Genome-Wide Identification and Analysis of the PHD Family Members in Gossypium tomentosum and Their Potential Roles in Response to Abiotic Stress

Plant homeobox domain (PHD) proteins are a class of zinc-finger proteins that play pivotal regulatory roles in plant responses to environmental stresses. Research on the identification and analysis of PHDs in Gossypium tomentosum (G. tomentosum) remains limited. The present study conducted a genome-wide analysis of the PHD members in G. tomentosum and examined their properties and functions. A total of 71 PHDs have been identified, designated as GtPHD1–GtPHD71, through a combination of profile HMM-based searches, BLAST searches, and canonical features of PHD domains. Multiple sequence alignment of the G. tomentosum PHD domains revealed a characteristic signature: X(0,1)-C-X(1,2)-C-X(6,12)-[VLI]-X-C-X(0,2)-[DPK]-X(1,2)-C-X(4,5)-H-X2-C-X(9,18)-[YWF]-X-C-X2-C. A comprehensive investigation encompassing RT–qPCR, promoter analysis, and transcription factor analysis concluded that G. tomentosum PHDs likely play critical regulatory roles in response to abiotic stresses, including drought, hypoxia, and low temperature.