Additional file 1: Figures S1. of DNA methylation changes facilitated evolution of genes derived from Mutator-like transposable elements

a) shows the phylogenetic tree of 10 Oryza and 1 Leersia species. Based on the presence and absence of MULEs on the phylogenetic tree, we inferred the origination time points of the MULEs measured with divergence time of the 11 species. We listed the origination time index on the phylogenetic tree as 1-9, e.g. “1” represents MULEs originated after each species diverged, “4” represents MULEs originated before Asian rice diverged but after Asian rice split from the rest of Oryza species, 9 represents MULEs originated before the AA and BB genome rice diverged. Then for each of the 9 Oryza 2 species, we grouped their MULEs based on its origination time index. b) We categorized MULEs based on their origination time points (shown in ‘a’) inferred from presence and absence of MULEs in the phylogenetic tree of Oryza species, and drew the density distribution of the amplification time of MULEs, which were estimated based on the sequence divergence of MULEs and their most similar paralogs, in each origination time point category for 9 species, respectively. Figure S2. Methylation level distribution of parental sequences of MULE-derived genes and randomly selected non-TE genic-regions in across the O. nivara genome. Figure S3. Methylation level of MULE-derived putative genes a) in O. sativa ssp. japonica genome; b) the genes derived from MULEs overlapped between Ferguson et al. and us.; c) in O. nivara genome. Figure S4. Analysis of methylation levels of genic-MULEs with the overlapped data set of Ferguson et al. and us. a) Methylation level of MULE internal sequences; b) Methylation level of entire MULEs and flanking regions. Figure S5. Analysis of TE-coverage and TIR similarity of genic-MULEs with the overlapped data set of Ferguson et al and us. Figure S6. Analysis of methylation levels of genic-MULEs in O. nivara genome. a) Methylation level of MULE internal sequences; b) Methylation level of entire MULEs and flanking regions. Figure S7. Analysis of TE-coverage of genic-MULEs in O. nivara genome. Figure S8. The Marey’s and recombination rate map of O. sativa ssp. japonica genome. The Blue line is based on LOESS function and the red line is based on cubic splines. (DOCX 3.19 mb

Historical Introgression of the Downy Mildew Resistance Gene <i>Rpv12</i> from the Asian Species <i>Vitis amurensis</i> into Grapevine Varieties

<div><p>The Amur grape (<i>Vitis amurensis</i> Rupr.) thrives naturally in cool climates of Northeast Asia. Resistance against the introduced pathogen <i>Plasmopara viticola</i> is common among wild ecotypes that were propagated from Manchuria into Chinese vineyards or collected by Soviet botanists in Siberia, and used for the introgression of resistance into wine grapes (<i>Vitis vinifera</i> L.). A QTL analysis revealed a dominant gene <i>Rpv12</i> that explained 79% of the phenotypic variance for downy mildew resistance and was inherited independently of other resistance genes. A Mendelian component of resistance–a hypersensitive response in leaves challenged with <i>P. viticola</i>–was mapped in an interval of 0.2 cM containing an array of coiled-coil NB-LRR genes on chromosome 14. We sequenced 10-kb genic regions in the <i>Rpv12⁺</i> haplotype and identified polymorphisms in 12 varieties of <i>V. vinifera</i> using next-generation sequencing. The combination of two SNPs in single-copy genes flanking the NB-LRR cluster distinguished the resistant haplotype from all others found in 200 accessions of <i>V. vinifera</i>, <i>V. amurensis</i>, and <i>V. amurensis</i> x <i>V. vinifera</i> crosses. The <i>Rpv12⁺</i> haplotype is shared by 15 varieties, the most ancestral of which are the century-old ‘Zarja severa’ and ‘Michurinets’. Before this knowledge, the chromosome segment around <i>Rpv12⁺</i> became introgressed, shortened, and pyramided with another downy mildew resistance gene from North American grapevines (<i>Rpv3</i>) only by phenotypic selection. <i>Rpv12⁺</i> has an additive effect with <i>Rpv3⁺</i> to protect vines against natural infections, and confers foliar resistance to strains that are virulent on <i>Rpv3⁺</i> plants.</p> </div

Phenotypic distribution of downy mildew resistance.

<p>Two families segregating for <i>Rpv12⁺</i> (panel <b>A</b>) and for the combination of <i>Rpv12⁺</i> and <i>Rpv3⁺</i> (panel <b>B</b>) were analysed. Resistance scores in panel <b>A</b> are based on the OIV452 parameter (1 = most sensitive, 9 = most resistant) scored on field-grown seedlings under natural infection. Resistance scores in panel <b>B</b> are based on the cumulative OIV452 parameter (∑OIV452 = sum of daily OIV452 scores from 3 to 8 dpi) in artificially inoculated leaf discs. The average phenotypic value in the upper left corner of the panels <b>A</b>–<b>B</b> refers to individuals grouped by their allelic status at the <i>Rpv12</i> and <i>Rpv3</i> genes, which was estimated based on the flanking markers UDV014/UDV370 for <i>Rpv12</i>, and on UDV305/UDV737 for <i>Rpv3 </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061228#pone.0061228-DiGaspero1" target="_blank">[8]</a>. Recombinants in those intervals were excluded from this estimate. QTL plots that explain the phenotypic variance shown in panel <b>B</b> are given in panel <b>C</b>.</p

Host–pathogen interaction observed between host and pathogen genotypes.

<p>Leaf discs of four host genotypes including (panels <b>A</b>, <b>E</b>) a double homozygous recessive grapevine (<i>Rpv12⁻</i> and <i>Rpv3⁻</i>), (panels <b>B</b>, <b>F</b>) a grapevine carrying <i>Rpv3⁺</i> in the absence of <i>Rpv12⁺</i>, (panels <b>C</b>, <b>G</b>) a grapevine carrying <i>Rpv12⁺</i> in the absence of <i>Rpv3⁺</i>, and (panels <b>D</b>, <b>H</b>) a double heterozygous grapevine for both <i>Rpv12⁺</i> and <i>Rpv3⁺</i> were inoculated with two isolates of <i>P. viticola</i>, (panels <b>A</b>–<b>D</b>) <i>Rude</i> (<i>avrRpv3⁺</i>/<i>avrRpv12⁺</i>) and (panels <b>E</b>–<b>H</b>) <i>Pv127</i> (<i>avrRpv3⁻</i>/<i>avrRpv12⁺</i>). Pictures were taken at 6 dpi.</p