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

Genome Research

Volumn 13, Issue 3, 2003, Pages 358-368

  Liu, Ge ^a   Thomas, Jim ^b   Touchman, Jeff ^b   Blakesley, Bob ^b   Bouffard, Gerry ^b   Beckstrom Sternberg, Steve ^b   McDowell, Jenny ^b   Maskeri, Baishali ^b   Thomas, Pam ^b   Zhao, Shaying ^c   Bailey, Jeffrey A ^a   Sahinalp, S Cenk ^a   Alkan, Can ^a   Tuzun, Eray ^a   Green, Erick D ^b   Eichler, Evan E ^a  

^a UNIVERSITY HOSPITALS OF CLEVELAND   (United States)

^b NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^c Institute for Genome Research   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SUBSTITUTION; ARTICLE; BABOON; CHIMPANZEE; CONTROLLED STUDY; DNA TRANSPOSITION; GENE DELETION; GENE FREQUENCY; GENE INSERTION; GENE MUTATION; GENETIC ANALYSIS; GENETIC VARIABILITY; HUMAN; HUMAN GENOME; MOLECULAR CLONING; NONHUMAN; PRIMATE; PRIORITY JOURNAL; PROSIMIAN; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

ANIMALS; EVOLUTION, MOLECULAR; GENOME; GENOME, HUMAN; HUMANS; LEMUR; PAPIO; POINT MUTATION; PONGO PYGMAEUS; PRIMATES; RETROELEMENTS; SEQUENCE ALIGNMENT; VARIATION (GENETICS);

LEMUR; MAMMALIA; PAN TROGLODYTES; PAPIO HAMADRYAS; PRIMATES; STREPSIRHINI;

EID: 0037350508     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.923303     Document Type: Article

References (51)

1. Alkan, C., Tuzun, E., Eicher, E.E., Bailey, J.A., and Sahinalp, S.C. 2002. MaM: Multiple alignment manipulator. Currents in computational molecular biology 2002. pp. 3-4. Celera Genomics, Rockville, MD.
2. Aparicio, S., Chapman, J., Stupka, E., Putnam, N., Chia, J.M., Dehal, P., Christoffels, A., Rash, S., Hoon, S., Smit, A., et al. 2002. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297: 1301-1310.
3. Bailey J.A., Gu, Z., Clark, R.A., Reinert, K., Samonte, R.V., Schwartz, S., Adams, M.D., Myers, E.W., Li, P.W., and Eichler, E.E. 2002. Recent segmental duplications in the human genome. Science 297: 1003-1007.
4. Bailey, W.J., Fitch, D.H., Tagle, D.A., Czelusniak, J., Slightom, J.L., and Goodman, M. 1991. Molecular evolution of the ψ η-globin gene locus: Gibbon phylogeny and the hominoid slowdown. Mol. Biol. Evol. 8: 155-184.
5. Batzer, M.A. and Deininger, P.L. 2002. Alu repeats and human genomic diversity. Nat. Rev. Genet. 3: 370-379.
6. Bohossian, H.B., Skaletsky, H., and Page, D.C. 2000. Unexpectedly similar rates of nucleotide substitution found in male and female hominids. Nature 406: 622-625.
7. Britten, R.J. 2002. Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels. Proc. Natl. Acad. Sci. 99: 13633-13635.
8. Chen, F.C. and Li, W.H. 2001. Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. Am. J. Hum. Genet. 68: 444-456.
9. Chen, F.C., Vallender, E.J., Wang, H., Tzeng, C.S., and Li, W.H. 2001. Genomic divergence between human and chimpanzee estimated from large-scale alignments of genomic sequences. J. Hered. 92: 481-489.
10. Chiaromonte, F., Yang, S., Elnitski, L., Yap, V.B., Miller, W., and Hardison, R.C. 2001. Association between divergence and interspersed repeats in mammalian noncoding genomic DNA. Proc. Natl. Acad. Sci. 98: 14503-14508.
11. Cooper, G., Rubinsztein, D.C., and Amos, W. 1998. Ascertainment bias cannot entirely account for human microsatellites being longer than their chimpanzee homologues. Hum. Mol. Genet. 7: 1425-1429.
12. Dehal, P., Predki, P., Olsen, A.S., Kobayashi, A., Folta, P., Lucas, S., Land, M., Terry, A., Ecale Zhou, C.L., Rash, S., et al. 2001. Human chromosome 19 and related regions in mouse: Conservative and lineage-specific evolution. Science 293: 104-111.
13. Deininger, P.L. and Batzer, M.A. 1999. Alu repeats and human disease. Mol. Genet. Metab. 67: 183-193.
14. Deininger, P.L. and Batzer, M.A. 2002. Mammalian retroelements. Genome Res. 12: 1445-1465.
15. Ebersberger, I., Metzler, D., Schwarz, C., and Paabo, S. 2002. Genomewide comparison of DNA sequences between humans and chimpanzees. Am. J. Hum. Genet. 70: 1490-1497.
16. Eichler, E.E. and DeJong, P.J. 2002. Biomedical applications and studies of molecular evolution: A proposal for a primate genomic library resource. Genome Res. 12: 673-678.
17. Felsenfeld, A., Peterson, L, Schloss, J., and Guyer, M. 1999. Assessing the quality of the DNA sequence from the Human Genome Project. Genome Res. 9: 1-4.
18. Fujiyama, A., Watanabe, H., Toyoda, A., Taylor, T.D., Itoh, T., Tsai, S.F., Park, H.S., Yaspo, M.L., Lehrach, H., Chen, Z., et al. 2002. Construction and analysis of a human-chimpanzee comparative clone map. Science 295: 131-134.
19. Gilbert N., Lutz-Prigge, S., and Moran, J.V. 2002. Genomic deletions created upon LINE-1 retrotransposition. Cell 110: 315-325.
20. Goodman, M. 1999. The genomic record of humankind's evolutionary roots. Am. J. Hum. Genet. 64: 31-39.
21. Goodman, M., Barnabas, J., Matsuda, G., and Moore, G.W. 1971. Molecular evolution in the descent of man. Nature 233: 604-613.
22. Horai, S., Hayasaka, K., Kondo, R., Tsugane, K., and Takahata, N. 1995. Recent African origin of modern humans revealed by complete sequences of hominoid mitochondrial DNAs. Proc. Natl. Acad. Sci. 92: 532-536.
23. Hurles, M.E. 2001. Gene conversion homogenizes the CMT1A paralogous repeats. BMC Genomics 2: 11-19.
24. International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-920.
25. Kaessmann, H., Wiebe, V., and Paabo, S. 1999. Extensive nuclear DNA sequence diversity among chimpanzees. Science 286: 1159-1162.
26. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16: 111-120.
27. Koop, B.F., Miyamoto, M.M., Embury, J.E., Goodman, M., Czelusniak, J., and Slightom, J.L. 1986. Nucleotide sequence and evolution of the orangutan ε globin gene region and surrounding Alu repeats. J. Mol. Evol. 24: 94-102.
28. Kumar, S. and Hedges, S.B. 1998. A molecular timescale for vertebrate evolution. Nature 392: 917-920.
29. Kumar, S., Tamura, K., Jakobsen, I.B., and Nei, M. 2001. MEGA2: Molecular evolutionary genetics analysis software. Bioinformatics 17: 1244-1245.
30. Li, W. 1997. Molecular evolution. pp. 177-213. Sinauer Associates, Sunderland, MA.
31. Li, W.H. and Tanimura, M. 1987.The molecular clock runs more slowly in man than in apes and monkeys. Nature 326: 93-96.
32. Martin, R.D. 1990. Primate origins and evolution: A phylogenetic reconstruction. pp. 558-559. University Press, Princeton, NJ.
33. Moran, J.V., DeBerardinis, R.J., and Kazazian, Jr., H.H. 1999. Exon shuffling by L1 retrotransposition. Science 283: 1530-1534.
34. Mural, R.J., Adams, M.D., Myers, E.W., Smith, H.O., Miklos, G.L., Wides, R., Halpern, A., Li, P.W., Sutton, G.G., Nadeau, J., et al. 2002. A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science 296: 1661-1671.
35. Myers, E.W. and Miller, W. 1988. Optimal alignments in linear space. Comput. Appl. Biosci. 4: 11-17.
36. Parsons, J. 1995. Miropeats: Graphical DNA sequence comparisons. Comput. Appl. Biosci. 11: 615-619.
37. Pellicciari, C., Formenti, D., C.A. Redi, and M.R. M.G. 1982. DNA content variability in primates. J. Hum. Evol. 11: 131-141.
38. Perna, N.T., Batzer, M.A., Deininger, P.L., and Stoneking, M. 1992. Alu insertion polymorphism: A new type of marker for human population studies. Hum. Biol. 64: 641-648.
39. Powell, J.R. and Caccone, A. 1990. The TEACL method of DNA-DNA hybridization: Technical considerations. J. Mol. Evol. 30: 267-272.
40. Ruvolo, M. 1997. Molecular phylogeny of the hominoids: Inferences from multiple independent DNA sequence data sets. Mol. Biol. Evol. 14: 248-265.
41. Shen, M.-R., Batzer, M., and Deininger, P. 1991. Evolution of the master Alu gene(s). J. Mol. Evol. 33: 311-320.
42. Sibley, C.G. and Ahlquist, J.E. 1984. The phylogeny of the hominoid primates, as indicated by DNA-DNA hybridization. J. Mol. Evol. 20: 2-15.
43. Sibley, C.G., Comstock, J.A., and Ahlquist, J.E. 1990. DNA hybridization evidence of hominoid phylogeny: A reanalysis of the data. J. Mol. Evol. 30: 202-236.
44. Smit, A.F. 1999. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr. Opin. Genet. Dev. 9: 657-663.
45. Smith, J. 1992. Evolutionary biology. Byte-sized evolution. Nature 355: 772-773.
46. Smith, N.G., Webster, M.T., and Ellegren, H. 2002. Deterministic mutation rate variation in the human genome. Genome Res. 12: 1350-1356.
47. Thomas, J.W., Prasad, A.B., Summers, T.J., Lee-Lin, S.Q., Maduro, V.V., Idol, J.R., Ryan, J.F., Thomas, P.J., McDowell, J.C., and Green, E.D. 2002. Parallel construction of orthologous sequence-ready clone contig maps in multiple species. Genome Res. 12: 1277-1285.
48. Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton, G.G., Smith, H.O., Yandell, M., Evans, C.A., Holt, R.A., et al. 2001. The sequence of the human genome. Science 291: 1304-1351.
49. Webster, M.T., Smith, N.G., and Ellegren, H. 2002. Microsatellite evolution inferred from human-chimpanzee genomic sequence alignments. Proc. Natl. Acad. Sci. 99: 8748-8753.
50. Zhao, S., Malek, J., Mahairas, G., Fu, L., Nierman, W., Venter, J.C., and Adams, M.D. 2000. Human BAC ends quality assessment and sequence analyses. Genomics 63: 321-332.
51. Zuckerkandl, E. and Pauling, L. 1965. Molecules as documents of evolutionary history. J. Theor. Biol. 8: 357-366.