## Results and Discussion
### Cell Wall Organisation and Transport Processes Regulation by Meloidogyne javanica  
This study showed that genes related to cell wall synthesis, degradation, modification, and cell wall proteins were differentially expressed following nematode attack (Figure 8A and Table S6). Figure 7: Heat map representation of differential regulation of transcription factors. (**A**) Represents various families of TFs under the regulation of _Meloidogyne javanica_. (**B**) AP2/ERF family. (**C**) WRKY family. (**D**) MYB family. (**E**) DOF family (The heat map represents a subset of the differentially expressed family of TFs. Refer to supporting information for all transcription factors family displaying differential expression). In addition, genes encoding for hydrolytic enzymes involved in pectin degradation such as polygalacturonase (PG), pectate lyases (PL), and pectin esterase (PE) were differentially expressed at 3 and 7 dpi by nematode infestation (Table S5). Further, genes encoding for pectin methylesterase inhibitor (PMEI) were largely down-regulated (10 out of 12 genes) (Figure 8A and Table S5). More PMEI genes were suppressed at 7 dpi compared to 3 dpi. Repression of PMEI by nematode attack shows that the activity of PME was activated leading to the breakdown of pectin bonds, increasing the vulnerability of the cell wall to microbial pectic enzymes, and other degrading enzymes, culminating to a susceptible response. We also detected xyloglucan endotransglucose/hydrolase and expansin encoding genes, cell wall modifying enzymes under differential regulation following nematode attack. Of these, 19 out of 21 genes encoding for xyloglucan endotransglucose/hydrolase were suppressed. Two genes (PGSC0003 DMG400004670 and PGSC0003 DMG400021877) were down-regulated at 3 dpi were up-regulated at 7 dpi. Moreover, 4 genes encoding for expansin and expansin-like were precisely up-regulated at 7 dpi (Figure 8A and Table S5). Xyloglucan endotransglucose/hydrolase and expansin enzymes have cell wall loosening properties required for plant cell wall expansion during plant development. Therefore, we can hypothesis that _M. Javanica_ induces cell wall modifying enzymes at 7 dpi for expansion and enlargement of GCS a crucial event for nematode development. Further, we identified the alternation of genes related to beta-glucanase, 18 out of 29 genes down-regulated during disease progression (Figure 8A and Table S5). Plant cell wall modification, the deposition of callose a 1,3-\(\beta\) glucan cell wall polymer, is associated with cell wall thickening at the site of pathogen attack acting as a physical barrier derailing further pathogen invasion [57]. Therefore, suppression of beta-glucanase genes is probable to interfere with plant cell wall reinforcement to ward off further nematode invasion, hence successful _M. javanica_ colonization. With the increased demand for nutrients in nematode feeding cells, nematodes deploy specialized membrane transporters to control the flow of nutrients in and out of the NFS [58]. Several genes encoding for peptide transporters (31 genes), major intrinsic proteins (22 genes), amino acid transporters  
Figure 8: Heat map representation of gene expression patterns of genes associated with cell wall architecture (**A**) and transport activity (**B**). (The heat map illustrates a subset of genes from each group. Refer to supporting information for all differentially expressed genes in each group). (32 genes), metabolite transporters (27 genes), and sugar transporters (16 genes) were differentially expressed. Overall, we found that 55.29% of transporter encoding genes in the DEGs were up-regulated following nematode infestation (Figure 8B and Table S5). The activation of genes encoding amino acid transporters (17 genes) and sugar transporters (7 genes) indicates regulation of amino acid and carbohydrate metabolism, respectively. Similarly, the induction of sugar transporters increases soluble sugar content in RKN infested tomato plants, which is crucial for nematode development [59].