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Comparative Study
. 2003 Mar;13(3):358-68.
doi: 10.1101/gr.923303.

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

Ge Liu  1 ; NISC Comparative Sequencing Program; Shaying Zhao, Jeffrey A Bailey, S Cenk Sahinalp, Can Alkan, Eray Tuzun, Eric D Green, Evan E Eichler
Affiliations
Comparative Study

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

Ge Liu et al. Genome Res. 2003 Mar.

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 x 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.

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Figures

Figure 1.
Figure 1.
Single-nucleotide variation. A scatter plot of genetic distances (changes/bp) determined from nonoverlapping 3-kb sliding windows for human–chimpanzee (51 loci, 5.0 Mb, 9684 windows), human–baboon (42 loci, 5.0 Mb, 8893 windows), and human–lemur (9 loci, 0.62 Mb, 841 windows) sequence alignments. These were plotted against human divergence times of 5.5, 25, and 55 Mya for chimpanzee, baboon, and lemur alignments, respectively. Suboptimal alignments were excluded. The means and their standard deviations are shown.
Figure 2.
Figure 2.
Human vs. lemur genome comparison. Nine orthologous genomic regions between human and lemur were concatenated for each species (lemur: top, human: bottom), and regions of conservation were visualized (parasight). Red bars demarcate the extent of each orthologous alignment. Repeat content for each region is depicted as a colored track: SINE, blue; LINE, pink; DNA transposon, salmon; LTR, cyan; low complexity and simple repeat, red. The human genomic sequence is ∼19% larger.
Figure 3.
Figure 3.
Primate genome size variation. Repetitive and unique portions of aligned orthologous sequences were identified by RepeatMasker (version 3.0, slow option). Relative fractions were based on the larger primate genome. Significance of the difference in genome size was determined by a permutation test (10,000 replicates, see Methods). Asterisks over species bars indicate significant differences in overall lengths, and those between species bars indicate significant differences in either repetitive or unique lengths between two species. *, P < 0.05; **, P < 0.01.
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