Proportions of <i>Brassica napus</i> genes encoding receptor-like proteins (RLPs), secreted peptides (SPs) or nucleotide-binding leucine-rich repeat receptors (NLRs) within chromosomal intervals (loci) for resistance against <i>Sclerotinia sclero</i>tiorum (necrotroph), <i>Leptosphaeria maculans</i> (extracellular) or <i>Plasmodiophora brassicae</i> (intracellular).

<p>(A) Proportions represent the numbers of RLP, SP or NLR genes within the mapped regions for resistance against <i>S</i>. <i>sclero</i>tiorum, <i>L</i>. <i>maculans</i> or <i>P</i>. <i>brassicae</i> divided by the total number of genes for each of the three families. Contingency tests show that proportions of RLP, SP and NLR genes are not equal for resistance against <i>P</i>. <i>brassicae</i> (<i>χ</i>^<i>2</i> = 9.84, <i>P</i> = 0.007). (B) Proportions represent the total number of LRR genes (RLP, SP and NLR) within mapped regions for resistance divided by the total number of LRR genes (black bars). These proportions were compared to those for all of the genes within mapped regions for resistance divided by the total number of genes within the genome (white bars). Differences between these two proportions were not significant (contingency table, <i>χ</i>^<i>2</i> = 1.90, <i>P</i> = 0.39).</p

Test for evidence of positive selection in coding sequences of <i>Brassica napus R</i> genes and candidate genes for resistance against <i>Leptosphaeria maculans</i>.

<p>Test for evidence of positive selection in coding sequences of <i>Brassica napus R</i> genes and candidate genes for resistance against <i>Leptosphaeria maculans</i>.</p

Symptoms and expression of candidate <i>R</i> genes after inoculation of susceptible <i>Brassica napus</i> cultivar Topas DH16516 with <i>Leptosphaeria maculans</i> isolate 00–100.

<p>(A) Appearance of cotyledons 0, 2, 4, 6 and 8 days post-inoculation (dpi) with <i>L</i>. <i>maculans</i>. (B) Heat maps of differentially expressed genes (DEG) encoding receptor-like proteins (RLPs), secreted peptides (SPs) and nucleotide-binding leucine-rich repeat receptors (NLRs). The expression of each gene is based on regularized logarithmic transformation (rld) of the average of the best three biological replicates. Expression patterns are grouped into initial endophytic (0–2 dpi), intermediate (4 dpi) and late necrotrophic (6–8 dpi) stages of colonization [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198201#pone.0198201.ref022" target="_blank">22</a>]. (C, D) Classification of different gene families into different expression categories. Circles (from inside to outside) represent NLR, RLP and SP genes. (C) General expression patterns, reads per kilobase million (RPKM), did not differ between RLP, SP and NLR genes (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198201#pone.0198201.s004" target="_blank">S4 Table</a>, <i>χ</i>^<i>2</i> = 2.51, <i>P</i> = 0.64). (D) Percentages of differentially expressed genes (% DEG) at the three stages of colonization are shown. Induced expression patterns differed between RLP, SP and NLR genes (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198201#pone.0198201.s005" target="_blank">S5 Table</a>, <i>χ</i>^<i>2</i> = 22.13, <i>P</i> = 0.0002).</p

Distribution of candidate genes for resistance against pathogens in the genome of <i>Brassica napus</i>.

<p>All 19 (10 A and 9 C) chromosomes are displayed in grey as concentric circles according to the published <i>B</i>. <i>napus</i> genome sequence [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198201#pone.0198201.ref021" target="_blank">21</a>]. Genes encoding nucleotide-binding leucine-rich repeat receptors (NLRs), receptor-like proteins (RLPs) and secreted peptides (SPs) are color-coded in orange, blue and red, respectively. The center of this diagram shows homeologous relationships on the A and C sub-genomes between orthologous RLP and SP gene pairs in blue and red, respectively.</p

Phylogenetic tree and structural model of the leucine-rich repeat (LRR) domain of <i>Brassica napus</i> gene <i>LepR3</i> for resistance against <i>Leptosphaeria maculans</i>.

<p>(A) Maximum likelihood phylogenetic tree of genes belonging to the <i>LepR3</i>/<i>Rlm2</i> locus. Coding sequences were used to generate the tree. The Jukes-Cantor model [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198201#pone.0198201.ref028" target="_blank">28</a>] was used. The tree with the greatest log-likelihood is shown. Numbers indicate bootstrap values of 1,000 replicates. A discrete Gamma distribution was used to model evolutionary rate differences between sites. The rate variation model allowed for some sites to be evolutionarily invariable. Branch lengths are measured as the number of substitutions per site (scale bar). Branches designate species abbreviations: Bna = <i>Brassica napus</i>, Bra = <i>B</i>. <i>rapa</i> and Bju = <i>B</i>. <i>juncea</i>, followed by cultivar names or IDs, or accession numbers; BnaGlacier: AJG42078, BnaWestar: AJG42083, Bra 006-1-1: AJG42088, Bna-Marnoo: AJG42089, BjuAC-Vulkan: AJG42090, BnaSurpass: AGC13588, BraTorch: AJG42087. Gene IDs for genes that encode a receptor-like protein (RLP) are given after <i>Arabidopsis thaliana</i> accession numbers. Sequences from <i>B</i>. <i>napus</i> cultivars Glacier and Surpass, underlined in blue and red, respectively, have <i>Rlm2</i> and <i>LepR3</i> alleles, respectively, of the resistance gene on chromosome A10. Alleles identical to those from Glacier and Surpass were sequenced from three and two different cultivars, respectively. The sequence of cultivar Westar (no known <i>R</i> gene against <i>L</i>. <i>maculans</i>) was identical to sequences from eight other cultivars. (B) The modeled LRR domain starts at amino acid 27 and ends at amino acid 804. Seven amino acids predicted to be under positive selection are shown as vdW spheres. Residues in yellow (A234) and red (A306, E455, R467, Y638, A723) are supported at the 95% and 99% confidence level, respectively, using a comparison of 11 coding sequences. The residue in blue (Y120) is supported at the 95% level using four coding sequences.</p