Rapid evolution of yeast centromeres in the absence of drive

Genetics

Volumn 178, Issue 4, 2008, Pages 2161-2167

  Bensasson, Douda ^a,b   Zarowiecki, Magdalena ^a,c   Burt, Austin ^a   Koufopanou, Vassiliki ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY OF MANCHESTER   (United Kingdom)

^c DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SUBSTITUTION; ARTICLE; CENTROMERE; CONTROLLED STUDY; DNA POLYMORPHISM; GENETIC VARIABILITY; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SACCHAROMYCES; AT RICH SEQUENCE; CHROMOSOME; DNA SEQUENCE; GENETIC POLYMORPHISM; GENETIC SELECTION; GENETICS; MOLECULAR GENETICS; MUTATION; PHYLOGENY; SACCHAROMYCES CEREVISIAE;

ANIMALIA; SACCHAROMYCES; SACCHAROMYCES PARADOXUS;

FUNGAL DNA;

AT RICH SEQUENCE; BASE SEQUENCE; CENTROMERE; CHROMOSOMES, FUNGAL; DNA, FUNGAL; EVOLUTION, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; PHYLOGENY; POLYMORPHISM, GENETIC; SACCHAROMYCES CEREVISIAE; SELECTION (GENETICS); SEQUENCE ANALYSIS, DNA;

EID: 44449161646     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.107.083980     Document Type: Article

References (42)

1. AKASHI, H., 2001 Gene expression and molecular evolution. Curr. Opin. Genet. Dev. 11: 660-666.
2. BAKER, R. E., and K. ROGERS, 2005 Genetic and genomic analysis of the AT-rich centromere DNA element II of Saccharomyces cerevisiae. Genetics 171: 1463-1475.
3. BAKER, R. E., and K. ROGERS, 2006 Phylogenetic analysis of fungal centromere H3 proteins. Genetics 174: 1481-1492.
4. BRUDNO, M., C. B. DO, G. M. COOPER, M. F. KIM, E. DAVYDOV et al., 2003 LAGAN and multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 13: 721-731.
5. BUSSELL, J. J., N. M. PEARSON, R. KANDA, D. A. FILATOV and B. T. LAHN, 2006 Human polymorphism and human-chimpanzee divergence in pseudoautosomal region correlate with local recombination rate. Gene 368: 94-100.
6. CHIMPANZEE SEQUENCING AND ANALYSIS CONSORTIUM, 2005 Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69-87.
7. CLARKE, L., 1998 Centromeres: proteins, protein complexes, and repeated domains at centromeres of simple eukaryotes. Curr. Opin. Genet. Dev. 8: 212-218.
8. CLARKE, L., and J. CARBON, 1983 Genomic substitutions of centromeres in Saccharomyces cerevisiae. Nature 305: 23-28.
9. CLIFTEN, P., P. SUDARSANAM, A. DESIKAN, L. FULTON, B. FULTON et al., 2003 Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301: 71-76.
10. DUJON, B., D. SHERMAN, G. FISCHER, P. DURRENS, S. CASAREGOLA et al., 2004 Genome evolution in yeasts. Nature 430: 35-44.
11. EWING, B., and P. GREEN, 1998 Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res. 8: 186-194.
12. FAY, J. C., and J. A. BENAVIDES, 2005 Hypervariable noncoding sequences in Saccharomyces cerevisiae. Genetics 170: 1575-1587.
13. GALTIER, N., M. GOUY and C. GAUTIER, 1996 SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput. Appl. Biosci. 12: 543-548.
14. GOFFEAU, A., B. G. BARRELL, H. BUSSEY, R. W. DAVIS, B. DUJON et al., 1996 Life with 6000 genes. Science 274: 546.
15. GREIG, D., M. TRAVISANO, E. J. LOUIS and R. H. BORTS, 2003 A role for the mismatch repair system during incipient speciation in Saccharomyces. J. Evol. Biol. 16: 429-437.
16. HAAF, T., and H. F. WILLARD, 1997 Chromosome-specific alpha-satellite DNA from the centromere of chimpanzee chromosome 4. Chromosoma 106: 226-232.
17. HADDRILL, P. R., B. CHARLESWORTH, D. L. HALLIGAN and P. ANDOLFATTO, 2005 Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content. Genome Biol. 6: R67.
18. HALL, T. A., 1999 BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41: 95-98.
19. HENIKOFF, S., and Y. DALAL, 2005 Centromeric chromatin: What makes it unique? Curr. Opin. Genet. Dev. 15: 177-184.
20. HENIKOFF, S., K. AHMAD and H. S. MALIK, 2001 The centromere paradox: stable inheritance with rapidly evolving DNA. Science 293: 1098-1102.
21. HIRSH, A. E., H. B. FRASER and D. P. WALL, 2005 Adjusting for selection on synonymous sites in estimates of evolutionary distance. Mol. Biol. Evol. 22: 174-177.
22. HUDSON, R. R., M. KREITMAN and M. AGUADE, 1987 A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153-159.
23. JOHNSON, L. J., V. KOUFOPANOU, M. R. GODDARD, R. HETHERINGTON, S. M. SCHAFER et al., 2004 Population genetics of the wild yeast Saccharomyces paradoxus. Genetics 166: 43-52.
24. KELLIS, M., N. PATTERSON, M. ENDRIZZI, B. BIRREN and E. S. LANDER, 2003 Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241-254.
25. KELLIS, M., B. W. BIRREN and E. S. LANDER, 2004 Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428: 617-624.
26. KOUFOPANOU, V., J. HUGHES, G. BELL and A. BURT, 2006 The spatial scale of genetic differentiation in a model organism: the wild yeast Saccharomyces paradoxus. Philos. Trans. R. Soc. B 361: 1941-1946.
27. LEE, H. R., W. L. ZHANG, T. LANGDON, W. W. JIN, H. H. YAN et al., 2005 Chromatin immunoprecipitation cloning reveals rapid evolutionary patterns of centromeric DNA in Oryza species. Proc. Natl. Acad. Sci. USA 102: 11793-11798.
28. LEVINSON, G., and G. A. GUTMAN, 1987 Slipped-strand mispairing - a major mechanism for DNA-sequence evolution. Mol. Biol. Evol. 4: 203-221.
29. LITI, G., and E. J. LOUIS, 2005 Yeast evolution and comparative genomics. Annu. Rev. Microbiol. 59: 135-153.
30. LITI, G., D. B. H. BARTON and E. J. LOUIS, 2006 Sequence diversity, reproductive isolation and species concepts in Saccharomyces. Genetics 174: 839-850.
31. MA, J., R. A. WING, J. L. BENNETZEN and S. A. JACKSON, 2007 Plant centromere organization: a dynamic structure with conserved functions. Trends Genet. 23: 134-139.
32. MALIK, H. S., and S. HENIKOFF, 2002 Conflict begets complexity: the evolution of centromeres. Curr. Opin. Genet. Dev. 12: 711-718.
33. MURPHY, T. D., and G. H. KARPEN, 1998 Centromeres take flight: alpha satellite and the quest for the human centromere. Cell 93: 317-320.
34. NAUMOV, G. I., E. S. NAUMOVA and P. D. SNIEGOWSKI, 1997 Differentiation of European and Far East Asian populations of Saccharomyces paradoxus by allozyme analysis. Int. J. Syst. Bacteriol. 47: 341-344.
35. SCHEIN, M., Z. YANG, T. MITCHELL-OLDS and K. J. SCHMID, 2004 Rapid evolution of a pollen-specific oleosin-like gene family from Arabidopsis thaliana and closely related species. Mol. Biol. Evol. 21: 659-669.
36. SHAPIRO, J. A., X. Q. HUANG, C. ZHANG, M. J. HUBISZ, J. LU et al., 2007 Adaptive genic evolution in the Drosophila genomes. Proc. Natl. Acad. Sci. USA 104: 2271-2276.
37. SULLIVAN, B. A., M. D. BLOWER and G. H. KARPEN, 2001 Determining centromere identity: cyclical stories and forking paths. Nat. Rev. Genet. 2: 584-596.
38. SWOFFORD, D. L., 1999 PAUP* Phylogenetic Analysis Using Parsimony. Sinauer, Sunderland, MA.
39. THORNTON, K., 2003 libsequence: a C++ class library for evolutionary genetic analysis. Bioinformatics 19: 2325-2327.
40. VENTURA, M., F. ANTONACCI, M. F. CARDONE, R. STANYON, P. D'ADDABBO et al., 2007 Evolutionary formation of new centromeres in macaque. Science 316: 243-246.
41. VILELLA, A. J., A. BLANCO-GARCIA, S. HUTTER and J. ROZAS, 2005 VariScan: analysis of evolutionary patterns from large-scale DNA sequence polymorphismdata. Bioinformatics 21: 2791-2793.
42. WRIGHT, S. I., and B. CHARLESWORTH, 2004 The HKA test revisited: a maximum-likelihood-ratio test of the standard neutral model. Genetics 168: 1071-1076.