## Results and Discussion  
Analysis of Meloidogyne javanica Infestation and Functional Annotation of Differentially Expressed Genes  
To establish whether _Solanum tuberosum_ cv. Mondial is susceptible or tolerant to _M. javanica_, five-week-old potato plants were inoculated with 1000 J2s eggs and the control mock-inoculated with sterile water. At eight weeks post-inoculation, the results showed that _S. tuberosum_ cv. Mondial plants infested with _M. javanica_ have a reproduction factor (Rf \(>\) 1) of 3.11 and galling index of 5 (Figure 1A). Based on the GI (\(>\)100 per root system) _S. tuberosum_ cv. Mondial potato cultivar was classified as highly susceptible. Figure 1B,C illustrate mature galls at eight weeks after inoculation exhibited either as single or egg masses, confirming _M. javanica_ infectivity and ability to reproduce and complete their life cycle on this potato cultivar. To understand the molecular basis of this compatible interaction between _M. javanica_ and _S. tuberosum_ cv. Mondial, RNA sequencing was performed at two infestation stages: 3 and 7 dpi. These time points correspond to nematode stages of induction of feeding sites at 3 dpi and nutrient acquisition stage that starts from 7 dpi to 8 weeks after infestation [5]. Approximately 1.3 billion paired-end reads were generated yielding an average of 23 million high-quality reads for individual samples. Successfully mapped reads onto the _S. tuberosum_ reference genome (v4.03) [26] accounted for 78-86% of the total number of reads generated per sample (Table S2). Log\({}_{2}\) fold change \(\geq\)\(\pm\)1 and adjusted \(p\)-value (FDR) \(<\) 0.05 were used as cut off values to obtain DEGs through pairwise comparison between the mock-inoculated and infested samples at 3 and 7 dpi. Overall, 4948 genes were differentially expressed at 3 dpi. Of these, 2867 were down-regulated and 2081 up-regulated. At 7 dpi, fewer genes (4484) were differentially expressed compared to 3 dpi. The number of down-regulated genes at 7 dpi (2871) wassimilar to that observed at 3 dpi (2867); however, there were 22% fewer genes up-regulated at 7 dpi compared to those at 3 dpi (Figure 2A and Table S3). Collectively, 3108 genes were differentially regulated at both 3 and 7 dpi: 2069 down- and 1022 up-regulated. For both time points, a total of 3652 out of 6324 (57.75%) of the DEGs were down-regulated compared to only 42.25% which were up-regulated (Figure 2A,B and Table S3). Figure 1: Responses of _Solanum tuberosum_ cv. Mondial potato cultivar to _Meloidogyne javanica_ infestation. (**A**) Reproductive factor and the number of galls induced by _Meloidogyne javanica_ (**B**) and (**C**) displays nematode damage on potato roots, the egg masses stained pink and a mature gall, respectively. Figure 2: Schematic representation of differentially expressed genes in potato roots following _Meloidogyne javanica_ infestation (**A**) Number of differentially expressed genes detected at 3 and 7 dpi compared to the mock-inoculated samples. ‘Down’ designates down-regulated genes. ‘Up’ designates up-regulated genes. (**B**) Venn diagram of the distribution of differentially expressed genes between 3 and 7 dpi. Yellow and blue ovals represent up-regulated and down-regulated differentially expressed genes at 3 dpi, respectively. [PERSON] and green ovals indicate the genes up-regulated and down-regulated at 7 dpi, respectively. One possible explanation of this scenario is that down-regulation of genes might be essential for proper formation of galls induced by RKN as reported previously by [PERSON] et al. (2018). Secondly, as an obligate biotroph, _M. javanica_ establishes an intricate relationship with its host; therefore, a larger suppression of defense-related genes is also plausible. GO enrichment analyses revealed the main regulatory trends in root tissues in response to _M. javanica_ infestation. The GO terms were grouped into three main functional categories at adjusted _p_-value < 0.05 and categorized using WEGO software ([PERSON] et al., 2018).