## Results and Discussion
### Regulation of Proteolysis Processes by Meloidogyne javanica  
Gene Ontology enrichment analyses showed that genes involved in primary metabolism were overrepresented among the down-regulated genes (Table S5). Protein degradation was among the significantly altered processes involved in metabolism. In this study, genes coding for various classes of proteolytic enzymes were identified as differentially expressed include cysteine proteases, aspartate proteases, AAA-type, metacaspase, metalloproteinase, subtilases, and serine proteases. The immense turnover of cellular proteins during nematode feeding can enhance a compatible nematode interaction due to regulation of plant immunity associated with proteolysis process.  
Further, we found several genes involved in ubiquitin-proteasome system (UPS), the main protein degradation pathway in a cell. Various classes of E3 ubiquitin ligases enzymes that play a central role during protein ubiquitination process were differentially expressed. This includes SKP1-CUL1-F-box-protein (SCF) and the U-box domain RING finger protein-encoding genes which were co-regulated, 102 down- and 105 genes up-regulated (Table S5). The fact that the UPS regulates degradation of many proteins in the cell affecting various cellular processes such as signal transduction, hormone signaling, and immune responses [60], makes it an attractive target for pathogen virulence factors including nematode effectors [61; 62].  
Collectively, this study uncovers the molecular networks regulated during compatible interaction between potato and _M. javanica_. Our results lay a foundation for functional studies in the future for genes highlighted to have a role in mediating susceptibility to _M. javanica_ infestation to reveal their precise role in this interaction. In addition to providing further insights on plant-mematode interactions, further studies in the area development of target-specific control strategies against _Meloidogyne_ species will originate.  
**Supplementary Materials:** The following are available online at [[http://www.mdpi.com/2076-2607/8/9/1443/s1](http://www.mdpi.com/2076-2607/8/9/1443/s1)]([http://www.mdpi.com/2076-2607/8/9/1443/s1](http://www.mdpi.com/2076-2607/8/9/1443/s1)), Table S1: List of primer used for RT-qPCR for validation of RNA-seq results; Table S2: Mapping summary of RNA-Seq reads from _Solanum tuberosum_ samples using the reference genome (v4.03); Table S3: Differentially expressed genes induced by _Meloidogyne javanica_ at 3 and 7 dpi; Table S4: Gene ontology enrichment analysis; Table S5: Differentially expressed biotic stress-related genes induced by _Meloidogyne javanica_ at 3 and 7 dpi as defined by Mapman analysis; Table 56: Classification of differentially expressed transcription factors; Figure S1: The expression profile of genes experimentally validated using real-time qPCR in response to _Meloidogyne javanica_ infestation; Figure S2: Mapman visualization of genes involved in secondary biosynthetic pathways at (A) 3 dpi and (B) 7 dpi after challenge by _Meloidogyne javanica_.  
**Author Contributions:** L.N.M. conceived, designed this study, funding acquisition, and supervision. T.N.M. set-up the experiment for nematode inoculations, analyzed and visualized data, and wrote the original draft. D.B.-R. carried out the bioinformatics work. L.N.M. and D.B.-R. revised the manuscript. All authors have read and agreed to the published version of the manuscript.  
**Funding:** This research study was funded by the National Research Foundation (NRF), South Africa through Competitive Funding for Rated Researchers (CFRR) 98993, Bioinformatics and Functional Genomics (BFG) 93685, and Potatoes South Africa (PSA). DB-R was supported by the University of Pretoria Post-Doctoral Fellowship. TM was funded by Potato South Africa and the NRF Scare Skills/Innovation Scholarships. Any findings and/or recommendations expressed here are those of the author(s) and the NRF does not accept any liability in this regard.  
**Conflicts of Interest:** The authors declare no conflict of interest.