role in cell wall synthesis. WRKY genes are a family of transcription factors that regulate various plant processes, including stress responses, development, and secondary metabolism ( Wang et al., 2010 ; Feng et al., 2022 ). WRKY genes can affect secondary cell wall thickening by binding to the promoters of other transcription factors that activate secondary wall synthesis ( Wang et al., 2010 ).…”

Comprehensive Analysis of WUSCEL-Related Homeobox Gene Family in Ramie (Boehmeria nivea) Indicates Its Potential Role in Adventitious Root Development

“…Ramie and Arabidopsis have 11 ortholog gene pairs, against 6 between the former and rice. These conserved genes might have similar functions across different species [51]. Because gene duplication is crucial in the evolution process, gene functions, and plant diversity [52], we investigated the presence of segmental and tandem duplications in the orthologues gene pairs (Table S5).…”

“…The rate of the nonsynonymous (Ka) and synonymous (Ks) substitutions among the segmentally duplicated pairs ranged from 0.0361 (BnWOX10/14) to 1.6615 (BnWOX6A/ Maker00021031). The substitution rates were defined as Ka/Ks >1 (positive or diversifying selection), <1 (negative or purifying selection), and Ka/Ks = 1 as neutral mutation [51]. From the result (Table S5), we can deduce that all the duplicated genes have undergone purifying selection within the WOX family, except for BnWOX6A and its homolog that went through diversifying selection, which may be expected, as the homolog is not a WOX gene.…”