Additional file 1: of A genome-wide survey of DNA methylation in hexaploid wheat

Supplementary data file includes Figures S1–S11, Tables S1–S12 and Notes 1–4. (PDF 107087 kb

Additional file 2: of A modified sequence capture approach allowing standard and methylation analyses of the same enriched genomic DNA sample

Figure S2. Design of the 12 Mbp wheat gene capture array. The 110 Mbp design target sequence for the capture probe set is as described by Gardiner et al. (Gardiner et al., 2015). The RNA baits for this SureSelect Methyl-Seq Target Enrichment system are all 120 bp in length, unique, non-repetitive and are evenly placed across the available wheat genic target sequence according to the design illustrated. (PDF 187 kb

Additional file 3: of A modified sequence capture approach allowing standard and methylation analyses of the same enriched genomic DNA sample

Table S1. Drought tolerance associated genes. 120-mer probes were tiled end-to-end across these genes of particular interest [15–18]. (PDF 81 kb

Additional file 1: of A modified sequence capture approach allowing standard and methylation analyses of the same enriched genomic DNA sample

Figure S1. Depth of coverage summarised for the non-bisulphite treated samples per extended bait sequence reference contig. Reference extended bait sequence contigs here are organized using POPseq chromosomal pseudomolecules. a) Displays data for the NBTS sample and b) displays data for the NBTF sample. (PDF 1425 kb

Comparison of expression profiles for contrasts between treatment groups at 13°C.

<p>Panel A indicates those genes up-regulated (upper) and down-regulated (lower) by anoxia treatment. Panel B presents the same profiles following removal of the outlier genes as described in the Methods section. Panel C shows that the anoxic response (A7/A1 contrast) was inversely correlated with the subsequent reoxygenation response (R7/A7 contrast). Panel D illustrates the diverse profiles for 75 outlier genes grouped into 16 clusters.</p

Bar-charts to illustrate the responses of genes of the glycolytic pathway to anoxia for 1 (A1/N7 log₂ ratio) and 7 days (A7/N7), followed by re-oxygenation for a further 7 days (R7/N7).

<p>Representative gene probes were selected from all probes that aligned by BLASTx to the indicated gene identity irrespective of significance in the array analysis, as indicated by FDR <5%. The circles indicate features discussed in the text. Gene abbreviations: hk - hexokinase; pfk - phosphofructokinase, muscle b or platelet p isoforms; aldo or Baldo - aldolase with multiple isoforms; tpi - triosephosphate isomerase; gapdh - glyceraldehyde-3-phosphate dehydrogenase; pgam - phosphoglycerate mutase; eno - enolase; pk-m - pyruvate kinase-muscle; pdh - pyruvate dehydrogenase; mdh - malate dehydrogenase Isoforms are indicated.</p

Heat map representing the log₂ fold-change values between contrasted treatments for the 844 genes found to be differentially expressed in at least one of the contrasts.

<p>Each of the 16 columns represents a different contrast between treatment groups, as indicated in the key to the right, and as illustrated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109978#pone-0109978-g001" target="_blank">Figure 1</a>; note that the 13A7 group was the denominator in most of these contrasts. The value of fold-change between contrasted treatments for each gene was indicated by the coloured scale, with red indicating a value>1 and blue indicating a value <1. Genes were clustered into 1-6 groups using the K-means technique, each possessing broadly the same profile across all contrasts.</p

Bar-charts displaying types of <i>p</i>-value distributions for contrasts between selected treatments.

<p>A random distribution would be represented by an equal representation of <i>p</i>-values across the full range, generating a flat histogram, as in the 8R7/8N7 contrast, top left panel. In some contrasts, the proportion of genes with p<0.05 was much greater indicating a non-random distribution, as in the 13A7/13A1 contrast, bottom right panel. The proportion of these gene probes that were randomly included in this category (i.e. the false discovery rate) was estimated by backwards extrapolation of the horizontal line above <i>p</i>>0.2. The two other contrasts represent intermediate conditions in which DE genes were evident but were difficult to extract as significant due to large proportions of false positives.</p

List of gene ontology (GO) categories judged as being (i) enriched in differentially expressed (DE, FDR <5%) genes according to the hypergeometric test, or (ii) displaying a significant non-random order in the <i>p</i>-rank test.

<p>The contrasts for the former test relate to all DE genes (A) or all down-regulated DE genes (B). For the <i>p</i>-rank test they relate to contrasts between temperatures under anoxia (13A7/8A7, C) and for anoxia treatment (13A7/13N7, D). GO terms have been grouped into the indicated high-level categories, which are not linked to formal GO categories.</p

Nucella_CoAssembly

Co-assembly data: list of contigs and singleton