Bidirectional Best Hits Miss Many Orthologs in Duplication-Rich Clades such as Plants and Animals
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Bidirectional best hits (BBH), which entails identifying the pairs of genes in two different genomes that are more similar to each other than either is to any other gene in the other genome, is a simple and widely used method to infer orthology. A recent study has analyzed the link between BBH and orthology in bacteria and archaea and concluded that, given the very high consistency in BBH they observed among triplets of neighboring genes, a high proportion of BBH are likely to be bona fide orthologs. However, limited by their analysis setup, the previous study could not easily test the reverse question: which proportion of orthologs are BBH? In this follow-up study, we consider this question in theory and answer it based on conceptual arguments, simulated data, and real biological data from all three domains of life. Our analyses corroborate the findings of the previous study, but also show that because of the high rate of gene duplication in plants and animals, as much as 60% of orthologous relations are missed by the BBH criterion.
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Errors from score-based estimates can be mitigated by analysis of phylogenetic trees of genes, because phylogenetic trees distinguish variable sequence evolution rates (branch lengths) from the order in which sequences diverged (tree topology) and hence clarify orthology and paralogy relationships.
“Such errors can be mitigated by the analysis of phylogenetic trees of genes [17], as phylogenetic trees are able to distinguish variable sequence evolution rates (branch lengths) from the order in which sequences diverged (tree topology) and hence clarify orthology and paralogy relationships (Fig. 1).”
From OrthoFinder: phylogenetic orthology inference for comparative genomics (2019) · cites this paper as [17]
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Whelan, S., & Goldman, N. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003851 · Cited by 2,849 · see citing works
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OrthoFinder: phylogenetic orthology inference for comparative genomics
Emms, D. M., & Kelly, S. (2019) · Genome Biology · doi:10.1186/s13059-019-1832-y · Cited by 7,676 · see citing works
- Authors
- Dalquen, D. A., & Dessimoz, C.
- Affiliations
- SIB Swiss Institute of Bioinformatics (CH)
- Corresponding author
- Dalquen, Daniel A.
- Dessimoz, Christophe
- ORCID
- Dessimoz, Christophe
- Venue
- Genome Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-09-06
- Volume
- 5
- Issue
- 10
- Pages
- 1800-1806
- ISSN
- 1759-6653 (ISSN-L)
- PMC
- PMC3814191
- OpenAlex
- W2136258184
- Cited by
- 86
- References
- 1
- Citations by year
- 2026: 3 · 2025: 5 · 2024: 8 · 2023: 3 · 2022: 6 · 2021: 2 · 2020: 10 · 2019: 11 · 2018: 5 · 2017: 9 · 2016: 7 · 2015: 14 · 2014: 2 · 2013: 1
- FWCI
- 3.01
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by-nc
- Locations
- Genome Biology and Evolution (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Funders
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (136461)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Keywords
- orthology inference, gene duplication, ortholog detection, plants, animals, bacteria, archaea, simulated data
- MeSH terms
- Algorithms, Animals, Phylogeny, Plants, Conserved Sequence, Evolution, Molecular, Gene Duplication
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