## Results and Discussion
### Pathogen Perception and Regulation of Defense Response Genes by Meloidogyne javancia Infestation
For instance, we identified nine genes coding osmotin34 (PR-5), where 7 genes were up-regulated at 7 dpi (Figure 5 and Table S5). Additionally, 11 genes encoding basic chitinase and chitinase-like family protein (PR-3 and PR-4) were detected with nine genes up-regulated at 7 dpi (Figure 5 and Table S5). Rapid generation of reactive oxygen species (ROS) is one of the early PTI cellular events that trigger several defense responses such as activation of several defense genes and cell wall reinforcement [39]. In this study, respiratory burst homolog (RBOHs) and Riboflavin synthase-like superfamily which are important players in production of ROS in plants, were down-regulated both at 3 and/or 7 dpi (Figure 5 and Table S5). In a resistant tomato genotype, ROS was strongly induced in response to RKN infestation mediating the R-gene resistant response [41]. Moreover, genes coding for peroxididases (50 genes) were detected mostly down-regulated (70%) during disease development. Emerging evidence shows that RKN can utilize the host ROS scavenging system to reduce the damaging effects of oxygen species [42; 43]. Here, we detected one gene encoding for peroxiredoxin (PGSC0003 DMG401002721), the main detoxifying antioxidant enzyme in the plant-nematode interface [44], being up-regulated at both time points. Glutathione S transferase (GSTs) encoding genes were also identified in this study. The majority of these were up-regulated at both time points (of these, 19 genes out of 25 were up-regulated (Figure 5 and Table S5). The production of anti-nematode compounds in the form of secondary metabolites play a critical role in induced plant immune responses against PPNs [39]. Analysis of genes related to secondary metabolism alterations was revealed in phenylpronanids, lignin, flavonoids, isoprenoid, and phenols biosynthetic pathways (Figure S2). The three genes encoding for key enzymes (phenylalanine ammonia-lyase (_PAL_), cinnamate 4-hydroxylase (_CH4_), and 4-comarate CoA-ligase 2 (_4 CL_) essential for the synthesis of phenylpropanoids and downstream synthesis of other metabolites such as flavonoids, lignin, and SA [45] were down-regulated in this study (Table S5). Other downstream genesdetected to be differentially regulated include chalcone synthase, chalcone-flavone, and cinnamyl alcohols dehydrogenase involved in flavonoids and lignin pathway (Table S5). This can imply that nematode interacts with phenylpropanol metabolism to interfere with defense compounds that originate from this biosynthetic pathway. Further, genes encoding for enzymes involved in isoprenoid biosynthetic pathway such as hydroxymethylglutaryl-CoA synthase and hydroxy methylglutaryl CoA reductase 1 were identified with more genes detected at 7 dpi than 3 dpi. A higher proportion of these genes were largely up-regulated, 34 out of 48 genes (Table S5). Studies show that isoprenoids have various key roles in plant physiology including synthesis of key phytohormones (cytokinins, abscisic acid, gibberells, and brassinosteroids) as well as plant defense compounds [46]. Taken together, we can hypothesize that _M. javanica_ alters isoprenoid biosynthetic pathway to modulate hormone signaling which determines the outcome of plant-nematode interaction as reviewed by [PERSON] and [PERSON] [47]. Furthermore, up-regulation of genes related to secondary metabolism suggests mounting of a defense response as a result of damage caused by _M. javanica_ feeding.