Fig. 2: Subgenome gene expression divergence is associated with epigenetic modifications. | Nature Genetics

Fig. 2: Subgenome gene expression divergence is associated with epigenetic modifications.

From: The genome and GeneBank genomics of allotetraploid Nicotiana tabacum provide insights into genome evolution and complex trait regulation

Fig. 2

a,b, Gene expression divergence between the N. sylvestris and N. tabacum S subgenomes (a) and between the N. tomentosiformis and N. tabacum T subgenomes (b). c–f, CG, CHG and CHH methylation differences among ancestral genomes and the corresponding N. tabacum subgenome for genes upregulated (c) or downregulated (d) in the S subgenome and upregulated (e) or downregulated (f) in the T subgenome. Sample size is 1,302 (c), 723 (d), 1,236 (e) and 804 (f). P values from left to right are 1.98 × 10−17, 2.20 × 10−72, 6.81 × 10−3, 2.28 × 10−4, 2.44 × 10−14, 7.06 × 10−3, 9.77 × 10−3, 1.00 × 10−15, 2.04 × 10−3, 2.90 × 10−11, 1.80 × 10−19 and 6.23 × 10−3. g, Overlap of differentially expressed homoeologous gene pairs between the two subgenomes of N. tabacum (blue) and two ancestor genomes (red). h, Relationships of homologous or homoeologous gene expression fold changes between two subgenomes of N. tabacum (y axis) and two ancestor genomes (x axis). Dashed vertical and horizontal lines indicate log2(fold change) > 2. i, Overlap of homoeologous gene expression changes. The overlap between Ssub up and Tsub up indicates that a pair of homoeologous genes were both upregulated in the N. tabacum subgenome, while the overlap between Ssub down and Tsub up indicates that one gene from the S subgenome was downregulated but its homolog was upregulated in the T subgenome. j, Boxplot illustrating that homoeologous gene expression is strongly biased toward the S subgenome by simultaneously upregulating genes in the S subgenome and suppressing their homoeologs in the T subgenome. The sample size is 33 and P values are 2.21 × 10−2 and 1.52 × 10−5 from left to right. k,l, Comparison of CHG methylation levels between the ancestor genome and corresponding subgenomes for homoeologous genes strongly biased toward the S (k) and T (l) genomes. In the boxplots, the center line is the median, box limits are the first and third quartiles and whiskers are the minimum and maximum. A two-sided t-test was performed to generate the significances for all pairwise comparisons. *P < 0.05, **P < 0.01 and ***P < 0.001. 2k, 2 kilobase; FDR, false discovery rate; TES, transcript end site; TSS, transcript starting site.

Back to article page