Genomewide association between insertions/deletions and the nucleotide diversity in bacteria

Molecular Biology and Evolution

Volumn 26, Issue 10, 2009, Pages 2353-2361

  Zhu, Liucun ^a   Wang, Qiang ^a   Tang, Ping ^a   Araki, Hitoshi ^a,b   Tian, Dacheng ^a  

^a NANJING UNIVERSITY   (China)

^b SWISS FEDERAL INSTITUTE OF AQUATIC SCIENCE AND TECHNOLOGY   (Switzerland)

Author keywords

Bacteria; Genome; Indel; Molecular evolution; Nucleotide diversity

Indexed keywords

NUCLEOTIDE;

ARTICLE; BACTERIAL GENOME; CONTROLLED STUDY; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC VARIABILITY; INDEL MUTATION; MOLECULAR EVOLUTION; NONHUMAN;

BACTERIA; BASE SEQUENCE; GENETIC VARIATION; GENOME, BACTERIAL; MUTAGENESIS, INSERTIONAL; PHYLOGENY; SEQUENCE DELETION; TIME FACTORS;

BACTERIA (MICROORGANISMS); EUKARYOTA; PROKARYOTA;

EID: 70349934568     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msp144     Document Type: Article

References (19)

1. Bresler SE, Lanzov VA, Blinkova AA. 1967. Mechanism of genetic recombination during bacterial conjugation of Escher-ichia coli K-12. I. Heterogeneity of the progeny of conjugated cells. Genetics. 56:105-116.
2. de Visser JA. 2002. The fate of microbial mutators. Microbiology. 148:1247-1252.
3. Drake JW. 1991. A constant rate of spontaneous mutation in DNA-based microbes. Proc Natl Acad Sci USA. 88: 7160-7164.
4. Duret L. 2009. Mutation patterns in the human genome: more variable than expected. PLoS Biol. 7:217-219.
5. Feil EJ, Holmes EC, Bessen DE, et al. (12 co-authors). 2001. Recombination within natural populations of pathogenic bacteria: short-term empirical estimates and long-term phylogenetic consequences. Proc Natl Acad Sci USA. 98: 182-187.
6. Foster PL. 2004. Adaptive mutation in Escherichia coli. J Bacteriol. 186:4846-4852.
7. Foster PL. 2005. Stress responses and genetic variation in bacteria. Mutat Res. 569:3-11.
8. Giraud A, Matic I, Tenaillon O, Clara A, Radman M, Fons M, Taddei F. 2001. Costs and benefits of high mutation rates: adaptive evolution of bacteria in the mouse gut. Science. 291:2606-2608.
9. Hodgkinson A, Ladoukakis E, Eyre-Walker A. 2009. Cryptic variation in the human mutation rate. PLoS Biol. 7:e1000027. doi:10.1371/journal.pbio.1000027.
10. Jiggins FM. 2002. The rate of recombination in Wolbachia bacteria. Mol Biol Evol. 19:1640-1643.
11. Jukes TH, Cantor CR. 1969. Evolution of protein molecules. In: Munro HN, editor. Mammalian protein metabolism. New York: Academic Press. p. 21-132.
12. Li W-H. 1997. Molecular evolution. Sunderland (MA): Sinauer Associates.
13. Moran NA. 2002. Microbial minimalism: genome reduction in bacterial pathogens. Cell. 108:583-586.
14. Nei M. 1987. Molecular evolutionary genetics. New York: Columbia University Press.
15. 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.
16. Sniegowski PD, Gerrish PJ, Lenski RE. 1997. Evolution of high mutation rates in experimental populations of E. coli. Nature. 387:703-705.
17. Taddei F, Radman M, Maynard-Smith J, Toupance B, Gouyon PH, Godelle B. 1997. Role of mutator alleles in adaptive evolution. Nature. 387:700-702.
18. 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 indels in eukaryotes. Nature. 455:105-108.
19. Vetsigian K, Goldenfeld N. 2005. Global divergence of microbial genome sequences mediated by propagating fronts. Proc Natl Acad Sci USA. 102:7332-7337.