Extended Data Fig. 6: Changes in gene expression between cybrids with a Ler nucleus (panel a), an Ely nucleus (panel b) and changes they have in common (panel c).

Cybrid genotypes are indicated as Nucleotype^Plasmotype. The triangle in panel a shows cybrid comparisons with a Ler nuclear background (for plasmotypes Ely, Ler and Bur) and panel b shows cybrid comparisons with an Ely nuclear background for the same plasmotypes. Significantly differentially expressed (DE) genes between cybrid comparisons are indicated with black numbers. These DE genes are subdivided in upregulated genes (green numbers in superscript) and downregulated genes (red numbers in subscript), following the direction of the arrows between cybrids (that is the change from an Ely to a Ler plasmotype in a Ler nuclear background resulted in 726 DE genes, of which 426 were upregulated and 300 were downregulated). The green triangle in panel c shows what differentially expressed genes the comparisons in panels a and b have in common. For example, the Ler and Ely nuclear backgrounds show a common response of 78 DE genes when the Ely plasmotype is changed for a Ler plasmotype. The absence of one of the comparisons in this triangle is due to the absence of shared DE genes. The common effect of changing an Ely plasmotype for either Bur of Ler was derived by assessing what DE genes are similar along the axes in the green triangle c. These 78 and 150 genes have 40 shared DE genes (see Supplementary Table 6). For the raw data see Supplementary Data 3.