Homoeologs: What Are They and How Do We Infer Them?

By Natasha M. Glover, Henning Redestig, Christophe Dessimoz. 2016

179 citations recorded by the source corpus.

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.

Subfields: Ecology, Evolution, Behavior and Systematics, Molecular Biology, Plant Science

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Citations in the corpus

OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more (2020, background): “We have added one allopolyploid species (Xenopus lavis) to the existing ones (Triticum aestivum, Gossypium hirsutum, Brassica napus), for which we also compute homoeologs, which are the related genes resulting from allopolyploidisation (7).”
Polyploidy, the Nucleotype, and Novelty: The Impact of Genome Doubling on the Biology of the Cell (2019, background): “For example, unequal expression (including silencing) of homoeologous loci has been studied extensively in allopolyploids (Yoo et al. 2014; Glover et al. 2016), whereas regulation of genes on the four homologous chromosomes of genetic autopolyploids has received little attention.”
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces (2017, unknown): “For example, we now cover three allopolyploid plant genomes (bread wheat, rapeseed and upland cotton) and provide homoe-ology predictions among them (18).”