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Functional and evolutionary implications of gene orthology

Nature Reviews Genetics volume 14, pages 360–366 (2013)Cite this article

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Abstract

Orthologues and paralogues are types of homologous genes that are related by speciation or duplication, respectively. Orthologous genes are generally assumed to retain equivalent functions in different organisms and to share other key properties. Several recent comparative genomic studies have focused on testing these expectations. Here we discuss the complexity of the evolution of gene–phenotype relationships and assess the validity of the key implications of orthology and paralogy relationships as general statistical trends and guiding principles.

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Figure 1: Decay of the number of one-to-one orthologues with the increase of the intergenomic evolutionary distance.
Figure 2: Functional divergence versus sequence divergence for orthologues and paralogues.

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Acknowledgements

T.G. is supported by funds from the European Research Council and the Spanish Ministry of Economy and Competitiveness. E.V.K. is supported by intramural funds of the US Department of Health and Human Services (to the US National Library of Medicine).

Author information

Authors and Affiliations

  1. Toni Gabaldón is at the Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG) and Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain.,

    Toni Gabaldón

  2. Eugene V. Koonin is at the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland 20894, USA.,

    Eugene V. Koonin

Authors
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Corresponding authors

Correspondence to Toni Gabaldón or Eugene V. Koonin.

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Glossary

Alternative transcription

The expression of multiple transcripts with different structures from the same gene locus.

Bidirectional best hit

(BBH). A pair of genes that show the greatest sequence similarity to each other in a complete, reciprocal comparison of the gene (protein) sequences from a pair of compared genomes.

Co-orthologue

A gene in a species (or group of species) that is jointly orthologous to the same gene (or genes) in another species (or group of species).

Domain accretion

In evolution, the addition of sequences encoding extra structural domains to protein-coding genes.

Gene Ontology

(GO). A collaborative bioinformatic project aiming at providing an ontology of defined terms representing gene product properties.

In-paralogues

Paralogous genes that originate from a lineage-specific duplication that postdates that reference ancestral species.

Non-homologous and isofunctional

When referring to proteins, these are proteins that in different species carry out equivalent biological functions but are not homologous.

Orthologues

Homologous genes related by speciation.

Orthologous groups

Sets of genes that are inferred to have evolved from a single ancestral gene in the reference ancestral species.

Out-paralogues

Paralogous genes that originate from a duplication that antedates that reference ancestral species.

Paralogues

Homologous genes related by duplication.

Xenologues

Homologous genes that originate from horizontal gene transfer.

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Gabaldón, T., Koonin, E. Functional and evolutionary implications of gene orthology. Nat Rev Genet 14, 360–366 (2013). https://doi.org/10.1038/nrg3456

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