Mutagenesis from meiotic recombination is not a primary driver of sequence divergence between Saccharomyces species

Molecular Biology and Evolution

Volumn 25, Issue 11, 2008, Pages 2439-2444

  Noor, Mohamed A F ^a  

^a DUKE UNIVERSITY   (United States)

Author keywords

Divergence; Diversity; Recombination; Saccharomyces

Indexed keywords

DOUBLE STRANDED DNA;

ARTICLE; CROSSING OVER; DNA SEQUENCE; DOUBLE STRANDED DNA BREAK; GENE SEQUENCE; GENETIC RECOMBINATION; GENETIC VARIABILITY; MEIOSIS; MUTAGENESIS; MUTAGENICITY; MUTATION RATE; NONHUMAN; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS; YEAST;

CROSSING OVER, GENETIC; DNA BREAKS, DOUBLE-STRANDED; DNA, FUNGAL; EVOLUTION, MOLECULAR; MEIOSIS; MUTAGENESIS; RECOMBINATION, GENETIC; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; SPECIES SPECIFICITY;

SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 54149106525     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msn186     Document Type: Article

References (45)

1. Aguade M, Miyashita N, Langley CH. 1989. Reduced variation in the yellow-achaete-scute region in natural populations of Drosophila melanogaster. Genetics. 122:607-615.
2. Aquadro CF. 1997. Insights into the evolutionary process from patterns of DNA sequence variability. Curr Opin Genet Dev. 7:835-840.
3. Baudat F, Nicolas A. 1997. Clustering of meiotic double-strand breaks on yeast chromosome III. Proc Natl Acad Sci USA. 94:5213-5218.
4. Begun DJ, Aquadro CF. 1992. Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster. Nature. 356:519-520.
5. Begun DJ, Holloway AK, Stevens K, et al. (13 co-authors). 2007. Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biol. 5:e310.
6. Bennetzen JL, Hall BD. 1982. Codon selection in yeast. J Biol Chem. 257:3026-3031.
7. Blanchette M, Kent WJ, Riemer C, et al. (12 co-authors). 2004. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14:708-715.
8. Blitzblau HG, Bell GW, Rodriguez J, Bell SP, Hochwagen A. 2007. Mapping of meiotic single-stranded DNA reveals double-strand-break hotspots near centromeres and telomeres. Curr Biol. 17:2003-2012.
9. Buhler C, Borde V, Lichten M. 2007. Mapping meiotic single-strand DNA reveals a new landscape of DNA double-strand breaks in Saccharomyces cerevisiae. PLoS Biol. 5:e324.
10. Charlesworth B, Morgan MT, Charlesworth D. 1993. The effect of deleterious mutations on neutral molecular variation. Genetics. 134:1289-1303.
11. Coop G, Myers SR. 2007. Live hot, die young: transmission distortion in recombination hotspots. PLoS Genet. 3:e35.
12. Demogines A, Wong A, Aquadro C, Alani E. 2008. Incompatibilities involving yeast mismatch repair genes: a role for genetic modifiers and implications for disease penetrance and variation in genomic mutation rates. PLoS Genet. 4:e1000103.
13. Doniger SW, Fay JC. 2007. Frequent gain and loss of functional transcription factor binding sites. PLoS Comput Biol. 3:e99.
14. Doniger SW, Huh J, Fay JC. 2005. Identification of functional transcription factor binding sites using closely related Saccharomyces species. Genome Res. 15:701-709.
15. Esposito MS, Bruschi CV. 1993. Diploid yeast cells yield homozygous spontaneous mutations. Curr Genet. 23: 430-434.
16. Faith JJ, Pollock DD. 2003. Likelihood analysis of asymmetrical mutation bias gradients in vertebrate mitochondrial genomes. Genetics. 165:735-745.
17. Fay JC, Benavides JA. 2005. Hypervariable noncoding sequences in Saccharomyces cerevisiae. Genetics. 170:1575-1587.
18. Filatov DA, Gerrard DT. 2003. High mutation rates in human and ape pseudoautosomal genes. Gene. 317:67-77.
19. Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Cherry JM. 2006. Saccharomyces cerevisiae S288C genome annotation: a working hypothesis. Yeast. 23:857-865.
20. Galtier N, Duret L. 2007. Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution. Trends Genet. 23:273-277.
21. Gerton JL, DeRisi J, Shroff R, Lichten M, Brown PO, Petes TD. 2000. Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae. Proc Natl Acad Sci USA. 97:11383-11390.
22. Goffeau A, Barrell BG, Bussey H, et al. (16 co-authors). 1996. Life with 6000 genes. Science. 274(546):563-567.
23. Haddrill PR, Charlesworth B, Halligan DL, Andolfatto P. 2005. Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content. Genome Biol. 6:R67.
24. Halligan DL, Keightley PD. 2006. Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison. Genome Res. 16:875-884.
25. Hawk JD, Stefanovic L, Boyer JC, Petes TD, Farber RA. 2005. Variation in efficiency of DNA mismatch repair at different sites in the yeast genome. Proc Natl Acad Sci USA. 102:8639-8643.
26. Heck JA, Argueso JL, Gemici Z, Reeves RG, Bernard A, Aquadro CF, Alani E. 2006. Negative epistasis between natural variants of the Saccharomyces cerevisiae MLH1 and PMS1 genes results in a defect in mismatch repair. Proc Natl Acad Sci USA. 103:3256-3261.
27. Hellmann I, Ebersberger I, Ptak SE, Paabo S, Przeworski M. 2003. A neutral explanation for the correlation of diversity with recombination rates in humans. Am J Hum Genet. 72: 1527-1535.
28. Hunter N, Chambers SR, Louis EJ, Borts RH. 1996. The mismatch repair system contributes to meiotic sterility in an interspecific yeast hybrid. EMBO J. 15:1726-1733.
29. 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.
30. Kliman RM, Irving N, Santiago M. 2003. Selection conflicts, gene expression, and codon usage trends in yeast. J Mol Evol. 57:98-109.
31. Kulathinal RJ, Bennett SM, Fitzpatrick CL, Noor MA. 2008. Fine-scale mapping of recombination rate in Drosophila refines its correlation to diversity and divergence. Proc Natl Acad Sci USA. 105:10051-10056.
32. Lercher MJ, Hurst LD. 2002. Human SNP variability and mutation rate are higher in regions of high recombination. Trends Genet. 18:337-340.
33. Lynch M, Sung W, Morris K, et al. (11 co-authors). 2008. A genome-wide view of the spectrum of spontaneous mutations in yeast. Proc Natl Acad Sci USA. 105:9272-9277.
34. Magni GE, Von Borstel RC. 1962. Different rates of spontaneous mutation during mitosis and meiosis in yeast. Genetics. 47:1097-1108.
35. Mancera E, Bourgon R, Brozzi A, Huber W, Steinmetz LM. 2008. High-resolution mapping of meiotic crossovers and non-crossovers in yeast. Nature. 454:479-485.
36. MaynardSmith J, Haigh J. 1974. The hitch-hiking effect of a favourable gene. Genet Res. 23:23-35.
37. Nachman MW. 2002. Variation in recombination rate across the genome: evidence and implications. Curr Opin Genet Dev. 12:657-663.
38. Neumann R, Jeffreys AJ. 2006. Polymorphism in the activity of human crossover hotspots independent of local DNA sequence variation. Hum Mol Genet. 15:1401-1411.
39. Nordborg M, Charlesworth B, Charlesworth D. 1996. The effect of recombination on background selection. Genet Res. 67:159-174.
40. Petes TD, Merker JD. 2002. Context dependence of meiotic recombination hotspots in yeast: the relationship between recombination activity of a reporter construct and base composition. Genetics. 162:2049-2052.
41. Roselius K, Stephan W, Stadler T. 2005. The relationship of nucleotide polymorphism, recombination rate and selection in wild tomato species. Genetics. 171:753-763.
42. Stephan W, Langley CH. 1998. DNA polymorphism in lycopersicon and crossing-over per physical length. Genetics. 150:1585-1603.
43. Strathern JN, Shafer BK, McGill CB. 1995. DNA synthesis errors associated with double-strand-break repair. Genetics. 140:965-972.
44. Tenaillon MI, U'Ren J, Tenaillon O, Gaut BS. 2004. Selection versus demography: a multilocus investigation of the domestication process in maize. Mol Biol Evol. 21:1214-1225.
45. Wu TC, Lichten M. 1994. Meiosis-induced double-strand break sites determined by yeast chromatin structure. Science. 263:515-518.