Genome-wide identification and expression analysis of WRKY transcription factor family members in seashore paspalum under salt stress
Xuanyang Wu, Zicheng Tian, Ting Wang, Xiaochen Hu, Qi Sun, Yuzhu Wang, Wen-Jie Lu, Zhanfeng Ren, Jingyu Qi, Xueli Wu
Abstract
Although WRKY transcription factors (TFs) are established key regulators of plant stress responses, their contributions to highly salt-tolerant halophytes remain poorly understood. This study presents the first comprehensive genome-wide characterization of the WRKY gene family in the exceptionally salt-tolerant halophyte, seashore paspalum (<italic>Paspalum vaginatum</italic>). Using HMM profile searches and conserved domain analysis, 126 nonredundant PvWRKY sequences were identified. These were subsequently classified phylogenetically by comparison to Arabidopsis orthologs into established groups: Group I (n = 22), Group II (n = 58, subgroups IIa-IIe), and Group III (n = 46). Protein characterization revealed unstable hydrophilic PvWRKYs predominantly localized to the nucleus (84.92%), consistent with their transcriptional regulatory roles. Promoter <italic>cis</italic>-element analysis identified enrichment in stress-responsive motifs, with ABA-responsive elements (ABRE; present in 116 genes) and MeJA-responsive elements (detected in 115 genes), highlighting hormonal integration in salt adaptation. Intraspecific collinearity and tandem duplication events on chromosomes 2, 3, 5, and 9 suggested evolutionary expansion via gene duplication. Transcriptome and quantitative reverse transcription (qRT-PCR) analyses revealed spatiotemporal expression dynamics under salt stress: <italic>PvWRKY105/117/126</italic> exhibited root-specific upregulation during prolonged stress, whereas <italic>PvWRKY84/58/90</italic> were leaf-predominant responders. Functional annotation (GO) linked <italic>PvWRKY</italic>s to root development (GO:0048364), oxidative stress response, and MAPK signaling, with protein-protein interaction (PPI) networks identifying <italic>PvWRKY52</italic> as a central hub interacting with key stress regulators (MKS1, MPK3/MPK4). Additionally, <italic>PvWRKY123</italic> showed ABA signaling synergism via ABI4/ABI5 interactions, while <italic>PvWRKY86</italic> was associated with SUMOylation-mediated regulation through BZIP8 and SUMO1. This genome-wide exploration of the WRKY family in seashore paspalum emphasizes its regulatory potential in salt adaptation and offers a foundation for future functional analyses.