Comparative analyses of multi-species sequences from targeted genomic regions (original) (raw)

• Letter
• Published: 14 August 2003
• J. W. Touchman1,2,13 nAff12,
• R. W. Blakesley1,2,
• G. G. Bouffard1,2,
• S. M. Beckstrom-Sternberg1,2,
• E. H. Margulies1,
• M. Blanchette3,
• A. C. Siepel3,
• P. J. Thomas2,
• J. C. McDowell2,
• B. Maskeri2,
• N. F. Hansen2,
• M. S. Schwartz3,
• R. J. Weber3,
• W. J. Kent3,
• D. Karolchik3,
• T. C. Bruen3,
• R. Bevan3,
• D. J. Cutler4,
• S. Schwartz5,
• L. Elnitski5,
• J. R. Idol1,
• A. B. Prasad1,
• S.-Q. Lee-Lin1,
• V. V. B. Maduro1,
• T. J. Summers1,
• M. E. Portnoy1,
• N. L. Dietrich2,
• N. Akhter2,
• K. Ayele2,
• B. Benjamin2,
• K. Cariaga2,
• C. P. Brinkley2,
• S. Y. Brooks2,
• S. Granite2,
• X. Guan2,
• J. Gupta2,
• P. Haghighi2,
• S.-L. Ho2,
• M. C. Huang2,
• E. Karlins2,
• P. L. Laric2,
• R. Legaspi2,
• M. J. Lim2,
• Q. L. Maduro2,
• C. A. Masiello2,
• S. D. Mastrian2,
• J. C. McCloskey2,
• R. Pearson2,
• S. Stantripop2,
• E. E. Tiongson2,
• J. T. Tran2,
• C. Tsurgeon2,
• J. L. Vogt2,
• M. A. Walker2,
• K. D. Wetherby2,
• L. S. Wiggins2,
• A. C. Young2,
• L.-H. Zhang2,
• K. Osoegawa6,
• B. Zhu6,
• B. Zhao6,
• C. L. Shu6,
• P. J. De Jong6,
• C. E. Lawrence7,
• A. F. Smit8,
• A. Chakravarti4,
• D. Haussler3,9,
• P. Green10,
• W. Miller5 &
• …
• E. D. Green1,2

Nature volume 424, pages 788–793 (2003)Cite this article

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Abstract

The systematic comparison of genomic sequences from different organisms represents a central focus of contemporary genome analysis. Comparative analyses of vertebrate sequences can identify coding1,2,3,4,5,6 and conserved non-coding4,6,7 regions, including regulatory elements8,9,10, and provide insight into the forces that have rendered modern-day genomes6. As a complement to whole-genome sequencing efforts3,5,6, we are sequencing and comparing targeted genomic regions in multiple, evolutionarily diverse vertebrates. Here we report the generation and analysis of over 12 megabases (Mb) of sequence from 12 species, all derived from the genomic region orthologous to a segment of about 1.8 Mb on human chromosome 7 containing ten genes, including the gene mutated in cystic fibrosis. These sequences show conservation reflecting both functional constraints and the neutral mutational events that shaped this genomic region. In particular, we identify substantial numbers of conserved non-coding segments beyond those previously identified experimentally, most of which are not detectable by pair-wise sequence comparisons alone. Analysis of transposable element insertions highlights the variation in genome dynamics among these species and confirms the placement of rodents as a sister group to the primates.

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References

1. Batzoglou, S., Pachter, L., Mesirov, J. P., Berger, B. & Lander, E. S. Human and mouse gene structure: comparative analysis and application to exon prediction. Genome Res. 10, 950–958 (2000)
   Article CAS Google Scholar
2. Roest Crollius, H. et al. Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence. Nature Genet. 25, 235–238 (2000)
   Article CAS Google Scholar
3. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001)
   Article Google Scholar
4. Chen, R., Bouck, J. B., Weinstock, G. M. & Gibbs, R. A. Comparing vertebrate whole-genome shotgun reads to the human genome. Genome Res. 11, 1807–1816 (2001)
   Article CAS Google Scholar
5. Aparicio, S. et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297, 1301–1310 (2002)
   Article ADS CAS Google Scholar
6. Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520–562 (2002)
   Article Google Scholar
7. Dubchak, I. et al. Active conservation of noncoding sequences revealed by three-way species comparisons. Genome Res. 10, 1304–1306 (2000)
   Article CAS Google Scholar
8. Gottgens, B. et al. Analysis of vertebrate SCL loci identifies conserved enhancers. Nature Biotechnol. 18, 181–186 (2000)
   Article CAS Google Scholar
9. Hardison, R. C. Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet. 16, 369–372 (2000)
   Article CAS Google Scholar
10. Pennacchio, L. A. & Rubin, E. M. Genomic strategies to identify mammalian regulatory sequences. Nature Rev. Genet. 2, 100–109 (2001)
    Article CAS Google Scholar
11. Rommens, J. M. et al. Identification of the cystic fibrosis gene: chromosome walking and jumping. Science 245, 1059–1065 (1989)
    Article ADS CAS Google Scholar
12. Felsenfeld, A., Peterson, J., Schloss, J. & Guyer, M. Assessing the quality of the DNA sequence from The Human Genome Project. Genome Res. 9, 1–4 (1999)
    CAS PubMed Google Scholar
13. Schwartz, S. et al. Human–mouse alignments with BLASTZ. Genome Res 13, 103–107 (2003)
    Article CAS Google Scholar
14. Schwartz, S. et al. MultiPipMaker and supporting tools: alignments and analysis of multiple genomic DNA sequences. Nucleic Acids Res. 31, 3518–3524 (2003)
    Article CAS Google Scholar
15. Murphy, W. J. et al. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294, 2348–2351 (2001)
    Article ADS CAS Google Scholar
16. Poux, C., Van Rheede, T., Madsen, O. & de Jong, W. W. Sequence gaps join mice and men: phylogenetic evidence from deletions in two proteins. Mol. Biol. Evol. 19, 2035–2037 (2002)
    Article CAS Google Scholar
17. Huelsenbeck, J. P., Larget, B. & Swofford, D. A compound Poisson process for relaxing the molecular clock. Genetics 154, 1879–1892 (2000)
    CAS PubMed PubMed Central Google Scholar
18. Cooper, G. M. et al. Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes. Genome Res. 13, 813–820 (2003)
    Article CAS Google Scholar
19. Siepel, A. & Haussler, D. Proc. 7th Annual Int. Conf. Research in Computational Molecular Biology (ACM, New York, 2003)
    Google Scholar
20. Hardison, R. C. et al. Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res. 13, 13–26 (2003)
    Article CAS Google Scholar
21. Green, P. et al. Transcription-associated mutational asymmetry in mammalian evolution. Nature Genet. 33, 514–517 (2003)
    Article CAS Google Scholar
22. Frazer, K. A. et al. Genomic DNA insertions and deletions occur frequently between humans and nonhuman primates. Genome Res. 13, 341–346 (2003)
    Article CAS Google Scholar
23. Britten, R. J. Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels. Proc. Natl Acad. Sci. USA 99, 13633–13635 (2002)
    Article ADS CAS Google Scholar
24. Springer, M. S., Murphy, W. J., Eizirik, E. & O'Brien, S. J. Placental mammal diversification and the Cretaceous/Tertiary boundary. Proc. Natl Acad. Sci. USA 100, 1056–1061 (2003)
    Article ADS CAS Google Scholar
25. Li, W. H., Ellsworth, D. L., Krushkal, J., Chang, B. H. & Hewett-Emmett, D. Rates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis. Mol. Phylogenet. Evol. 5, 182–187 (1996)
    Article CAS Google Scholar
26. Kumar, S. & Subramanian, S. Mutation rates in mammalian genomes. Proc. Natl Acad. Sci. USA 99, 803–808 (2002)
    Article ADS CAS Google Scholar
27. Shizuya, H. et al. Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc. Natl Acad. Sci. USA 89, 8794–8797 (1992)
    Article ADS CAS Google Scholar
28. Thomas, J. W. et al. Parallel construction of orthologous sequence-ready clone contig maps in multiple species. Genome Res. 12, 1277–1285 (2002)
    Article CAS Google Scholar
29. Burge, C. & Karlin, S. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268, 78–94 (1997)
    Article CAS Google Scholar
30. Kent, W. J. et al. The human genome browser at UCSC. Genome Res. 12, 996–1006 (2002)
    Article CAS Google Scholar

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Acknowledgements

We thank J. Weissenbach and H. Roest Crollius for Tetraodon BACs; M. Diekhans for computational expertise; N. Goldman and Z. Yang for advice on phylogenetic analyses; and F. Collins and J. Mullikin for critically reading the manuscript. We acknowledge the support of the National Human Genome Research Institute (National Institutes of Health) and the Howard Hughes Medical Institute.

Author information

Author notes

1. J. W. Thomas
   Present address: Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, 30322, USA
2. J. W. Touchman
   Present address: Translational Genomics Research Institute, Phoenix, Arizona, 85004

Authors and Affiliations

1. Genome Technology Branch, National Human Genome Research Institute,
   J. W. Thomas, J. W. Touchman, R. W. Blakesley, G. G. Bouffard, S. M. Beckstrom-Sternberg, E. H. Margulies, J. R. Idol, A. B. Prasad, S.-Q. Lee-Lin, V. V. B. Maduro, T. J. Summers, M. E. Portnoy & E. D. Green
2. NIH Intramural Sequencing Center, National Institutes of Health, Bethesda, Maryland, 20892, USA
   J. W. Touchman, R. W. Blakesley, G. G. Bouffard, S. M. Beckstrom-Sternberg, P. J. Thomas, J. C. McDowell, B. Maskeri, N. F. Hansen, N. L. Dietrich, N. Akhter, K. Ayele, B. Benjamin, K. Cariaga, C. P. Brinkley, S. Y. Brooks, S. Granite, X. Guan, J. Gupta, P. Haghighi, S.-L. Ho, M. C. Huang, E. Karlins, P. L. Laric, R. Legaspi, M. J. Lim, Q. L. Maduro, C. A. Masiello, S. D. Mastrian, J. C. McCloskey, R. Pearson, S. Stantripop, E. E. Tiongson, J. T. Tran, C. Tsurgeon, J. L. Vogt, M. A. Walker, K. D. Wetherby, L. S. Wiggins, A. C. Young, L.-H. Zhang & E. D. Green
3. Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California, 95064, USA
   M. Blanchette, A. C. Siepel, M. S. Schwartz, R. J. Weber, W. J. Kent, D. Karolchik, T. C. Bruen, R. Bevan & D. Haussler
4. Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21287, USA
   D. J. Cutler & A. Chakravarti
5. Department of Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
   S. Schwartz, L. Elnitski & W. Miller
6. Children's Hospital Oakland Research Institute, Oakland, California, 94609, USA
   K. Osoegawa, B. Zhu, B. Zhao, C. L. Shu & P. J. De Jong
7. The Wadsworth Center for Laboratories and Research, New York State Department of Health, Albany, New York, 12201, USA
   C. E. Lawrence
8. The Institute for Systems Biology, Seattle, Washington, 98103, USA
   A. F. Smit
9. Howard Hughes Medical Institute, University of California, Santa Cruz, California, 95064, USA
   D. Haussler
10. Howard Hughes Medical Institute and Department of Genome Sciences, University of Washington, Seattle, Washington, 98195, USA
    P. Green
11. Department of Biology, Arizona State University, Tempe, Arizona, 85287, USA
    J. W. Touchman

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1. J. W. Thomas
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2. J. W. Touchman
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3. R. W. Blakesley
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4. G. G. Bouffard
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5. S. M. Beckstrom-Sternberg
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6. E. H. Margulies
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7. M. Blanchette
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8. A. C. Siepel
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9. P. J. Thomas
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10. J. C. McDowell
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11. B. Maskeri
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21. L. Elnitski
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22. J. R. Idol
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23. A. B. Prasad
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24. S.-Q. Lee-Lin
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25. V. V. B. Maduro
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26. T. J. Summers
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37. J. Gupta
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38. P. Haghighi
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39. S.-L. Ho
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40. M. C. Huang
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41. E. Karlins
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42. P. L. Laric
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43. R. Legaspi
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44. M. J. Lim
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45. Q. L. Maduro
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46. C. A. Masiello
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47. S. D. Mastrian
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48. J. C. McCloskey
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49. R. Pearson
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50. S. Stantripop
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51. E. E. Tiongson
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52. J. T. Tran
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53. C. Tsurgeon
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54. J. L. Vogt
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55. M. A. Walker
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64. P. J. De Jong
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65. C. E. Lawrence
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Corresponding author

Correspondence toE. D. Green.

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Thomas, J., Touchman, J., Blakesley, R. et al. Comparative analyses of multi-species sequences from targeted genomic regions.Nature 424, 788–793 (2003). https://doi.org/10.1038/nature01858

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• Received: 11 April 2003
• Accepted: 16 June 2003
• Issue Date: 14 August 2003
• DOI: https://doi.org/10.1038/nature01858

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