Genome-wide identification and analysis of the <i>PAL</i> genes from the orchids <i>Apostasia shenzhenica, Dendrobium catenatum</i> and <i>Phalaenopsis equestris</i>

Abstract

Phenylalanine ammonia-lyase (PAL) is a key gateway enzyme that connects the phenylpropanoid pathway to primary metabolism. The phenylpropanoid pathway plays a vital role in the growth and environmental adaptation of many plants leading to the production of valuable bioactive compounds with industrial and medical applications. In the present study, nine putative <i>PAL</i> genes from three orchids were identified; five in <i>Apostasia shenzhenica</i> and two each in <i>Dendrobium catenatum</i> and <i>Phalaenopsis equestris</i>. Eighteen motifs and four major conserved functional domains were identified as reported in PAL proteins of other species. All the nine PALs were stable based on their computed physicochemical properties and localized in the cytoplasm. The three-dimensional structures of PALs revealed a homo-tetrameric structure consisting of four identical subunits. A total of 21 cis-regulatory elements with known functions were identified from the promoter regions of all PALs which are responsible for various plant responses to light, stress and growth regulators like auxins, gibberellins and abscisic acid. Phylogenetic analysis showed that the studied PAL proteins clustered in two major clades (clade I and II), placing dicot and monocot PALs in two separate monophyletic clades. <i>In silico</i> gene expression of the identified <i>PALs</i> in different vegetative and reproductive tissues revealed the differential expressions based on tissue type and disclosed that the expression of <i>PAL</i> genes was upregulated in all the tissues examined with an exception of <i>PePAL</i> leaf samples where no expression was detected, however, the same being highly expressed in reproductive tissues (<i>PePAL1</i>-labellum; <i>PePAL2</i>-sepal). In case of <i>AsPALs</i>, the expression was found to be highest in reproductive tissues (<i>AsPAL</i>4-maximum in inflorescence). On the other hand, the expression of <i>DcPALs</i> was found to be highest in vegetative tissues (<i>DcPAL2-</i>maximum in root). Based on the medicinal importance of orchids and the significant role of <i>PAL</i> genes in synthesis of bioactive compounds, the functional characterization of <i>PAL</i> genes can be further exploited in genetic improvement of medicinal orchids.Communicated by Ramaswamy H. Sarma.