## 3 Discussion
### M. graminicola Express Their Core Set of Effectors  
Our comparative transcriptomic data also showed that _M. graminicola_ relies on the secretion of a set of effector proteins, in addition to CWDEs or peptidases, to establish infection within rice, whether susceptible or resistant cultivars. Effectors are produced by pathogens to facilitate parasitism and a small amount of _M. graminicola_ secreted proteins have been described [11; 12; 13; 14; 15]. Mining the _M. graminicola_ transcriptome returned eight novel candidate effectors in addition to those previously described in [PERSON] et al. [10]. Furthermore, we identified the orthologs of 12 effectors characterized in other _Meloidogyne_ species (Table S5).  
Indeed, we found that the majority of the 38 effector or candidate effector genes surveyed are expressed by pre-J2s (Figure 4). We showed that half of them have similar expression pattern in the early stages of parasitism and can be actively transcribed, whatever the host genotype. For instance, _Mg1376_ and _Mg366_, the closest _M. graminicola_ orthologs of _MgPDI_[15] and _Me-TCTP_[32], respectively, were highly expressed at all times sampled in both rice genotypes, which is consistent with their probable role in parasitism. _MgPDI_ and _Me-TCTP_ are expressed in pre-J2s esophageal glands and activated during plant infection until late developmental stages [15; 32]. _MgPDI_ encodes a disulfide isomerase probably secreted in the apoplast where it may be required for protecting the nematode from oxidative damage [15]. _Me-TCTP_ belongs to the translationally controlled tumor protein (TCTP) family and might be delivered by the nematode to the host cell cytoplasm where it is able to suppress programmed cell death and, by extension, plant immune defense responses [32]. Thus, expression of these two genes by _M. graminicola_ are probably required for counteracting some host defense reactions and protecting the nematode.  
In contrast, 16 DEGs-RvsS were identified among the 38 effectors and putatively secreted proteins surveyed (Figure 4). Like for CWDEs or peptidases, the majority of these DEGs-RvsS were expressed in pre-J2s and down-regulated in resistant plants later than in susceptible plants. This trend included several candidate effectors identified here are or previously [10], _MgGPP_[11], _Mg16820_[13] and the closest orthologs of _Mj-NULG1a_[33], _MilSE6_[35], and the chorismate mutase _Mi-CM_[34]. Like _MgPDI_ and _Me-TCTP_, _MgGPP_ is another effector that may be involved in the suppression of defense reactions of the host cell to promote parasitism [11]. Among the _M. graminicola_ genes highly expressed in pre-J2s,Mg448 encodes a C-type lectin that could also be involved in overcoming the host defenses as reported for _Mg01965_[14] and for the cyst nematode, _Heterodera glycines_[53].  
We identified here two other DEGs-RvsS whose expression profile deserved attention: _Mg44061_ was specifically expressed in resistant rice plants, only. Conversely, _Mg66296_ was not expressed at all in resistant plants and was specifically expressed at 4 dpi in the susceptible plants. No homology could be found for _Mg44061_ and _Mg66296_ in databases and both putatively encoded proteins have a predicted signal peptide for secretion. Functional analyses are required to assess the importance of these novel _M. graminicola_ pioneer genes for parasitism.