Chan YB, Ranwez V, Scornavacca C. Reconciliation-based detection of co-evolving gene families.
BMC Bioinformatics 2013;
14:332. [PMID:
24252193 PMCID:
PMC4225522 DOI:
10.1186/1471-2105-14-332]
[Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 11/13/2013] [Indexed: 02/07/2023] Open
Abstract
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 co-evolving gene families and thus help to unravel ancestral genome arrangements or undocumented gene interactions.
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