Genome-wide identification, characterization, and expression patterns of the PHD-Finger Family Genes in Wheat (Triticum aestivum L.): Molecular evolution and expression profiles during different stresses

Abstract The Plant homeodomain (PHD) transcription factors (TFs) are a class of proteins with conserved Cys4-His-Cys3 domains that play important roles in plant growth and development and in response to abiotic stresses. Although characterization of PHDs have been performed in plants, little is known about their function in wheat (Triticum aestivum), especially under stress conditions. This study, 244 TaPHDs were identified in wheat using the comparative genomics method. we renamed them TaPHD1-244 on their chromosomal distribution and almost all PHD proteins are located in the nucleus. According to the un-rooted neighbor joining phylogenetic tree, gene structure and motif analyses, the PHD genes were divided into 4 clades. A total of 149 TaPHD gene pairs were assigned to arise from duplicate events. Furthermore, 230 gene pairs come from itself, 119, 186, 168, 7, 2 and 6 gene pairs from T. aestivum and six other species (H. vulgareto, Z. mays, O. sativa, A. thaliana, B.rapa and G. raimondii). 548 interacting protein branches were identified as involve in the protein interaction network. Tissue-specific expression pattern analysis showed that we found that TaPHDs were highly expressed in the stigma and ovary during flowering, suggesting that the TaPHD gene plays an active role in the reproductive growth of wheat. In addition, qRT-PCR results further confirmed that these TaPHD genes were involved in wheat abiotic stress response. In conclusion, our study provides a theoretical basis for deciphering the molecular functions of TaPHDs, especially in response to abiotic stress.