Genome-wide identification and phylogenetic and syntenic comparison were performed for the genes responsible for phenylalanine ammonia lyase (PAL) and peroxidase A (POX A) enzymes in nine plant species representing very diverse groups like legumes (Glycine max and Medicago truncatula), fruits (Vitis vinifera), cereals (Sorghum bicolor, Zea mays, and Oryza sativa), trees (Populus trichocarpa), and model dicot (Arabidopsis thaliana) and monocot (Brachypodium distachyon) species. A total of 87 and 1045 genes in PAL and POX A gene families, respectively, have been identified in these species. The phylogenetic and syntenic comparison along with motif distributions shows a high degree of conservation of PAL genes, suggesting that these genes may predate monocot/eudicot divergence. The POX A family genes, present in clusters at the subtelomeric regions of chromosomes, might be evolving and expanding with higher rate than the PAL gene family. Our analysis showed that during the expansion of POX A gene family, many groups and subgroups have evolved, resulting in a high level of functional divergence among monocots and dicots. These results will act as a first step toward the understanding of monocot/eudicot evolution and functional characterization of these gene families in the future. 1. Introduction All plant species are continuously fighting with different biotic and abiotic stresses for their existence. The stresses like harsh environmental conditions, desiccation, UV radiation, and attack of microbial pathogens may affect growth and development in the plants and sometimes lead to their death. Although all plants have different natural defense mechanisms against these stresses, in most cases, plants activate the phenylpropanoid pathway in response to pathogen attack or to elicitors [1]. In the plant phenylpropanoid pathway, phenylalanine ammonia lyase (PAL) is a key enzyme that catalyses the first step in the pathway and not only leads to the accumulation of phytoalexins [2] but also contributes in growth and development of plants and responses to biotic stresses [3, 4]. The plant peroxidase (POX) genes are heme-containing glycoproteins present in large numbers in higher plants [5]. These genes are involved in defense against pathogen infection or insect attack, and several other physiological functions such as H2O2 removal, toxic reduction, oxidation, lignification, suberization, auxin catabolism, and wound healing in plants [5, 6]. Plants contain multiple isoforms for peroxidases, which respond to stresses in different or similar ways by making POX genes
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