Genome-wide identification and expression analysis of the PHD-finger gene family in Solanum tuberosum

Plant homeodomain (PHD) proteins are prevalent in eukaryotes and play important roles in plant growth, development and abiotic stress response. In this study, the comprehensive study of the PHD family (StPHD) was performed in potato (Solanum tuberosum L.). Seventy-two PHD genes (named StPHD1-72) were identified and grouped into 10 subfamilies based on phylogenetic analysis. Similar structure organizations were found within each subfamily according to the exon/intron structures and protein motif analysis. These genes were unequally scattered on the chromosomes of potato, with 9 pairs of segmental duplicated genes and 6 pairs of tandem duplicated genes showing that both segmental duplicated and tandem duplicated events contributed to the expansion of the potato PHD family. The gene ontology (GO) analysis suggests that StPHD mainly functioned at the intracellular level and was involved in various binding, metabolic and regulation processes. The analysis of expression patterns of StPHD genes showed that these genes were differentially expressed in 10 different tissues and responded specifically to heat, salt and drought stress based on the FPKM (Fragments per kilobase of transcript per million mapped reads) values of the RNA-seq data. Furthermore, the real-time quantitative PCR for 12 selected StPHD genes revealed the various levels of gene expression corresponding to abiotic stress. Our results provide useful information for a better understanding of PHD genes and provide the foundation for additional functional exploration of the potato PHD gene family.