The Evolution of Gene Duplicates in Angiosperms and the Impact of Protein-Protein Interactions and the Mechanism of Duplication

Genome Biology and Evolution
Jonas DefoortLorenzo Carretero-Paulet

Abstract

Gene duplicates, generated through either whole genome duplication (WGD) or small-scale duplication (SSD), are prominent in angiosperms and are believed to play an important role in adaptation and in generating evolutionary novelty. Previous studies reported contrasting evolutionary and functional dynamics of duplicate genes depending on the mechanism of origin, a behavior that is hypothesized to stem from constraints to maintain the relative dosage balance between the genes concerned and their interaction context. However, the mechanisms ultimately influencing loss and retention of gene duplicates over evolutionary time are not yet fully elucidated. Here, by using a robust classification of gene duplicates in Arabidopsis thaliana, Solanum lycopersicum, and Zea mays, large RNAseq expression compendia and an extensive protein-protein interaction (PPI) network from Arabidopsis, we investigated the impact of PPIs on the differential evolutionary and functional fate of WGD and SSD duplicates. In all three species, retained WGD duplicates show stronger constraints to diverge at the sequence and expression level than SSD ones, a pattern that is also observed for shared PPI partners between Arabidopsis duplicates. PPIs are preferentia...Continue Reading

Methods Mentioned

BETA
RNAseq
environmental stress

Software Mentioned

PAML
EdgeR
Trimmomatic
CORNET
BINGO
count
Htseq
CODEML
STRING
PLAZA

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