Fig. 1.
Transcriptomic variation among accessions in met1 mutants and wildtypes. a UMAP projections of transformed RNA-seq read counts in 19,473 genes similarly compared for wildtypes (left) and met1 mutants (right). These genes were further analyzed to identify DEGs across accessions, separately for WTs and met1 mutants. b UMAP representation of transformed RNA-seq counts from 158 samples (104 hetero- or homozygous met1 mutants and 54 wild-type plants) across 21,657 genes. Colors indicate accessions, and shapes indicate genotype. WT, wild-type; Mut Het, heterozygous met1 mutants; Mut Homo G1, first-generation homozygous met1 mutants; Mut Homo G2, second-generation homozygous met1 mutants. c Volcano plot of 3479 DEGs identified in a contrast between all met1 mutant samples and all wild-type samples. TE-associated DEGs (TE-DEGs) are colored purple, and Non-TE-DEGs yellow. d Chromosomal distribution of 3479 DEGs from the all-met1-against-all-wild-type contrast, and their log2(fold change) in mutants relative to the corresponding wildtypes. Upregulated DEGs are colored orange and downregulated DEGs green. e DEGs in the 18 accession-specific contrasts, compared to the all-met1-against-all-wild-type contrast (denoted by “A,” third column from the left). f Variation in numbers of upregulated and downregulated Non-TE-DEGs and TE-DEGs across different contrasts, bars colored similarly to d. For e and f, colors below bars indicate accession-specific contrasts. g Boxplots showing distribution of the coefficient of variation (CV) for expression level (measured in transformed read counts) across accessions, compared between 104 met1 mutant and 54 wild-type samples at 10,151 Non-TE-DEGs, 1,524 TE-DEGs, and 291 Universal DEGs. *** indicates Wilcoxon-test p-value <0.0001