## Results and Discussion
### Pathogen Perception and Regulation of Defense Response Genes by Meloidogyne javancia Infestation  
Plant recognition of _M. javancia_ presence, migration, and feeding is the initial step in triggering activation of downstream signaling cascades to induce defense responses. Large arsenals of plant receptors are responsible for recognition of phytonematodes and subsequent induction of basal plant defenses [38; 39]. Eight genes encoding for membrane-localized proteins, _mildew resistance locus o (MLO)_ family protein were down-regulated at 3 and/or 7 dpi (Figure 5, Table S5). Additionally, an important group of pattern recognition receptors (PRRs) was differentially regulated with the highest proportion down-regulated (62.86% of 175 genes). These include leucine-rich repeat receptor-like protein kinase (LRR-RLK), receptor-like protein kinases (RLP), and wall-associated receptor kinases (WAKs) (Table S5) indicating the importance of PRRs in mediating plant immunity to  
Figure 5: Heat map representation of selected differentially expressed genes associated with pathogen perception (**A**). Mitogen-activated protein kinase (MAPK) signaling pathways and calcium signaling pathways (**B**). Oxidative stress (**C**). Pathogenesis-related proteins and proteinase inhibitors (**D**). (The heat map illustrates a subset of genes from each group. Refer supporting information for all differentially expressed genes in each group). M. Javanica. Among the down-regulated LRR-RLK genes were two genes encoding for BAK1-interacting receptor-like kinase 1. Further, we found an LRR-RLK encoding gene, polygalacturonase inhibiting protein 2 (_PGIP 2_) down-regulated 7-fold at 3 dpi and 4-fold at 7 dpi (Figure 5 and Table S5). In addition to suppression of a cell wall-associated kinase, plant elicitor peptides (_PEPI_ receptor, three genes) encoding genes that perceive damage-associated molecular proteins (DAMPs) were down-regulated at both 3 and 7 dpi (Figure 5 and Table S5). These results suggest that _M. Javanica_ likely interferes with DAMP-mediated immunity subduing activation defense response. Transmission of perceived signals from the PRRs is mediated through the MAPK cascade and calcium (Ca2+) signaling pathway which transfers downstream components of plant immunity. In this regard, we found the expression of MAPKs genes was largely repressed (9 out of 11 genes) by nematode infestation (Figure 5 and Table S5). Furthermore, _M. Javanica_ repressed 88% of the genes involved in Ca2+ signaling pathway (66 out of 75 genes) (Table S5). The intracellular nucleotide-binding domain leucine-rich repeat (NBS-LRR) proteins are important in recognizing PPNs effectors leading to effector-triggered immunity. The majority of these NBS-LRR proteins are a major class of disease resistance (R) proteins encoding resistance R-genes [39]. In the current study, we identified 32 genes encoding for either toll-interleukin 1 receptor (TIR) domain or coiled-coil (CC), which are the two subgroups of NBS-LRR proteins. Of these, 20 genes were down-regulated at 3 and/or 7 dpi following nematode infestation interfering with the host immune response (Figure 5 and Table S5). PTI activation is associated with expression of pathogenesis-related (PR) proteins which defense-related genes expressed upon infection by diverse pathogens including nematode pests. These PR proteins contribute to systemic acquired resistance (SAR) and are induced through the action of signaling compounds such as SA, JA, and ET [40]. Generally, we detected a delayed activation of the PR genes as the majority of the PR encoding genes were up-regulated at 7 dpi (Figure 5 and Table S5). This could reflect a strategy adopted by the _M. Javanica_ to suppress defense response associated with PR proteins at early stages of invasion to ensure successful nematode infection. However, the induction of these PR proteins at 7 dpi could have other roles in mediating a successful _M. Javanica_ infestation.