Polyploid Origin of the Human Genome

Abstract

Accumulated evidence indicates strongly that two rounds of whole‐genome duplication (2R‐WGD) took place in the vertebrate lineage after its separation from invertebrate chordates; hence, the human genome can be regarded as paleooctoploid. The vertebrate genome often contains closely linked sets of paralogous genes (paralogues) on typically four different chromosomes. This genome architecture is widely believed to reflect the remnants of 2R‐WGD. In honour of Susumu Ohno, who initially proposed that the vertebrate genome underwent one or two rounds of tetraploidisation, paralogues that arose by 2R‐WGD are called ohnologues. Only 15% to 30% of human genes are members of the ohnologue families, indicating that most of the duplicated copies generated by 2R‐WGD were lost. Preferentially retained after WGD are dosage‐sensitive genes such as those encoding components of the complex biological machines or cascades.

Key Concepts:

  • 2R‐WGD took place in the vertebrate lineage after its separation from invertebrate chordates.

  • The strong evidence supporting 2R‐WGD is the occurrence of closely linked sets of paralogues on typically four different chromosomes.

  • WGD enabled duplicated genes to coevolve efficiently, thus leading to the formation of gene networks required for biological innovations.

  • After gene duplication, one of the duplicated copies becomes redundant and usually begins to accumulate deleterious mutations, resulting in its eventual loss.

  • An important requisite for the retention of duplicated genes is their divergence to acquire new functions or to partition the functions of their ancestral gene.

  • Dosage‐sensitive genes tend to be preferentially retained after WGD.

Keywords: genome paralogy; HOX genes; major histocompatibility complex; ‘one‐to‐four’ rule; tetraploidisation; whole‐genome duplication

Figure 1.

Two examples of genome paralogy in the human genome. Only a fraction of the gene families that share copies among paralogons are shown. For more detailed listing of such gene families see Table . Genes are arranged arbitrarily to emphasise the corresponding paralogues.

Figure 2.

Phylogenetic relationship of deuterostomes. Arrows indicate the timing of WGD. It is not established whether the second round of WGD occurred before or after the emergence of the jawless vertebrate. For this reason, the tree does not include the jawless vertebrate. A fish‐specific WGD is denoted as FSGD. Representative species are shown in parentheses. Mya, million years ago.

Figure 3.

Problems encountered when estimating the divergence time of paralogous copies. In (a), where paralogous copies diverged by WGD, the divergence time matches the age of WGD. As shown in (b), however, paralogous copies can also arise by tandem duplication that took place much earlier than the origin of vertebrates. In this case, the divergence time of paralogous copies does not match the age of WGD.

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Further Reading

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How to Cite close
Kasahara, Masanori(Jan 2013) Polyploid Origin of the Human Genome. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0005071.pub3]