BACKGROUND: Gene duplication, a major evolutionary path to genomic innovation, 
can occur at the scale of an entire genome. One such "whole-genome duplication" 
(WGD) event among the Ascomycota fungi gave rise to genes with distinct 
biological properties compared to small-scale duplications.
RESULTS: We studied the evolution of transcriptional interactions of 
whole-genome duplicates, to understand how they are wired into the yeast 
regulatory system. Our work combines network analysis and modeling of the 
large-scale structure of the interactions stemming from the WGD.
CONCLUSIONS: The results uncover the WGD as a major source for the evolution of 
a complex interconnected block of transcriptional pathways. The inheritance of 
interactions among WGD duplicates follows elementary "duplication subgraphs", 
relating ancestral interactions with newly formed ones. Duplication subgraphs 
are correlated with their neighbours and give rise to higher order circuits with 
two elementary properties: newly formed transcriptional pathways remain 
connected (paths are not broken), and are preferentially cross-connected with 
ancestral ones. The result is a coherent and connected "WGD-network", where 
duplication subgraphs are arranged in an astonishingly ordered configuration.