1. Volume 11, Issue 3, Pages 485-495 (March 2018)
Genic C-Methylation in Soybean Is Associated with Gene Paralogs Relocated to Transposable Element-Rich Pericentromeres 
Moaine El Baidouri, Kyung Do Kim, Brian Abernathy, Ying-Hui Li, Li-Juan Qiu, Scott A. Jackson 
Molecular Plant 
Volume 11, Issue 3, Pages (March 2018)
DOI: /j.molp
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2. Figure 1
Genomic and Transcriptional Features of Methylated Genes in Soybean.
(A) Classification of methylated genes. I: genes methylated in coding sequences (CDS) and in all three methylation contexts (CG, CHG, and CHH). II: genes methylated in all three contexts exclusively in introns. III: CG-body methylated genes. IV: unmethylated genes.
(B) TE percentages in gene body and the flanking regions 2 kbp upstream and downstream of the transcriptional start site (TSS) and transcriptional end site (TES) for each gene category.
(C) Distribution of each gene classification along the 20 soybean chromosomes (chromosomal arms versus pericentromere). Top: each chromosome compartment (chromosome arms and pericentromere) was divided into 20 equal windows from 5′ to 3′ end. Bottom: proportion of genes located in chromosomal arms (light gray) and pericentromeric regions (dark gray) for each gene category.
(D). Box plot of expression scores (log2(FPKM + 1)) for each gene category.
Molecular Plant  , DOI: ( /j.molp )
Copyright © 2018 The Authors Terms and Conditions

3. Figure 2 Gene Methylation Categories and Duplication Mode.
(A and B) Proportion of genes derived from different duplication modes in total genes (A) and for each gene category (B).
(C) Expression pattern of mC genes and their paralogs in different soybean tissues. Top: average expression score (log2(FPKM + 1)) in different tissues. Error bars represent SEM. Bottom: heatmap of expression score of mC genes (left) and their paralogs (right).
Molecular Plant  , DOI: ( /j.molp )
Copyright © 2018 The Authors Terms and Conditions

4. Figure 3
Comparison of Methylation of Translocated (Non-collinear) and Parental (Collinear) Paralogs.
(A) Total number of translocated versus parental paralogs identified in soybean genomes.
(B) Number of translocated versus parental paralogs where at least one pair is classified as an mC gene (category I).
Molecular Plant  , DOI: ( /j.molp )
Copyright © 2018 The Authors Terms and Conditions

5. Figure 4 G. max-Specific Gene C-Methylation Absent from G. soja.
(A) Two categories of G. max-specific mC genes: (1) gene C-methylation variation associated with presence/absence of TE (70 genes); (2) variant mC genes associated with shared TE between G. max and G. soja (n = 115).
(B) Chromosomal view showing a G. max-specific gene C-methylation and expression associated with TE insertion (Glyma14g12315 versus soyB_ ).
(C) Chromosomal view showing methylation and expression patterns of G. max-specific mC genes associated with a shared TE (Glyma13g21250 versus soyB_ ).
(D) Metaplot of average CG (red), CHG (blue), and CHH (green) methylation levels across G. max-specific mC genes (solid line) and their orthologs in G. soja (dotted line).
(E) Box plot of expression levels of G. max-specific mC genes and their orthologs from G. soja in leaves.
Molecular Plant  , DOI: ( /j.molp )
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6. Figure 5
Genic C-Methylation Variation in Wild and Domesticated Soybean Accessions.
(A) Number of shared mC genes within nine G. max and seven G. soja accessions. 1: number of unique mC genes that were not C-methylated in any other G. max or G. soja accessions. 7 or 9: common mC genes identified in nine or seven accessions for G. max and G. soja, respectively.
(B) Comparison of average TE distance between variant mC genes and total genes in each of the seven wild soybean G. soja accessions. Error bars represent SEM. ***P < 2.2e−16; Wilcoxon rank-sum test.
Molecular Plant  , DOI: ( /j.molp )
Copyright © 2018 The Authors Terms and Conditions