A comparative approach shows differences in patterns of numt insertion during hominoid evolution - PubMed (original) (raw)

A comparative approach shows differences in patterns of numt insertion during hominoid evolution

M I Jensen-Seaman et al. J Mol Evol. 2009 Jun.

Abstract

Nuclear integrations of mitochondrial DNA (numts) are widespread among eukaryotes, although their prevalence differs greatly among taxa. Most knowledge of numt evolution comes from analyses of whole-genome sequences of single species or, more recently, from genomic comparisons across vast phylogenetic distances. Here we employ a comparative approach using human and chimpanzee genome sequence data to infer differences in the patterns and processes underlying numt integrations. We identified 66 numts that have integrated into the chimpanzee nuclear genome since the human-chimp divergence, which is significantly greater than the 37 numts observed in humans. By comparing these closely related species, we accurately reconstructed the preintegration target site sequence and deduced nucleotide changes associated with numt integration. From >100 species-specific numts, we quantified the frequency of small insertions, deletions, duplications, and instances of microhomology. Most human and chimpanzee numt integrations were accompanied by microhomology and short indels of the kind typically observed in the nonhomologous end-joining pathway of DNA double-strand break repair. Human-specific numts have integrated into regions with a significant deficit of transposable elements; however, the same was not seen in chimpanzees. From a separate data set, we also found evidence for an apparent increase in the rate of numt insertions in the last common ancestor of humans and the great apes using a polymerase chain reaction-based screen. Last, phylogenetic analyses indicate that mitochondrial-numt alignments must be at least 500 bp, and preferably >1 kb in length, to accurately reconstruct hominoid phylogeny and recover the correct point of numt insertion.

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Figures

Figure 1

Figure 1

Examples of the use of the chimpanzee genomic sequence to accurately define the boundaries of the inserted numt. Shaded nucleotides represent BLAST-defined homology between human mtDNA and the human numt region. Boxed nucleotides are the actual nucleotides inserted, as inferred from comparison to chimpanzee sequence, the proxy for the pre-integration target site. Bold nucleotides indicate insertions in human, or deletions in chimpanzee. Sequences are labeled by species (H=Homo, P=Pan), followed by chromosome number (or “M” for the mitochondrial genome), followed by beginning position rounded to the nearest Mb for nuclear DNA or nearest bp for mitochondrial DNA.

Figure 2

Figure 2

a–c) Examples of microhomology found at numt-nuclear junctions. Black background with white text shows the conservatively defined microhomology used the quantitative analysis, while the shaded nucleotides show possible additional stretches of microhomology. The six junctions shown here exhibit 0, 0, 1, 3, 4, and 5bp of microhomology. Sequences are labeled as in Figure 1. d) Distribution of lengths of microhomology observed at the 37 human-specific numts compared to that described by other for other types of DNA double-strand break repair.

Figure 2

Figure 2

a–c) Examples of microhomology found at numt-nuclear junctions. Black background with white text shows the conservatively defined microhomology used the quantitative analysis, while the shaded nucleotides show possible additional stretches of microhomology. The six junctions shown here exhibit 0, 0, 1, 3, 4, and 5bp of microhomology. Sequences are labeled as in Figure 1. d) Distribution of lengths of microhomology observed at the 37 human-specific numts compared to that described by other for other types of DNA double-strand break repair.

Figure 3

Figure 3

Examples of small duplications accompanying numt integration, derived from flanking direct repeats (a,b), tandem direct repeats (c,d), and inverted repeats (e,f). Shaded nucleotides indicate the duplication while boxed nucleotides indicate the numt and bold nucleotides indicate indels. The underlined nucleotides in c show a perfect complement between the preintegration sequence and the mitochondrial DNA.

Figure 4

Figure 4

a) Transposable element content in 100bp windows flanking human-specific numts. Each column shows the major classes of transposable elements estimated from 7400bp (37 numts × 2 flanking regions × 100bp). Dashed line indicates the average (33.8%) of the total transposable element content found in 10,000 randomly generated data sets (each data set consisted of 37 regions × 2 flanking regions × 100bp). b) Distribution of the total transposable element content of the 10,000 randomly generated data sets, along with the values from the first 100bp and the second 100bp from the flanking regions of the 37 human-specific numts. Asterisk indicates the average of the distribution.

Figure 4

Figure 4

a) Transposable element content in 100bp windows flanking human-specific numts. Each column shows the major classes of transposable elements estimated from 7400bp (37 numts × 2 flanking regions × 100bp). Dashed line indicates the average (33.8%) of the total transposable element content found in 10,000 randomly generated data sets (each data set consisted of 37 regions × 2 flanking regions × 100bp). b) Distribution of the total transposable element content of the 10,000 randomly generated data sets, along with the values from the first 100bp and the second 100bp from the flanking regions of the 37 human-specific numts. Asterisk indicates the average of the distribution.

Figure 5

Figure 5

Observed (above branch) and expected (below branch) distribution of hominoid numt insertions, determined with cross-species PCR, and shown on the universally accepted phylogeny. Bayesian posterior probability estimates of divergence times are given below, taken from Raaum et al. (2005), and used to calculate the expected number of numts on each branch. A significant excess of numts have inserted into the common ancestor of humans and the great apes, following their divergence with gibbons (p < 0.05; indicated by a thick branch).

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