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).