More single-nucleotide mutations surround small insertions than small deletions in primates

Human Mutation

Volumn 33, Issue 7, 2012, Pages 1099-1106

  Huang, Shengfeng ^a   Yu, Ting ^a   Chen, Zelin ^a   Yuan, Shaochun ^a   Chen, Shangwu ^a   Xu, Anlong ^a  

^a SUN YAT SEN UNIVERSITY   (China)

Author keywords

Deletion; Genome; Human population; Insertion; Primate; Selection; Single nucleotide mutation

Indexed keywords

CYTOSINE; GUANINE;

ARTICLE; BASE PAIRING; CONCENTRATION (PARAMETERS); EXON; GENE DELETION; GENE INSERTION; GENE REPLICATION; GENE SEQUENCE; GENETIC RECOMBINATION; GENETIC SELECTION; GENOMICS; HETEROZYGOSITY; INTRON; MOLECULAR EVOLUTION; MOLECULAR MECHANICS; NONHUMAN; PHENOTYPE; PRIMATE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; HETEROZYGOTE; MUTAGENESIS, INSERTIONAL; MUTATION; PRIMATES; SEQUENCE DELETION;

PRIMATES;

EID: 84861902210     PISSN: 10597794     EISSN: 10981004     Source Type: Journal    
DOI: 10.1002/humu.22085     Document Type: Article

References (38)

1. Ball EV, Stenson PD, Abeysinghe SS, Krawczak M, Cooper DN, Chuzhanova NA. 2005. Microdeletions and microinsertions causing human genetic disease: common mechanisms of mutagenesis and the role of local DNA sequence complexity. Hum Mutat 26:205-213.
2. Bhangale TR, Rieder MJ, Livingston RJ, Nickerson DA. 2005. Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genes. Hum Mol Genet 14:59-69.
3. Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, Haussler D, Miller W. 2004. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 14:708-715.
4. 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.
5. Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, Green ED, Sidow A, Batzoglou S. 2003. LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res 13:721-731.
6. Cardoso-Moreira MM, Long M. 2010. Mutational bias shaping fly copy number variation: implications for genome evolution. Trends Genet 26:243-247.
7. Cartwright RA. 2009. Problems and solutions for estimating indel rates and length distributions. Mol Biol Evol 26:473-480.
8. Chen CH, Chuang TJ, Liao BY, Chen FC. 2009a. Scanning for the signatures of positive selection for human-specific insertions and deletions. Genome Biol Evol 2009:415-419.
9. Chen FC, Chen CJ, Li WH, Chuang TJ. 2007. Human-specific insertions and deletions inferred from mammalian genome sequences. Genome Res 17:16-22.
10. Chen JQ, Wu Y, Yang H, Bergelson J, Kreitman M, Tian D. 2009b. Variation in the ratio of nucleotide substitution and indel rates across genomes in mammals and bacteria. Mol Biol Evol 26:1523-1531.
11. De S, Babu MM. 2010. A time-invariant principle of genome evolution. Proc Natl Acad Sci USA 107:13004-13009.
12. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792-1797.
13. Fan Y, Wang W, Ma G, Liang L, Shi Q, Tao S. 2007. Patterns of insertion and deletion in Mammalian genomes. Curr Genomics 8:370-378.
14. Hardison RC, Roskin KM, Yang S, Diekhans 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.
15. Hinds DA, Kloek AP, Jen M, Chen X, Frazer KA. 2006. Common deletions and SNPs are in linkage disequilibrium in the human genome. Nat Genet 38:82-85.
16. Hubbard TJ, Aken BL, Ayling S, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Clarke L and others. 2009. Ensembl 2009. Nucleic Acids Res 37:D690-D697.
17. Jukes TH, Cantor CR. 1969. Evolution of protein molecules. In Mammalian protein metabolism. New York: Academic. p 21-132.
18. Katoh K, Asimenos G, Toh H. 2009. Multiple alignment of DNA sequences with MAFFT. Methods Mol Biol 537:39-64.
19. Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423:241-254.
20. Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. 2003. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA 100:11484-11489.
21. Kvikstad EM, Chiaromonte F, Makova KD. 2009. Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions. Genome Res 19:1153-1164.
22. Kvikstad EM, Tyekucheva S, Chiaromonte F, Makova KD. 2007. A macaque's-eye view of human insertions and deletions: differences in mechanisms. PLoS Comput Biol 3:1772-1782.
23. Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G, Lin Y, MacDonald JR, Pang AW. 2007. The diploid genome sequence of an individual human. PLoS Biol 5:e254.
24. Lunter G. 2007. Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes. Bioinformatics 23:i289-i296.
25. McDonald MJ, Wang WC, Huang HD, Leu JY. 2011. Clusters of nucleotide substitutions and insertion/deletion mutations are associated with repeat sequences. PLoS Biol 9:e1000622.
26. Messer PW, Arndt PF. 2007. The majority of recent short DNA insertions in the human genome are tandem duplications. Mol Biol Evol 24:1190-1197.
27. Myers S, Bottolo L, Freeman C, McVean G, Donnelly P. 2005. A fine-scale map of recombination rates and hotspots across the human genome. Science 310:321-324.
28. Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ and others. 2010. The UCSC Genome Browser database: update 2010. Nucleic Acids Res 38:D613-D619.
29. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. 2003. Human-mouse alignments with BLASTZ. Genome Res 13:103-107.
30. Stamatoyannopoulos JA, Adzhubei I, Thurman RE, Kryukov GV, Mirkin SM, Sunyaev SR. 2009. Human mutation rate associated with DNA replication timing. Nat Genet 41:393-395.
31. Tanay A, Siggia ED. 2008. Sequence context affects the rate of short insertions and deletions in flies and primates. Genome Biol 9:R37.
32. Tarailo-Graovac M, Chen N. 2009. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinformatics Chapter 4:Unit 4.10.
33. Taylor MS, Ponting CP, Copley RR. 2004. Occurrence and consequences of coding sequence insertions and deletions in Mammalian genomes. Genome Res 14:555-566.
34. Thompson JD, Gibson TJ, Higgins DG. 2002. Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics Chapter 2:Unit 2 3.
35. Tian D, Wang Q, Zhang P, Araki H, Yang S, Kreitman M, Nagylaki T, Hudson R, Bergelson J, Chen JQ. 2008. Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes. Nature 455:105-108.
36. Weddington N, Stuy A, Hiratani I, Ryba T, Yokochi T, Gilbert DM. 2008. ReplicationDomain: a visualization tool and comparative database for genome-wide replication timing data. BMC Bioinformatics 9:530.
37. Zhang W, Sun X, Yuan H, Araki H, Wang J, Tian D. 2008. The pattern of insertion/deletion polymorphism in Arabidopsis thaliana. Mol Genet Genomics 280:351-361.
38. Zhu L, Wang Q, Tang P, Araki H, Tian D. 2009. Genomewide association between insertions/deletions and the nucleotide diversity in bacteria. Mol Biol Evol 26:2353-2361.