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  • Review Article
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The functional repertoires of metazoan genomes

Nature Reviews Genetics volume 9, pages 689–698 (2008)Cite this article

Key Points

  • Predicting the number of protein-coding genes that are present in a genome is complicated by the presence of pseudogenes, by misannotations of non-coding sequence, by the incompleteness of assemblies and by structural variation. Nevertheless, it seems that gene counts in metazoan genomes vary by less than twofold between approximately 13,000 and 23,000.

  • Different genes in a species evolve at different rates. At one end of the spectrum genes involved in transcriptional and developmental regulation, and other housekeeping genes, tend to duplicate and change their coding and non-coding sequences slowly. At the other end of the spectrum, genes with products that are involved in sensing and responding to the environment tend to experience elevated rates of evolutionary change.

  • Approximately 1% of the human genome lies within protein-coding sequence. A further ∼2% does not encode protein but seems to be functional in divergent mammals, such as mice and humans. Up to an additional 7% of the human genome might be lineage specific: it is functional only in closely related primate species.

  • Vertebrate genomes seem to contain between two and five times more functional sequence than fruitfly genomes.

  • The majority of mammalian transposable elements exhibit no evidence of constraint and therefore are unlikely to be functional. Mobile genetic elements seem to contribute only a minority of eutherian specific and functional sequence.

  • Rates of chromosomal rearrangements vary dramatically across the metazoa but are unlikely to contribute greatly to phenotypic change.

  • Chromosomal rearrangements seem to be concentrated within 'fragile' GC-rich sequence. Increases in GC-content might result from sustained high rates of biased gene conversion.

  • Such mutational biases, together with a reduced efficacy of purifying selection in regions of sustained low recombination, might better explain the landscape of amniotic and nematode chromosomes than models invoking episodes of adaptive evolution.

Abstract

Metazoan genomes are being sequenced at an increasingly rapid rate. For each new genome, the number of protein-coding genes it encodes and the amount of functional DNA it contains are known only inaccurately. Nevertheless, there have been considerable recent advances in identifying protein-coding and non-coding sequences that have remained constrained in diverse species. However, these approaches struggle to pinpoint genomic sequences that are functional in some species but that are absent or not functional in others. Yet it is here, encoded in lineage-specific and functional sequence, that we expect physiological differences between species to be most concentrated.

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Figure 1: Metazoan phylogeny.
Figure 2: A neutral insertion and deletion (indel) model.
Figure 3: Conserved sequence in the fruitfly and the human.
Figure 4: Fragile breakage model.
Figure 5: Nematode chromosomal organization.

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Acknowledgements

I am grateful to all in my group for assistance. My apologies go out to all authors whose work was not cited in this Review owing to space restrictions.

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  1. Department of Physiology, MRC Functional Genomics Unit, University of Oxford, Anatomy and Genetics, Le Gros Clark Building, South Parks Road, Oxford, OX1 3QX, UK

    Chris P. Ponting

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OPTIC: Clade genomics web server

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Glossary

Hill–Robertson interference

When recombination fails to break down linkage disequilibrium between alleles at selected loci the ability of selection to act on these alleles tends to be reduced.

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Ponting, C. The functional repertoires of metazoan genomes. Nat Rev Genet 9, 689–698 (2008). https://doi.org/10.1038/nrg2413

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