Homeodomain leucine zipper (HD-ZIP) gene family in Apostasia shenzhenica Z. J. Liu & L. J. Chen (Orchidaceae): In silico identification and characterization

Abstract

The homeodomain leucine zipper (HD-ZIP) gene family constitutes an important class of transcription factors found in plants that play crucial roles in various aspects of growth, development and stress regulation. Despite this, there have been minuscule reports on identification and characterization of HD-ZIP gene family in orchids. The present study identifies 31 putative genes (AsHD-ZIP) in Apostasia shenzhenica, using in silico approaches. All of the identified transcription factors were grouped into four subfamilies (HD-ZIP I to IV) based on the distribution of various conserved domains and motifs i.e., HD-ZIP I (homeodomain and leucine zipper), HD-ZIP II (homeodomain, leucine zipper and CPSCE), HD-ZIP III (homeodomain, leucine zipper, MEKHLA and START) and HD-ZIP IV (homeodomain, leucine zipper and START). Prediction of physicochemical properties, protein structures, protein-protein interactions, gene ontology, and gene structures further validated this classification. Phylogenetic analysis showed clustering of all subgroups separately along with their orthologs in Arabidopsis thaliana, Oryza sativa, Dendrobium catenatum and Phalaenopsis equestris. Furthermore, spatio-temporal expression profiling and presence of cis-regulatory elements confirmed tissue specific expression. As HD-ZIP genes are vital players in regulation of plant growth and development as well as in biotic and abiotic stress responses, this study provides a foundation for genetic improvement in orchids through functional validation and characterization of HD-ZIP gene family.