Table 1.
Number of Solanum tuberosum group phureja genes that encode NBS-domains with homology to plant resistance proteins.
Figure 1.
Phylogenetic construction of the NBS-LRR proteins in Solanum tuberosum group phureja.
The neighbor-joining tree was constructed using the sequences of 110 NBS-containing proteins using MEGA4 software [31]. Sequences were trimmed to extract just the NBS domain. Bootstrap values are indicated on the branches. Each protein is encoded by its full PGSC code followed by its type (CNL, TNL, TN and so on); green, blue and red branches correspond to CC(I), CC(II) and TIR clades respectively. Functional annotation and chromosome location for each protein are positioned in the right margin.
Figure 2.
MEME analysis of NBS and LRR regions between CC(I) and CC(II) proteins.
(a) NBS domain analysis. Different color boxes represent different subdomains. CC(I) and CC(II) were analyzed separately. Even though CC(II) has two different configurations, (subdomains 7-4 and 8-2) they are clustered together due to strong similarities on principal subdomains (P-loop, kinases and GLPL. Figure S5). (b) Predominant LRR motifs are also different between these two groups; CC(I) proteins have smaller and more abundant LRR. Different color letters represent amino acid belonging to different families.
Figure 3.
Distribution of Solanum tuberosum group phureja sequences that are predicted to encode NBS resistance proteins.
Gray bars represent all 12 linkage groups in potato. Boxes across each bar designate the location of each gene. Color code: CNL (green), TNL (red) or a partial NBS gene (yellow). Distance in Megabases is shown at the top of each column.
Table 2.
Distribution of pseudogenes across the chromosomes and by domain group.
Figure 4.
(a) This cluster is positioned at ∼50 Mb in chromosome 9. The exact position of each gene-model is represented by a green rectangle. For reference we include the relative expression of each gene as obtained by RNAseq of leaves in normal condition and leaves infected with Phytophthora infestans. As these genes encode homologs to an Rpi protein we expected that the expression would increase during infection. (b) Structure of the proteins encoded by the genes in (a). At the top we can see a representation of the reference Rpi-vnt1 gene. All the genes presented are encoded within the cluster except for PGSC0003DMG400020584 that is placed at position 33 kb of the same scaffold. These proteins share a very high homology with the reference protein.
Figure 5.
Alternative splicing of a TIR-NBS-LRR resistance gene.
Three different primer pairs (orange, red and black) were used to explore alternative splicing in the gene PGSC0003DMP400023191 with homology to a TMV resistance gene. cDNA from 14 week old DM plants was amplified and products with different sizes were cloned and sequenced. cDNA sequence was then blasted to the resistance gene DNA sequence at scaffold PGSC0003DMB000000105. Dotted lines represent introns.