Identification and expression analysis of the WRKY gene family during different developmental stages in Lycium ruthenicum Murr. fruit

Abstract

Background The WRKY gene family, one of the major transcription factor families in plants, plays crucial regulatory roles in physiological and biological developmental processes, and the adaptation of plants to the environment. However, the systematic study of WRKY structure, expression profiling, and regulatory functions has not been extensively reported in Lycium ruthenicum, although these aspects have been comprehensively studied in most plant species. Methods In this study, the WRKY genes were identified from a L. ruthenicum transcriptome database by using bioinformatics. The identification, phylogenetic analysis, zinc-finger structures, and conserved motif prediction were extensively explored. Moreover, the expression levels of 23 selected genes with fragments per kilobase of exons per million mapped reads (FPKM) >5 were assayed during different fruit developmental stages with real-time quantitative polymerase chain reaction (RT-qPCR). Results A total of 73 putative WRKY proteins in the L. ruthenicum transcriptome database were identified and examined. Forty-four proteins with the WRKY domain were identified and divided into three major groups with several subgroups, in accordance with those in other plant species. All 44 LrWRKY proteins contained one or two conserved WRKY domains and a zinc-finger structure. Conserved motif prediction revealed conservation of the WRKY DNA-binding domain in L. ruthenicum proteins. The selected LrWRKY genes exhibited discrete expression patterns during different fruit developmental stages. Interestingly, five LrWRKYs (-20, -21, -28, -30, and -31) were expressed remarkably throughout the fruit developmental stages. Discussion Our results reveal the characteristics of the LrWRKY gene family, thus laying a foundation for further functional analysis of the WRKY family in L. ruthenicum.

Genome-Wide Analysis of Snapdragon WRKY and VQ Gene Families and Their Expression in Response to Drought and Cold Stresses

“…2). This was consistent with that the WRKYGKK variant was frequently occurred in Group IIc of plant WRKY genes [4,7,9,55,[57][58][59]. It has been showed that variation of the WRKYGQK core sequence might affect the binding ability of the WRKY transcription factor to the W-box motif [60,61].…”

Identification of WRKY gene family in Dioscorea opposita Thunb. reveals that DoWRKY71 enhanced the tolerance to cold and ABA stress

“…Multiple sequence alignment of DoWRKY proteins shows that all DoWRKY proteins except DoWRKY50 contain WRKYGQK conserved sequences. However, the members of group IIc, such as DoWRKY50, differ by one amino acid, with the glutamine (Q) being substituted by a lysine (K)to form WRKYGKK, a pattern consistent with what is observed in Lycium ruthenicum ( Tiika et al, 2020 ). It has been reported that the DNA binding activity of the N-terminal WRKY domain is not as strong as that of C-terminal, and there are more variations in the N-terminal WRKY domain ( Maeo et al, 2001 ).…”

“…WRKY transcription factors (TFs) are the seventh largest family of regulatory genes screened from higher plants ( Tiika et al, 2020 ). The name of the WRKY family is derived from their conserved WRKYGQK amino acidcore sequences in the N-terminal region.…”

Genome-wide identification of the Liriodendron chinense WRKY gene family and its diverse roles in response to multiple abiotic stress

“…To verify the accuracy of abiotic stress transcriptome data, we performed qRT-PCR experiments of 10 genes with different expression levels, including high or low expression, LchiWRKY7 and 44 were low expression (0 < Log2FC < 3) in the three stresses and other genes ( LchiWRKY5 , 18 , 19 , 25 , 27 , 33 , and 36 ) were high expression (Log2FC > 3) at different time points of the three stresses [ 38 ] (Figs. 8 , 9 and 10 ).…”