Abstract
BackgroundGene 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.ResultsWe 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.ConclusionsThe 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.
Highlights
Gene duplication, a major evolutionary path to genomic innovation, can occur at the scale of an entire genome
It represents the network formed by all duplication subgraphs for which at least one extra interaction has been inherited after the whole-genome duplication (WGD)
We will refer to this structure as the "WGD network"
Summary
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. An organism can respond to internal and environmental cues by the coordinated activation of large sets of genes through transcriptional regulation. This process can be described as a complex "network" of interactions, connecting binding sites of regulatory proteins (transcription factors, TFs) to regulatory DNA regions of their target genes [1]. Gene duplication can occur with different functional consequences [4,5] at the scale of a single gene
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