Patterns of subgenome and allelic gene expression. (IMAGE)
Caption
Patterns of subgenome and allelic gene expression. (A) Cytokinin (CTK)-induced in vitro flowering and auxin (IAA)-induced in vitro rejuvenation of B. odashimae. The pictures from left to right represent the vegetative shoots, flowering shoots, and flower anatomy of B. odashimae, respectively. (B) PCA of the first two principal components of subgenome expression profiles across 11 different developmental stages under different hormone treatments. (C) PCA plot of the first two principal components of allele expression profiles across 11 stages. (D) Transcript abundance across all samples for expressed genes among subgenome A, B, and C of Hap I. (E) Transcript abundance across all samples for expressed genes among Hap I, Hap II, and Hap III. (F) The violin plot of biased expression for homoeologous genes of subgenome A and subgenome C across all samples. (G) Proportions of alleles with allelic expression bias across 11 different samples. There are three categories: small allele expression differences (ASE) genes, large ASE genes, and balanced genes without difference. (H) Absolute expression abundance for the small ASE genes (left) and large ASE genes (right). (I) Distances to the nearest TEs of small ASE genes (left) and large ASE (right). (J) Analysis of the number of differentially expressed genes among different haplotype pairs. (K) Distances to the nearest TEs for large ASE in different haplotypes. The line in the center of each plot (D, E, F, H, I, J, and K) represents the median value, and the bounds of each box indicate the first (25%) and third (75%) quartiles. Mann–Whitney–Wilcoxon test. *P < 0.05; **P < 0.01; ***P < 0.001 and ****P < 0.0001.
Credit
Horticulture Research
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