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  • Review Article
  • Published:

Computational approaches to unveiling ancient genome duplications

Nature Reviews Genetics volume 5, pages 752–763 (2004)Cite this article

Key Points

  • Many, if not most, eukaryotic model organisms have had their genome duplicated, sometimes more than once, in their evolutionary past. Such large-scale gene duplication events might explain major leaps in evolution and adaptive radiations of species. Owing to its putative impact on evolution, the search for traces of such events has received much attention of late.

  • Evidence for ancient large-scale gene duplication events comes from the detection and delineation of 'blocks' or 'segments' in the genome that are homologous; that is, that contain a set of homologous genes.

  • Extensive gene loss and gene translocations can obscure homology between two segments. In particular, after tens or hundreds of millions of years of evolution, too few homologous gene pairs might remain in close proximity to detect statistically significant collinearity. More sophisticated bioinformatics approaches are then needed to uncover homology between two segments.

  • One approach to uncover homology in the 'twilight zone' is to combine the gene content and gene order of multiple segments and build so-called genomic profiles. These profiles can then be used as more sensitive probes to sweep the rest of the genome to uncover additional homology.

  • Another strategy for uncovering duplicated segments that have become unrecognizable, because of differential gene loss, is to compare gene order information of a genome with that of the genome of another species. The comparative approach has been proven effective but relies on the assumption that gene order is largely conserved between the genomes of different species.

  • Dating duplication events provides another useful means to find evidence for large-scale gene duplication events. If it can be shown that many gene duplicates were created at about the same time, this can be considered strong evidence to show that most paralogous genes were created by one single event. Absolute dating can be based on synonymous substitution rates, or on the construction and analysis of linear phylogenetic trees.

  • Currently, more genomic sequences are being determined from species that probably carry remnants of whole-genome duplication events. On top of that, they might have experienced lineage-specific segmental duplications. Therefore, it is anticipated that more large-scale gene duplication events in eukaryotic genomes will be unveiled and that the detection of such events will soon become standard procedure.

Abstract

Recent analyses of complete genome sequences have revealed that many genomes have been duplicated in their evolutionary past. Such events have been associated with important biological transitions, major leaps in evolution and adaptive radiations of species. Here, we consider recently developed computational methods to detect such ancient large-scale gene duplication events. Several new approaches have been used to show that large-scale gene duplications are more common than previously thought.

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Figure 1: Gene homology matrix (GHM).
Figure 2: Hidden duplications and transitive homology.
Figure 3: Detection of genomic homology using a genomic profile.
Figure 4: Construction of a gene duplication landscape.
Figure 5: Age distributions of duplicated genes.

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Acknowledgements

I would like to thank all members of the Bioinformatics and Computational Biology Division for their interest and stimulating discussions. I am particularly grateful to Klaas Vandepoele, Cedric Simillion, Dirk Gevers, Jeroen Raes and Kathleen Marchal for critical readings of the manuscript, and to the Department of Plant Systems Biology for continuous support. I also gratefully acknowledge the constructive comments of the three anonymous reviewers.

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  1. Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, Technologiepark 927, Ghent, B-9052, Belgium

    Yves Van de Peer

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FURTHER INFORMATION

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Glossary

SYMPATRIC SPECIATION

Genetic divergence that leads to species formation in the same habitat.

BLOCK OR SEGMENTAL DUPLICATIONS

A duplication of several genes at the same time. The result is two genomic segments that share a similar set of genes and are therefore homologous.

TANDEM DUPLICATION

Duplication of (single) genes that create tandem repeats in the genome. The HOX genes are a well-known example of a gene family generated through tandem duplication.

ANCHOR POINT

A pair of homologous genes in a duplicated segment. Several anchor points in close proximity form strong evidence for a block duplication.

COLLINEARITY

Conservation in gene order and gene content between two genomic segments.

POLYPLOIDY

A polyploid organism has more than two sets of chromosomes.

E-VALUES

The expect value (E) is a parameter that describes the number of hits one can expect to see by chance when searching a database of a particular size. The lower the E-value, the more significant the match is, and the more probable that two sequences are homologous.

PARALOGUES

Homologous genes that have originated through gene duplication events; that is, by tandem, block or whole-genome duplication events.

GRAPH-CLUSTERING ALGORITHM

This is applied to separate, sparsely-connected, dense subgraphs (here gene families). This means that the graph is partitioned in such a way that the distance between the subgraphs (clusters) is maximized, whereas the sum of the distances within each subgraph is minimized.

NON-FUNCTIONALIZATION

When one of the two duplicate genes accumulates deleterious mutations in coding or regulatory sequences that ultimately renders the gene non-functional.

TRANSITIVE HOMOLOGY

When homology between two genes or genomic segments can only be inferred through a third gene or segment.

MULTIPLICON

A set of homologous genomic segments. The multiplication level of a multiplicon refers to the number of homologous segments that the multiplicon consists of.

GENOMIC PROFILES

A genomic profile is formed by genomic segments that combine gene order and gene content. These profiles can then be used to identify more concealed forms of homology.

PARALOGON

Homologous genomic segments created by partial or complete genome duplication.

PARANOME

The complete set of duplicated genes in a genome. The paranome can be formed by both small-scale and large-scale gene duplication events.

SYNTENY

Two loci are called syntenic when they are located on the same chromosome.

SILENT SUBSTITUTIONS

Nucleotide substitutions that do not lead to amino-acid replacements. They are considered to be neutral and to occur in a clocklike manner.

SYNONYMOUS SITE

One at which a nucleotide change does not alter the amino acid encoded.

TETRAPLOID

A tetraploid organism has four sets of homologous chromosomes, instead of the usual two.

AUTOTETRAPOLYPLOID

Tetraploidy, in which all the chromosomes come from the same species; that is, a tetraploid is formed by the doubling of its own genome.

ALLOTETRAPOLYPLOID

An allotetrapolyploid originates by the fusion of the genomes of two different, but closely-related species.

DIPLOIDIZATION

The evolutionary process whereby a polyploid species becomes a diploid again. The molecular basis of diploidization is not known yet.

LINEARIZED TREE

Linearized trees are phylogenetic trees that assume equal evolutionary rates in different lineages since their divergence from a common ancestor. As such trees assume a clocklike behaviour of the underlying molecular marker, a timescale can be superimposed on them.

MOLECULAR CLOCK

The hypothesis that, in any given gene or DNA sequence, mutations accumulate at an approximately constant rate in all evolutionary lineages as long as the gene or the DNA sequence retains its original function.

ISOZYME

Different forms of the same enzyme (synonymous with allozymes), which were used as some of the first biochemically-based genetic markers.

QUADRUPLICATE PARALOGY

Quadruplicate homology, where homology is found between four different genomic segments, is often considered to be evidence for two rounds of large-scale gene duplication (for example, Hox clusters).

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de Peer, Y. Computational approaches to unveiling ancient genome duplications. Nat Rev Genet 5, 752–763 (2004). https://doi.org/10.1038/nrg1449

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