Analysis of Primate Genomic Variation Reveals a Repeat-Driven Expansion of the Human Genome
- Ge Liu1,
- NISC Comparative Sequencing Program2,
- Shaying Zhao3,
- Jeffrey A. Bailey1,
- S. Cenk Sahinalp1,
- Can Alkan1,
- Eray Tuzun1,
- Eric D. Green2, and
- Evan E. Eichler1,4
- 1Department of Genetics, Center for Human Genetics and Center for Computational Genomics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 44106, USA; 2Genome Technology Branch and NIH Intramural Sequencing Center, National Human Genome Research Institute, Bethesda, Maryland 20892, USA; 3The Institute for Genome Research, Rockville, Maryland 20850, USA
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.
[Supplemental material is available online at www.genome.org.]
Footnotes
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↵4 Corresponding author.
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E-MAIL eee{at}po.cwru.edu, FAX (216) 368-3432.
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Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.923303.
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- Received October 22, 2002.
- Accepted January 2, 2003.
- Cold Spring Harbor Laboratory Press
