Regulation of LBPGs for maize seed Lysine biosynthesis.

<p>Regulation of LBPGs for maize seed Lysine biosynthesis.</p

Lysine biosynthesis pathway enzyme genes in maize.

<p>Lysine biosynthesis pathway enzyme genes in maize.</p

Comparison of lysine content.

<p>(A) Comparison of lysine biosynthesis pathway genes coexpressed genes (LBPGs) with the same number of randomly selected all genes set (Test) and with all genes set (All). (B) Comparison of DHDPS1-coexpressed genes (DHDPS1) and DHDPS2-coexpressed genes (DHDPS2) with all genes set (All). (** <i>P</i> < 0.01)</p

The motifs enriched in the LBPGs modules.

<p>The motifs enriched in 1-kb upstream sequences of the transcription start site of the LBPGs coexpressed module genes. (P-value was calculated by Ranksum test).</p

Phylogenetic trees of lysine biosynthesis pathway gene orthologs.

<p>Phylogenetic trees based on AK (aspartate kinase), ASD (aspartate-semialdehyde dehydrogenase), DHDPS (dihydrodipicolinate synthase), DapB (dihydrodipicolinate reductase), LL-DAP-AT (LL-diaminopimelate aminotransferase), DapF (diaminopimelate epimerase), and LysA (diaminopimelate decarboxylase) are shown. The AK tree contains two enzymes: the monofunctional enzyme AK (EC: 2.7.2.4; red branch) and the bifunctional enzyme HSDH (EC: 1.1.1.3; black branch)</p

Expression patterns of dihydrodipicolinate synthase (DHDPS) genes.

<p>(A) Expression levels reads per kilobase per million reads (RPKM) of DHDPS genes in 21 maize developmental stages. (B) Quantitative real-time PCR (qRT-PCR) validation of RNA-Seq-based DHDPS expression levels. qRT-PCR expression profiles (blue bars) of DHDPS genes closely match the RNA-Seq data (red lines). The correlation value (cor) was calculated using Pearson’s correlation coefficient. The error bars in the figure represent the standard deviation. (C) Heat map of expression profiles of DHDPS-coexpressed genes (Y axes). Numbers next to the heat map represent the number of days after pollination. (The error bars represent standard deviation).</p

Expression pattern of LBPGs coexpressed genes.

<p>The module eigengenes are used to represent the genes expression pattern within each module. Each bar represents one sample (days after pollination) and the color represents the module color, the LBPGs was list below the module name. The value of the module eigengenes for each sample is displayed on the y axis.</p

Additional file 5: Table S3. of Analyses of methylomes of upland and lowland switchgrass (Panicum virgatum) ecotypes using MeDIP-seq and BS-seq

Hypermethylated- and hypomethylated-DMRs flanking within 2000 bp of annotated genes. (XLSX 204 kb

Additional file 4: Table S2. of Analyses of methylomes of upland and lowland switchgrass (Panicum virgatum) ecotypes using MeDIP-seq and BS-seq

GO analysis of hypermethylated- and hypomethylated-DMRs. (XLSX 824 kb

Additional file 2: Table S1. of Analyses of methylomes of upland and lowland switchgrass (Panicum virgatum) ecotypes using MeDIP-seq and BS-seq

Overrepresentation hypergeometric test on Hypermethylated-DMRs and Hypomethylated-DMRs. (XLSX 9 kb