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Large tandem, higher order repeats and regularly dispersed repeat units contribute substantially to divergence between human and chimpanzee Y chromosomes

Paar, Vladimir; Glunčić, Matko; Basar, Ivan; Rosandić, Marija; Paar, Petar; Cvitković, Mislav (2011) Large tandem, higher order repeats and regularly dispersed repeat units contribute substantially to divergence between human and chimpanzee Y chromosomes. Journal of Molecular Evolution, 72 (1). pp. 34-55. ISSN 0022-2844

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Abstract

Comparison of human and chimpanzee genomes has received much attention, because of paramount role for understanding evolutionary step distinguishing us from our closest living relative. In order to contribute to insight into Y chromosome evolutionary history, we study and compare tandems, higher order repeats (HORs), and regularly dispersed repeats in human and chimpanzee Y chromosome contigs, using robust Global Repeat Map (GRM) algorithm. We find a new type of acceleration, human accelerated HOR region. In peripheral domains of 35mer human alphoid HORs, we find riddled features with ten additional repeat monomers. In chimpanzee we identify 30mer alphoid HOR. We construct alphoid HOR schemes showing significant human-chimpanzee difference, revealing rapid evolution after human-chimpanzee separation. We identify and analyze over 20 large repeat units, most of them reported here for the first time as: chimpanzee and human ~1.6 kb 3mer secondary repeat unit (SRU) and ~23.5 kb tertiary repeat unit (~0.55kb primary repeat unit, PRU) ; human 10848, 15775, 20309, 60910, and 72140 bp PRUs ; human 3mer SRU (~2.4 kb PRU) ; 715mer and 1123mer SRUs (5mer PRU) ; chimpanzee 5096, 10762, 10853, 60523 bp PRUs ; and chimpanzee 64624 bp SRU (10853 bp PRU). We show that substantial human-chimpanzee differences are concentrated in large repeat structures, at the level of as much as ~70% divergence, sizably exceeding previous numerical estimates for some selected noncoding sequences. Smeared over the whole sequenced assembly (25 Mb) this gives ~14% human-chimpanzee divergence. This is significantly higher estimate of divergence between human and chimpanzee than previous estimates.

Item Type: Article
Additional Information: The final publication is available at Springer via http://dx.doi.org/10.1007/s00239-010-9401-8
Uncontrolled Keywords: human genome; chimpanzee genome; Y chromosome; male-sspecific region; higher order repeat; tandem repeat; alpha satellite; global repeat map; evolution genetics; long-range regulatory elements
Subjects: NATURAL SCIENCES > Mathematics > Applied Mathematics and Mathematical Modeling
NATURAL SCIENCES > Physics > Biophysics and Medical Physics
NATURAL SCIENCES > Biology > Genetics, Evolution and Phylogenetics
BIOMEDICINE AND HEALTHCARE > Basic Medical Sciences > Human Genetics, Genomics and Proteomics
BIOTECHNICAL SCIENCES > Biotechnology > Bioinformatics
BIOTECHNICAL SCIENCES > Biotechnology > Biology
Divisions: Division of Physical Chemistry
Projects:
Project titleProject leaderProject codeProject type
KSA kompjutorsko istraživanje repeticija višeg reda i duplikona u humanom genomu[34485] Vladimir Paar119-0982464-1253MZOS
Depositing User: Mislav Cvitković
Date Deposited: 20 May 2015 14:45
Last Modified: 20 May 2015 14:45
URI: http://fulir.irb.hr/id/eprint/1935
DOI: 10.1007/s00239-010-9401-8

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