Phylogenetic and Structural Analysis of WRKY Genes in Weeping Forsythia

A phylogenetic tree using the neighbor-joining (NJ) method (Jones et al. 1992 (link)) was constructed using the obtained amino acid sequences. The NJ tree was constructed using MEGA 7.0 (Kumar et al., 2016 (link)) with the Poisson model, the pairwise deletion option, and 1,000 bootstrap resampling times. Finally, the phylogenetic tree was visualized using FigTree v1.4.4 (Rambaut 2009 ). TBtools (Chen et al. 2020a (link)) was used to visualize the introns and exons of all WRKY genes of weeping forsythia. The online database of MEME (https://meme-suite.org/meme/tools/meme, Bailey et al., 2009 (link)) was used to analyze the protein domains and conserved motifs of all WRKY genes in weeping forsythia. The analysis value of conserved motifs was set to 10, and the protein domains of WRKY family in weeping forsythia were visualized by TBtools (Chen et al. 2020a (link)). TBtools (Chen et al. 2020a (link)) was further used to extract the upstream 2 Kb sequence information of WRKY genes in weeping forsythia, and the online software PlantCARE (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/; Thijs et al., 2002 (link)) was predicted the possible cis-acting elements of WRKY genes, and the predicted results were visualized by TBtools (Chen et al. 2020a (link)).

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Yang Y.L., Cushman S.A., Wang S.C., Wang F., Li Q., Liu H.L, & Li Y. (2023). Genome-wide investigation of the WRKY transcription factor gene family in weeping forsythia: expression profile and cold and drought stress responses. Genetica, 151(2), 153-165.

Publication 2023

Amino acid sequences Deletion Exons Forsythia Genes Genes elements Introns Protein domains Tree

Corresponding Organization : Inner Mongolia Normal University

Other organizations : Henan Agricultural University, Northern Arizona University

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Variable analysis

independent variables

Amino acid sequences used to construct the phylogenetic tree

dependent variables

Phylogenetic tree constructed using the neighbor-joining (NJ) method

control variables

Poisson model
Pairwise deletion option
1,000 bootstrap resampling times

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