NLR transcripts

To look for the variation in the plant defense responses we carried out an in-depth study of the resistance NLR genes induced in the experiment. The transcriptome annotation predicted altogether 543 candidate NLR transcripts, and 51 of them were upregulated and 35 downregulated in resistant versus susceptible comparison. The clustering of the NLR transcripts resulted in 58 clusters containing 457 sequences and 54 singletons (Figure 5a). Cluster 69 with 22 transcripts had the highest number of transcripts. The BLAST query against Arabidopsis protein database for the longest transcript in this cluster returned a hit to the RPP13 gene. RPP13 has the highest amount of amino acid diversity in Arabidopsis and is involved in defense against Peronospora parasitica (Hall et al., 2009; Rose et al., 2004), an oomycete causing downy mildew in Brassicaceae. A closer look at the expressed NLR transcripts revealed that although many of the NLR transcripts are expressed across all genotypes, the differentially expressed NLRs differ between genotypes with no common NLR transcripts, as illustrated by Venn diagrams of all expressed and differentially expressed NLR transcripts (Figures 5b and c).