Genome-wide analysis of PHD family transcription factors in carrot (Daucus carota L.) reveals evolution and response to abiotic stress

The plant homeodomain (PHD)-finger proteins are universally found in eukaryotes. In animals, the structure and function of PHD-finger proteins have been well studied. The PHD family is one of the important transcription factor (TF) families that have crucial roles in different biological processes in plants. In this study, 106 putative TFs were identified from carrot based on the carrot genomic and transcriptomic sequences. According to the phylogenetic comparisons in Arabidopsis and Populus trichocarpa, the PHD proteins were distinguished into 11 groups (A–J, L). The amino acid sequence, phylogenetic tree, physical characterizations, and conserved motifs of the PHD family TFs were predicted and analyzed. The analysis on the PHD family TFs in different species revealed that the number of PHD TFs in different species had a close relationship with the evolution of plant. The expression profiles of the four selected DcPHD genes were detected in leaf, root, and stem of carrot. Gene expression appeared to be tissue-specific in carrot. To analyze the response of DcPHD genes to abiotic stress, the expression profiles of the four DcPHD genes that were selected from the subgroup I were also detected through quantitative real time-PCR under abiotic stress treatments. In carrot, the expression levels of some genes were up-regulated, whereas the others were down-regulated, such as DcPHD-I-15 under heat stress treatment at 1 h. Results show that different DcPHD genes had different relative expression levels in the same condition. In this study, we mainly introduced the progress in the research on the structure and function of PHD TFs in carrot. This study may offer rich information for in depth research on PHD factors, as well as becoming a useful reference for PHD evolutionary relationship in plants. Results provide novel insights into the stress responses of DcPHD genes and promote a better understanding of the construction and function of this gene in carrot.