Fig. 3: Fractional occupancies of genes and alleles under the reference scenario 1. | Nature Communications

Fig. 3: Fractional occupancies of genes and alleles under the reference scenario 1.

From: Unifying framework explaining how parental regulatory divergence can drive gene expression in hybrids and allopolyploids

Fig. 3

A Fractional occupancies of specific binding sites (of A and/or B-origin) weighted by their genomic dosages (note that A-derived binding sites have twice higher absolute numbers in species A with genotype AA than in AB hybrid and identical to AAB triploid). X- and \(y\)-axes are analogous to Fig. 1C. Types of individuals and strength of cross regulation are denoted by line colours and styles, respectively. Parental species with genotype AA is indicated by cyan, species with BB by yellow, their average expression (i.e. [expression of AA+ expression of BB]/2) are denoted by grey line, diploid hybrid AB by red, triploid hybrid AAB by black and triploid hybrid ABB by blue. Dotted lines show results for \(\rho=1\) (full cross-regulation), slashed lines show for \(\rho=2\) (limited cross-regulation) and full lines show \(\rho=10000\) (no cross-regulation). The insert with coloured schemes demonstrates how the simulation results correspond to expression level categories similarly as in Fig. 1A. Specifically, when fractional occupancy of parent A is higher than of parent B (right side of \(x\)-axis; \({f}_{{{\rm{A}}}} \, > \, {f}_{{{\rm{B}}}}\)), the levels of fractional occupancies in all hybrid forms (AB, AAB and ABB) are higher than average of their parents. B Comparison of fractional occupancies of alleles in hybrids (\({f}_{{{\rm{H}}}}^{{{\rm{A}}}}\) and \({f}_{{{\rm{H}}}}^{{{\rm{B}}}}\), respectively) relative to occupancies of their homologous alleles in parents (\({f}_{{{\rm{A}}}}\) and \({f}_{{{\rm{B}}}}\), respectively). X-axis shows the \({\log }_{2}({{f}_{{{\rm{H}}}}^{{{\rm{A}}}}/f}_{{{\rm{A}}}})\) ratio of Ahyb allele’s occupancy in hybrid relative to that in parental species A, \(y\)-axis shows the \({\log }_{2}({{f}_{{{\rm{H}}}}^{{{\rm{B}}}}/f}_{{{\rm{B}}}})\) ratio of Bhyb allele’s occupancy in hybrid relative to that in parental species B. Line colours and styles are analogous to panel A. Note: Reference scenario 1 assumes single specific site per chromosome and negligible concentration of free TFs. Square and diamond symbols along the lines provide the link between panels A and B by showing two reference values of \({\log }_{2}({{f}}_{{{\rm{A}}}}/{{f}}_{{{\rm{B}}}})\) expression divergence between parental species; square: \({\log }_{2}({{f}}_{{{\rm{A}}}}/{{f}}_{{{\rm{B}}}})=-1\) and diamond: \({\log }_{2}({{f}}_{{{\rm{A}}}}/{{f}}_{{{\rm{B}}}})=1\).

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