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Table S1 Chromosomal location and primer pairs of the loci that were independently experimentally validated by qRT-PCR

Table S2 List of 4684 putative novel transcriptionally active regions identified in nematode-infected rice root tissues, with their genomic location, the match found in the rice root transcriptome data of Kyndt et al. (2012a), BLASTn results against cDNA and genomic DNA of Oryza sativa cv ‘Japonica’, BLASTx results against rice proteins, SwissProt/trEMBL

Table S3 Results of parametric analysis of gene set enrichment of transcriptome data of root knot- or migratory root rot nematode-infected rice roots at 3 (early) or 7 d (late) after infection, showing the five most important up-regulated and five most down-regulated GO terms

Table S4 List of loci that are significantly differentially expressed in rice root tissues upon infection with M. graminicola (Mg) or H. oryzae (Ho), at 3 or 7 dai, including locus number or nTAR number, MSU6 annotation and the log2FC between infected and healthy tissues

Table S5 List of 382 loci that are significantly differentially expressed between root galls and uninfected root tips, but not differentially expressed upon root rot nematode infection, including locus number or nTAR number, MSU6 annotation and the log2FC between infected and healthy tissues

Table S6 List of 578 loci that are significantly differentially expressed between migratory root rot nematode-infected rice roots and healthy roots, but not differentially expressed upon root knot nematode infection, including locus number or nTAR-number, MSU6 annotation and the log2FC between infected and healthy tissues

nph4311-sup-0002-NotesS1.docxWord document112KNotes S1 Schematic representation and more detailed explanation of the bioinformatics workflow that was followed during the analysis of mRNA-Seq data obtained from nematode-infected and uninfected rice root tissues.