## 2 Results
### M. graminicola Genes Encoding Putative Effectors  
Among nematode molecules involved in host parasitism, several effector proteins others than CWDEs are secreted during infection. In the _M. graminicola_ Mg_v2 transcriptome, 18 other transcripts encoding predicted secreted proteins (i.e., with a signal peptide and absence of a transmembrane domain) were evidenced as \"DEGs-RvsS\" (Tables S3 and S5). In addition, we searched for already known _M. graminicola_ effectors and sequences homologs to _Meloidogyne_ effectors that were lacking a detectable signal peptide in our dataset (Table S5). We verified that most of these genes were present in the _M. graminicola_ draft genome even if they were not systematically identified as coding sequences (Table S5). Depending on effector gene, expression varied along time or stages, except _Mg1376_ and _Mg366_, the closest _M. graminicola_ orthologs of _MgPDI_[15] and _Me-TCTP_[32], respectively, which were highly expressed in all stages sampled (Figure 4, Table S5). The majority (78%) of the 38 genes surveyed are expressed by pre-J2s (Log2 CPM > 1) and more than half (22 of 38) had similar expression pattern in the early stages of parasitism whatever the host genotype (Figure 4). The 16 other effectors or putatively secreted proteins surveyed were classified DEGs-RvsS.  
Among _M. graminicola_ effectors or candidate effectors, _Mg44061_ (unknown function) was specifically expressed in resistant rice plants at 4 and 8 dpi. Conversely, _Mg66296_ (unknown function) was not expressed at all in resistant plants, and only detected at 4 dpi in susceptible rice. _Mg707_ and _Mg11937_, both encoding a venom allergen-like protein (VAP), were significantly up-regulated in resistant plants at 4 and 8 dpi. Expression of _Mg711_ (transthyrethin-like), _Mg1467_ (similar to _MgGPP_[11]), _Mg1071_ (lysozyme), _Mg39_ (similar to _Mg16820_[13]), _Mg448_ (C-type lectin), _Mg757_, _Mg233_, _Mg32557_ and _Mg4471_ (unknown functions) were similar in pre-J2s and 2 dpi and decreased later, but to a lesser extent in resistant plants compared to susceptible plants.  
Figure 4: Schematic representation of the gene expression patterns of 38 _Meloidogyne gruminicola_ genes encoding candidate effectors or homologs of _Meloidogyne_ effectors [10; 11; 12; 13; 14; 15; 16; 17; 18; 19; 20; 21; 22; 23; 24; 25; 26; 27; 28; 29; 30; 31; 32; 33; 34; 35; 36; 37; 38; 39; 40; 41; 42; 43; 44]. Each row represents a gene and each column represents a stage of nematode development (J2: pre-parasitic J2s, Nip: in susceptible rice plants, Tog: in resistant rice plants) either at 2, 4 or 8 dpi. The last column indicates if the gene was identified as a differentially expressed gene (DEG). The color key of the heatmap is given on the top of the figure. Values are expressed as Log2 of normalized Counts Per Million (CPM).  
Regarding the putative homologs of 12 virulence effectors characterized in other _Meloidogyne_ species, the majority shared the same expression patterns during infection of resistant or susceptible rice plants (\"DEG-across\" or no alteration of their expression), except _Mg1167_ (homology with _Mj-NULG1a_, [33]) which was down-regulated in susceptible plants, _Mg95_ (homology with _Mi-CM_, [34]) and _Mg709_ (homology with _MilSE6_, [35]) that were down-regulated in resistant plants later than in susceptible plants.  
In addition to _Mg92_ and _Mg448_, encoding proteins with a C-type lectin domain, we identified 6 other genes encoding proteins with a C-type lectin domain and a signal peptide for secretion which were highly expressed in pre-J2s and also down-regulated in resistant plants later than in susceptible plants (Table S3).