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.

Keywords: homoeology; homology; polyploidy; positional homoeology.

Figure 1

Subtypes of Homologous Genes (Genes of Common Ancestry). As the table shows, the definition of ‘homoeologs’ we recommend – genes that originated by speciation and that were subsequently brought back in a single genome through allopolyploidization – complements well other homology subtypes commonly used in evolutionary biology. In particular, the table highlights the parallels between homoeologs and orthologs and between homoeologs and ohnologs.

Figure 2

Evolutionary History of an Allopolyploid. An ancestral genome undergoes a speciation event, resulting in two diploid species. The genes, which descended from a common gene in the ancestor, are orthologs. Evolution occurs after speciation, including structural rearrangements, gene duplications, and gene movement. On polyploidization, genes that were once orthologs are now homoeologs. Homoeologous relationships can be one-to-one, one-to-many, or many-to-many depending on the number of duplications since speciation of the progenitors.

Figure I

Typical Chromosome Associations during Meiosis in (A) Autopolyploids and (B) Allopolyploids.

Figure I

Usage of Homeo- versus Homoeo- in the Literature. A search was performed via Scopus of the primary literature up to the end 2015 and included the search terms homoeology, homoeologous, homoeolog, and homoeologue versus their homeo- forms.