Distribution of short paired duplications in mammalian genomes

Proceedings of the National Academy of Sciences of the United States of America
Elizabeth E ThomasMichael Wigler

Abstract

Mammalian genomes are densely populated with long duplicated sequences. In this paper, we demonstrate the existence of doublets, short duplications between 25 and 100 bp, distinct from previously described repeats. Each doublet is a pair of exact matches, separated by some distance. The distribution of these intermatch distances is strikingly nonrandom. An unexpectedly high number of doublets have matches either within 100 bp (adjacent) or at distances tightly concentrated approximately 1,000 bp apart (nearby). We focus our study on these proximate doublets. First, they tend to have both matches on the same strand. By comparing nearby doublets shared in human and chimpanzee, we can also see that these doublets seem to arise by an insertion event that produces a copy without markedly affecting the surrounding sequence. Most doublets in humans are shared with chimpanzee, but many new pairs arose after the divergence of the species. Doublets found in human but not chimpanzee are most often composed of almost tandem matches, whereas older doublets (found in both species) are more likely to have matches spaced by approximately 1 kb, indicating that the nearly tandem doublets may be more dynamic. The spacing of doublets is highly con...Continue Reading

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Citations

Dec 13, 2006·Journal of Molecular Evolution·Emmanuel D Ladoukakis, Adam Eyre-Walker
Apr 22, 2006·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Patrick BassetJacques Hausser
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Dec 6, 2011·BMC Genomics·Anu SironenJohanna Vilkki
Apr 25, 2014·Proceedings of the National Academy of Sciences of the United States of America·Justin N Vaughn, Jeffrey L Bennetzen
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Jul 29, 2016·Magnetic Resonance in Medicine : Official Journal of the Society of Magnetic Resonance in Medicine·Kyong Hwan JinJong Chul Ye
Jan 22, 2005·Molecular Biology and Evolution·Saurabh Sinha, Eric D Siggia
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Feb 26, 2019·Journal of the American Statistical Association·Lorin CrawfordSayan Mukherjee
May 21, 2005·Physical Review Letters·Philipp W MesserMichael Lässig

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