Comparative genomic analysis of human and chimpanzee indicates a key role for indels in primate evolution

Journal of Molecular Evolution

Volumn 63, Issue 5, 2006, Pages 682-690

  Wetterbom, Anna ^a   Sevov, Marie ^a   Cavelier, Lucia ^a   Bergström, Tomas F ^a,b  

^a UPPSALA UNIVERSITY   (Sweden)

^b UPPSALA UNIVERSITY   (Sweden)

Author keywords

Chimpanzee; Comparative genomics; Indels; Primate evolution

Indexed keywords

DNA; SPACER DNA; UNTRANSLATED RNA;

AMINO ACID SUBSTITUTION; ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CHIMPANZEE; CHROMOSOME 21; CHROMOSOME 22; CODON; COMPARATIVE GENOMICS; COMPUTER PREDICTION; CONTROLLED STUDY; DNA TRANSCRIPTION; EVOLUTION; GENE DELETION; GENE INSERTION; GENE LOCATION; GENE MUTATION; GENE SEQUENCE; GENETIC VARIABILITY; GENOME ANALYSIS; GENOMICS; HUMAN; HUMAN VERSUS ANIMAL COMPARISON; INDEL; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; PRIMATE; PROTEIN EXPRESSION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STOP CODON;

ANIMALS; BASE SEQUENCE; CHROMOSOME MAPPING; DNA, INTERGENIC; EVOLUTION, MOLECULAR; GENOME; HUMANS; MOLECULAR SEQUENCE DATA; MUTAGENESIS, INSERTIONAL; OPEN READING FRAMES; PAN TROGLODYTES; PRIMATES; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE DELETION; VARIATION (GENETICS);

PAN; PAN TROGLODYTES; PRIMATES;

EID: 33751510984     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-006-0045-7     Document Type: Article

References (26)

1. Anzai T, Shiina T, Kimura N, Yanagiya K, Kohara S, Shigenari A, Yamagata T, Kulski JK, Naruse TK, Fujimori Y, Fukuzumi Y, Yamazaki M, Tashiro H, Iwarmoto C, Umehara Y, Imardshi T, Meyer A, Ikeo K, Gojobori T, Bahram S, Inoko H (2003) Comparative sequencing of human and chimpanzee MHC class I regions unveils insertions/deletions as the major path to genomic divergence. Proc Natl Acad Sci USA 100:7708-7713
2. Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S, Adams MD, Myers EW, Li PW, Eichler EE (2002) Recent segmented duplications in the human genome. Science 297:1003-1007
3. Birney E, Andrews D, Bevan P, Caccamo M, Cameron G, Chen Y, Clarke L, Coates G, Cox T, Cuff J, Curwen V, Cutts T, Down T, Durbin R, Eyras E, Fernandez-Suarez XM, Gane P, Gibbins B, Gilbert J, Hammond M, Hotz H, lyer V, Ka-hari A, Jekosch K, Kasprzyk A, Keefe D, Keenan S, Lehvaslaiho H, McVicker G, Melsopp C, Meidl P, Mongin E, Pettett R, Potter S, Proctor G, Rae M, Searle S, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Ureta-Vidal A, Woodwark C, Clamp M, Hubbard T (2004a) Ensembl 2004. Nucleic Acids Res 32 (Database Issue):D468-D470
4. Birney E, Clamp M, Durbin R (2004b) GeneWise and Genomewise. Genome Res 14:988-995
5. Bray N, Dubchak I, Pachter L (2003) AVID: A global alignment program. Genome Res 13:97-102
6. Britten RJ (2002) Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels. Proc Natl Acad Sci USA 99:13633-13635
7. Britten RJ, Rowen L, Williams J, Cameron RA (2003) Majority of divergence between closely related DNA samples is due to indels. Proc Natl Acad Sci USA 100:4661-4665
8. Chen FC, Vallender EJ, Wang H, Tzeng CS, Li WH (2001) Genomic divergence between human and chimpanzee estimated from large-scale alignments of genomic sequences. J Hered 92:481-489
9. Cheng Z, Ventura M, She X, Khaitovich P, Graves T, Osoegawa K, Church D, deJong P, Wilson RK, Paabo S, Rocchi M, Eichler EE (2005) A genome-wide comparison of recent chimpanzee and human segmental duplications. Nature 437:88-93
10. Choi DK, Suzuki Y, Yoshimura S, Togashi T, Hida M, Taylor TD, Wang Y, Sugano S, Hattori M, Sakaki Y (2001) Molecular cloning and characterization of a gene expressed in mouse developing tongue, mDscr5 gene, a homolog of human DSCR5 (Down syndrome Critical Region gene 5). Mamm Genome 12:347-351
11. Ebersberger I, Metzler D, Schwarz C, Paabo S (2002) Genomewide comparison of DNA sequences between humans and chimpanzees. Am J Hum Genet 70:1490-1497
12. Frazer KA, Chen X, Hinds DA, Pant PV, Patil N, Cox DR (2003) Genomic DNA insertions and deletions occur frequently between humans and nonhuman primates. Genome Res 13:341-346
13. Friedli M, Guipponi M, Bertrand S, Bertrand D, Neerman-Arbez M, Scott HS, Anto-narakis SE, Reymond A (2003) Identification of a novel member of the CLIC family, CLIC6, mapping to 21q22.12. Gene 320:31-40
14. Fujiyama A, Watanabe H, Toyoda A, Taylor TD, Itoh T, Tsai SF, Park HS, Yaspo ML, Lehrach H, Chen Z, Fu G, Saitou N, Osoegawa K, de Jong PJ , Suto Y, Hattori M, Sakaki Y (2002) Construction and analysis of a human-chimpanzee comparative clone map. Science 295:131-134
15. Glazko GV, Nei M (2003) Estimation of divergence times for major lineages of primate species. Mol Biol Evol 20:424-434
16. Hardison RC, Roskin KM, Yang S, Dieklians M, Kent WJ, Weber R, Elnitski L, Li J, O'Connor M, Kolbe D, Schwartz S, Furey TS, Whelan S, Goldman N, Smit A, Miller W Chiaromonte F, Haussler D (2003) Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res 13:13-26
17. Hentze MW, Kulozik AE (1999) A perfect message: RNA surveillance and nonsense-mediated decay. Cell 96:307-310 http://www.ensembl.org
18. Klucken J, Buchler C, Orso E, Kaminski WE, Porsch-Ozcurumez M, Liebisch G, Kapinsky M, Diederich W, Drobnik W, Dean M, Allikmets R, Schmitz G (2000) ABCG1 (ABC8), the human homolog of the Drosophila white gene, is a regulator of macrophage cholesterol and phospholipid transport. Proc Natl Acad Sci USA 97:817-822
19. Kumar S, Filipski A, Swarna V, Walker A, Hedges SB (2005) Placing confidence limits on the molecular age of the human-chimpanzee divergence. Proc Natl Acad Sci USA 102:18842-18847
20. Mikkelsen TS, Hillier LW, Eichler EE, Zody MC, Jaffe DB, Yang S, Enard W, Hellmann I, Lindblad-Toh K, Altheide TK (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437:69-87
21. Misawa K, Janke A (2003) Revisiting the Glires concept - phylogenetic analysis of nuclear sequences. Mol Phylogenet Evol 28:320-327
22. Shibuya K, Kudoh J, Minoshima S, Kawasaki K, Asakawa S, Shimizu N (2000) Isolation of two novel genes, DSCR5 and DSCR6, from Down syndrome critical region on human hromosome 21q22.2. Biochem Biophys Res Commun 271:693-698
23. Smit AFA, Green P (2006) http://repeatmasker.org
24. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
25. Watanabe H, Fujiyama A, Hattori M, Taylor TD, Toyoda A, Kuroki Y, Noguchi H, BenKahla A, Lehrach H, Sudbrak R, Kube M, Taenzer S, Galgoczy P, Platzer M, Scharfe M, Nordsiek G, Blocker H, Hellmann I, Khaitovich P, Paabo S, Reinhardt R, Zheng HJ, Zhang XL, Zhu GF, Wang BF, Fu G, Ren SX, Zhao GP, Chen Z, Lee YS, Cheong JE, Choi SH, Wu KM, Liu TT, Hsiao KJ, Tsai SF, Kim CG, Oota S, Kitano T, Kohara Y, Saitou N, Park HS, Wang SY, Yaspo ML, Sakaki Y (2004) DNA sequence and comparative analysis of chimpanzee chromosome 22. Nature 429:382-388
26. Zhu Y, Xu G, Patel A, McLaughlin MM, Silverman C, Knecht K, Sweitzer S, Li X, McDonnell P, Mirabile R, Zimmerman D, Boyce R, Tierney LA, Hu E, Livi GP, Wolf B, Abdel-Meguid SS, Rose GD, Aurora R, Hensley P, Briggs M, Young PR (2002) Cloning, expression, and initial characterization of a novel cytokine-like gene family. Genomics 80:144-150