Genome wide analysis of transcription factors of hd-zip gene family of arabidopsis thaliana

HD-ZIP proteins are a class of transcription factors family that have a conserved homeodomain in all of its factors. Homeo box; conserved part of home domain consists of 56 amino acids residues and involved in plant development from formation pattern to specification into different cell types. We retrieved the protein sequence of all the 48 transcription factors of HD-ZIP family and performed genome wide analysis and grouped them into four subfamilies. A comprehensive genome wide analysis in this study include mapping of all the transcription factors on 5 chromosomes of Arabidopsis thaliana, gene structure analysis by mapping introns and exons, multiple sequence alignment to find out conserved domain, phylogenetic analysis, promoter analysis by taking 1000bp upstream genomic sequence of all these transcription factors and motif analysis. This classification and analysis further categorized the transcription factors of 4 HD-ZIP subfamilies into different classes and revealed a deep evolutionary relationship among them and thus help to explore further functioning of these factors. These results help us to investigate functional homology among these factors on the basis of class grouping, comparison of tree with motifs that further depends upon the number of exons and introns.