## 2 Results
### M. graminicola Transcriptome
Thus, the highest reads number in the susceptible RNA-Seq library at 8 dpi reflects a higher amount of nematode tissues in Nipponbare roots rather than a higher nematode number. Differential Gene Expression Analysis from M. graminicola Transcriptomes in Susceptible and Resistant Rice Plants  
Count files were generated from mapped reads to determine the nematode gene expression levels in each library. Using the EdgeR software, the expression of 36,121 _M. graminicola_ transcripts could be examined across all samples (see M&M). Comparative gene expression analyses were performed to identify differentially expressed genes (DEGs) either up- or down-regulated between samples. The number of nematode DEGs across time was determined in susceptible (S) and resistant (R) samples by comparing the expression of genes at 2 dpi to that in pre-J2 stage, at 4 dpi to that at 2 dpi,and at 8 dpi to the expression at 4 dpi. In total, 2531 DEGs were identified, either common to R and S plant interaction or specific to one interaction (R only, S only) (Figure 1, Table S2). Overall, the highest number of nematode DEGs across was found between 2 dpi and the pre-J2 stage with more than 700 DEGs in R and 1100 DEGs in S, including 500 common to either R or S sample. Afterwards, much fewer nematode genes were regulated along time during the infection of resistant plants than during infection of susceptible plants (78% and 71% less DEGs at 4 and 8 dpi, respectively). This result may reflect that the majority of J2s in resistant plants did not suffer much change along this period, unable to feed and develop as well as they would in the susceptible plants. The number of nematode DEGs between resistant versus susceptible plants (here named DEGs-RvsS) was determined by comparing the expression of genes in R versus S at each time-point (Figure 2, Table S3). In total, 431 DEGs were identified (312 up-regulated; 119 down-regulated) (Figure 2a), of which 367 were unique (Figure 2b). At 2 dpi, only 13 DEGs-RvsS were found (12 up- and 1 down-regulated in R compared to S). More differences in nematode gene expression occurred at 4 dpi with 119 DEGs-RvsS (103 up- and 16 down-regulated) and 8 dpi with 299 DEGs-RvsS (197 up- and 102 down-regulated). The majority of the DEGs-RvsS activated in R were already expressed by pre-J2s, but lowered or totally ceased their expression in the susceptible rice (Table S3). Conversely, all DEGs-RvsS activated in S were not expressed by pre-J2s, and not or poorly expressed in the resistant rice. An annotation was associated with 67% of the DEGs-RvsS, which allowed identifying the functional categories impacted in _M. graminicola_ metabolism or physiology. Among genes expressed without annotation (and with hit in the _M. graminicola_ genome), two genes could be interesting: _Mg851_ and _Mg1167_ were both expressed in pre-J2s and later stages sampled; however, their expression was sustained at high level in resistant plants only (Table S3). Hereafter, we focus on the DEGs putatively involved in host infection and nematode development and highlight the differences we found in nematode gene expression during infection of resistant versus susceptible plants. As a matter of comparison, we also explored some categories highlighted in [PERSON] et al. (2017). Figure 1: Number of _Meloidogyne graminicola_ Differentially Expressed Genes across (“DEGs-across”) the early infection steps of rice susceptible (S) or resistant (R) plants.