## 2 Results  
### M. graminicola Transcriptome  
In this study, we used _M. graminicola_ RNA-Seq data retrieved from 14 (\(7\times 2\) replicates) cDNA libraries sequenced in our previous works [10; 22]. Libraries were obtained from pre-parasiticM. graminicola_ J2s, and from _O. sativa_ cv Nipponbare (susceptible) or _O. glaberrina_ TO5681 (resistant) plants challenged with _M. graminicola_. Root tips and galls, when formed, were collected at 2, 4, or 8 dpi. Time points 2, 4, and 8 dpi were chosen to focus on the early stages of the interaction, when gene expression differences may determine the nature of interaction between both partners. In our previous study, we generated a de novo _M. graminicola_ transcriptome composed of 66,396 transcripts, obtained from the pre-parasitic J2s and the susceptible libraries reads [10]. Combined Blastx results indicated that only 52% of the _M. graminicola_ sequences had similarities with recorded proteins from international databases [10], including with 14,875 (73%) of the 20,359 proteins predicted for _M. incognita_ in a first genome version [26]. Since then, a draft genome was described for _M. graminicola_, with 10,895 predicted genes [24], and the _M. incognita_ genome (third version) was much improved with 43,718 Coding DNA Sequences (CDS) [25]. Blast homology searches for the 66,396 assembled sequences, including now these 2 new genomes, were performed and we benefited from the results to clean our transcriptome. We eliminated sequences carrying the 2 following criteria: no hit in blast analyses and very low expression levels (Counts Per Million (CPM) values \(<\) 1 in all libraries). Moreover, we eliminated sequences with single expression data (reads detected in only one library) or two expression data when reads were not detected in replicate libraries, except sequences recording hits in the _M. graminicola_ draft genome. Hence, we propose here a novel _M. graminicola_ transcriptome version named Mg_v2, composed of 44,137 sequences (Table S1). In detail, Blastn homology searches for the 44,137 Mg_v2 sequences against the 10,895 _M. graminicola_ predicted CDS by [PERSON] et al. [24] retrieved 22,489 Mg_v2 sequences with at least one hit (51%) and against the genomic contigs retrieved 25,392 sequences (58%) (Table S1). In turn, 87% (9511) of the 10,895 predicted CDS [24] gave at least one hit on the 44,137 Mg_v2 sequences. This result indicates that the Mg_v2 transcriptome correctly covered the _M. graminicola_ draft genome, considering that all the nematode stages were not sampled here. Blastx performed against the 43,718 _M. incognita_ predicted proteins [25] found significant hits for 27,340 sequences (62%) of the Mg_v2 transcriptome, including 8111 sequences having no homologies with any of the _M. graminicola_ genomic sequences produced by [PERSON] et al. [24], thus probably pointing to genes lacking in the _M. graminicola_ draft genome sequence. Finally, taking into account of Blastx results against _Meloidogyne hapla_[27], _Caenorhabditis elegans_[28], and the Uniprot databases, we determined that the Mg_v2 transcriptome contains 7095 sequences (16%) with no homology at all. As expected, the percentage of reads that mapped on the _M. graminicola_ Mg_v2 transcriptome increased with time in the rice -nematode dual RNA-Seq libraries (Table S1). In the resistant libraries the nematode reads varied from 0.76-0.95% at 2 dpi to 3.81-4.34% at 8 dpi. In the susceptible RNA-Seq libraries, the percentage of _M. graminicola_ mapped reads increased from 0.41-0.58% at 2 dpi to 4.63-9.70% at 8 dpi. The nematode reads number along time is consistent with microscopic observation data showing that in our inoculation conditions almost the same number of J2s were present in Nipponbare and TO5681 roots after 7 days (Figure S1, [22]). However, all J2s in Nipponbare were feeding, had a sausage-like swollen body shape, when most of J2s were still vermiform in TO5681 roots and could not reproduce further.