title: Homoeologs: What Are They and How Do We Infer Them?
abstract: The evolutionary history of nearly all flowering plants includes a polyploidization event. Homologous genes resulting from allopolyploidy are commonly referred to as 'homoeologs', although this term has not always been used precisely or consistently in the literature. With several allopolyploid genome sequencing projects under way, there is a pressing need for computational methods for homoeology inference. Here we review the definition of homoeology in historical and modern contexts and propose a precise and testable definition highlighting the connection between homoeologs and orthologs. In the second part, we survey experimental and computational methods of homoeolog inference, considering the strengths and limitations of each approach. Establishing a precise and evolutionarily meaningful definition of homoeology is essential for understanding the evolutionary consequences of polyploidization.
authors.affiliation: Bayer CropScience NV, Technologiepark 38, 9052 Gent, Belgium; University College London, Gower Street, London WC1E 6BT, UK.
authors.forename: Natasha M
authors.initials: NM
authors.lastname: Glover
authors.affiliation: Bayer CropScience NV, Technologiepark 38, 9052 Gent, Belgium.
authors.forename: Henning
authors.initials: H
authors.lastname: Redestig
authors.affiliation: University College London, Gower Street, London WC1E 6BT, UK; University of Lausanne, Biophore, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, Biophore, 1015 Lausanne, Switzerland. Electronic address: c.dessimoz@ucl.ac.uk.
authors.forename: Christophe
authors.initials: C
authors.lastname: Dessimoz
mesh_terms: D019143:Evolution, Molecular; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics; D011123:Polyploidy
keywords: homoeology; homology; polyploidy; positional homoeology