Reconciliation-based detection of co-evolving gene families

Yao-Ban Chan (1) , Vincent Ranwez (2) , Celine Scornavacca (1)

1 UM2 - Université Montpellier 2 - Sciences et Techniques
2 UMR AGAP - Amélioration génétique et adaptation des plantes méditerranéennes et tropicales

Background Genes located in the same chromosome region share common evolutionary events more often than other genes (e.g. a segmental duplication of this region). Their evolution may also be related if they are involved in the same protein complex or biological process. Identifying co-evolving genes can thus shed light on ancestral genome structures and functional gene interactions. Results We devise a simple, fast and accurate probability method based on species tree-gene tree reconciliations to detect when two gene families have co-evolved. Our method observes the number and location of predicted macro-evolutionary events, and estimates the probability of having the observed number of common events by chance. Conclusions Simulation studies confirm that our method effectively identifies co-evolving families. This opens numerous perspectives on genome-scale analysis where this method could be used to pinpoint coevolving gene families and thus help to unravel ancestral genome arrangements or undocumented gene interactions.

Domaines: Biologie végétale; Sciences agricoles

Yao-Ban Chan, Vincent Ranwez, Celine Scornavacca. Reconciliation-based detection of co-evolving gene families. BMC Bioinformatics, 2013, 14, 15 p. ⟨10.1186/1471-2105-14-332⟩. ⟨hal-01189789⟩