Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome

Ge Liu, Jim Thomas, Jeff Touchman, Bob Blakesley, Gerry Bouffard, Stephen M Beckstrom-Sternberg, Jenny McDowell, Baishali Maskeri, Pam Thomas, Shaying Zhao, Jeffrey A. Bailey, S. Cenk Sahinalp, Can Alkan, Eray Tuzun, Erick D. Green, Evan E. Eichler

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109 Scopus citations

Abstract

We performed a detailed analysis of both single-nucleotide and large insertion/deletion events based on large-scale comparison of 10.6 Mb of genomic sequence from lemur, baboon, and chimpanzee to human. Using a human genomic reference, optimal global alignments were constructed from large (>50-kb) genomic sequence clones. These alignments were examined for the pattern, frequency, and nature of mutational events. Whereas rates of single-nucleotide substitution remain relatively constant (1-2 × 10-9 substitutions/site/year), rates of retrotransposition vary radically among different primate lineages. These differences have lead to a 15%-20% expansion of human genome size over the last 50 million years of primate evolution, 90% of it due to new retroposon insertions. Orthologous comparisons with the chimpanzee suggest that the human genome continues to significantly expand due to shifts in retrotransposition activity. Assuming that the primate genome sequence we have sampled is representative, we estimate that human euchromatin has expanded 30 Mb and 550 Mb compared to the primate genomes of chimpanzee and lemur, respectively.

Original languageEnglish (US)
Pages (from-to)358-368
Number of pages11
JournalGenome Research
Volume13
Issue number3
DOIs
StatePublished - Mar 1 2003
Externally publishedYes

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ASJC Scopus subject areas

  • Genetics

Cite this

Liu, G., Thomas, J., Touchman, J., Blakesley, B., Bouffard, G., Beckstrom-Sternberg, S. M., McDowell, J., Maskeri, B., Thomas, P., Zhao, S., Bailey, J. A., Sahinalp, S. C., Alkan, C., Tuzun, E., Green, E. D., & Eichler, E. E. (2003). Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome. Genome Research, 13(3), 358-368. https://doi.org/10.1101/gr.923303