Comprehensive in silico analysis of Phospholipase D gene family in economically important orchids

Abstract

• A total of 25 putative PLD proteins from the genomes of Phalaenopsis equestris (7) , Dendrobium catenatum (9) and Apostasia shenzhenica (9) were identified. • These proteins are comprised of two HKD domains and two additional domains; C2 and PXPH domains at N-terminal region. • The multiple sequence alignment, domain and motifs analysis revealed their conserved nature and homology structure simulation and Ramachadran plot analysis revealed the abundance of beta sheets in tertiary structures. • The presence of Root-specific element, DOF proteins binding domain, scaffold or matrix attachment region, pollen-specific, dehydration-responsive, light-responsive, gibberellin-responsive, ABA-responsive elements and Meja-responsive upstream cis- regulatory promoter elements indicated their role in various physiological processes. Phospholipase D (PLD) plays a fundamental role in various aspects of plant growth, development and stress responses. In present study, 25 putative PLD proteins from the genomes of Phalaenopsis equestris (7) , Dendrobium catenatum (9) and Apostasia shenzhenica (9) were identified on the basis of presence of two HKD domains and two additional domains; C2 and PXPH domains at N-terminal region. These proteins were clustered into five sub-groups (α, β, δ, ζ and φ) along with their orthologs in Arabidopsis thaliana and Oryza sativa upon phylogenetic analysis. Gene characterization divulged that most of the PePLD, DcPLD and AsPLD genes within the same sub-group exhibited similar exon-intron organization and highly conserved motifs. RNA-seq based spatio-temporal studies indicated differential expression in various vegetative and reproductive tissues. PePLDα 1 , DcPLDα 1 and AsPLDα 1 were showing significant expression in all the tissues, while for other genes the expression was limited either in vegetative or reproductive tissues. Homology structure simulation revealed the abundance of random coils in secondary structures and beta sheets in tertiary structures. The presence of specific upstream cis- regulatory promoter elements emphasized the role of PLD s in various physiological processes. This report is the first genome-wide characterization of the PLD gene family in orchids and shall provide new insight into the functional characterization of these genes.