Chromosome rearrangements and the evolution of genome structuring and adaptability

Molecular Biology and Evolution

Volumn 24, Issue 5, 2007, Pages 1130-1139

  Crombach, Anton ^a   Hogeweg, Paulien ^a  

^a UTRECHT UNIVERSITY   (Netherlands)

Author keywords

Evolution; Evolutionary adaptability; Genome structure; Individual oriented model; Retroposons

Indexed keywords

ARTICLE; CHROMOSOME REARRANGEMENT; EVOLUTION; EVOLUTIONARY ADAPTATION; GENE AMPLIFICATION; GENE DELETION; GENE INSERTION; GENE STRUCTURE; NONHUMAN; RETROPOSON;

ADAPTATION, BIOLOGICAL; CHROMOSOMES; EVOLUTION, MOLECULAR; GENE REARRANGEMENT; MODELS, GENETIC; MUTATION; RETROELEMENTS; SELECTION (GENETICS); TERMINAL REPEAT SEQUENCES; VARIATION (GENETICS);

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

EID: 34548304029     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msm033     Document Type: Article

References (30)

1. Biemont C, Vieira C. 2006. Genetics: junk DNA as an evolutionary force. Nature. 443:521-524.
2. 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.
3. Brown C, Todd K, Rosenzweig R. 1998. Multiple duplications of yeast hexose transport genes in response to selection in a glucose-limited environment. Mol Biol Evol. 15:931-942.
4. Cha RS, Kleckner N. 2002. ATR homolog Mec1 promotes fork progression, thus averting breaks in replication slow zones. Science. 297:602-606.
5. Cohen BA, Mitra RD, Hughes JD, Church GM. 2000. A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat Genet. 26:183-186.
6. Dunham M, Badrane H, Ferea T, Adams J, Brown P, Rosenzweig F, Botstein D. 2002. Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proc Natl Acad Sci USA. 99:16144-16149.
7. Edwards RJ, Brookfield JFY. 2003. Transiently beneficial insertions could maintain mobile DNA sequences in variable environments. Mol Biol Evol. 20:30-37.
8. Eichler EE, Sankoff D. 2003. Structural dynamics of eukaryotic chromosome evolution. Science. 301:793-797.
9. Ferea T, Botstein D, Brown P, Rosenzweig R. 1999. Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc Natl Acad Sci USA. 96:9721-9726.
10. Fischer G, James SA, Roberts IN, Oliver SG, Louis EJ. 2000. Chromosomal evolution in Saccharomyces. Nature. 405:451-454.
11. Fischer G, Neuvéglise C, Durrens P, Gaillardin C, Dujon B. 2001. Evolution of gene order in the genomes of two related yeast species. Genome Res. 11:2009-2019.
12. Hogeweg P. 2005. Self-organisation and evolution of social systems. In: Hemelrijk CK, editor. Interlocking of self-organisation and evolution. Cambridge: Cambridge University Press. p. 166-189.
13. Hughes AL, Friedman R. 2004. Transposable element distribution in the yeast genome reflects a role in repeated genomic rearrangement events on an evolutionary time scale. Genetica. 121:181-185.
14. Hughes TR, Roberts CJ, Dai H, et al. (12 co-authors). 2000. Widespread aneuploidy revealed by DNA microarray expression profiling. Nat Genet. 25:333-337.
15. Hurst LD, Pál C, Lercher MJ. 2004. The evolutionary dynamics of eukaryotic gene order. Nat Rev Genet. 5:299-310.
16. Infante JJ, Dombek KM, Rebordinos L, Cantoral JM, Young ET. 2003. Genome-wide amplifications caused by chromosomal rearrangements play a major role in the adaptive evolution of natural yeast. Genetics. 165:1745-1759.
17. Koszul R, Caburet S, Dujon B, Fischer G. 2004. Eucaryotic genome evolution through the spontaneous duplication of large chromosomal segments. EMBO J. 23:234-243.
18. Lambert S, Watson A, Sheedy DM, Martin B, Carr AM. 2005. Gross chromosomal rearrangements and elevated recombination at an inducible site-specific replication fork barrier. Cell. 121:689-702.
19. Lesage P, Todeschini AL. 2005. Happy together: the life and times of Ty retrotransposons and their hosts. Cytogenet Genome Res. 110:70-90.
20. Mieczkowski PA, Lemoine FJ, Petes TD. 2006. Recombination between retrotransposons as a source of chromosome rearrangements in the yeast Saccharomyces cerevisiae. DNA Repair (Amst). 5:1010-1020.
21. Murphy WJ, Larkin DM, van der Wind AE, et al. (25 co-authors). 2005. Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science. 309:613-617.
22. Pepper JW. 2003. The evolution of evolvability in genetic linkage patterns. Biosystems. 69:115-126.
23. Rouzic AL, Capy P. 2005. The first steps of transposable elements invasion: parasitic strategy vs. genetic drift. Genetics. 169:1033-1043.
24. Schacherer J, de Montigny J, Welcker A, Souciet JL, Potier S. 2005. Duplication processes in Saccharomyces cerevisiae haploid strains. Nucleic Acids Res. 33:6319-6326.
25. Schacherer J, Tourrette Y, Souciet JL, Potier S, Montigny JD. 2004. Recovery of a function involving gene duplication by retroposition in Saccharomyces cerevisiae. Genome Res. 14:1291-1297.
26. Seoighe C, Federspiel N, Jones T, et al. (20 co-authors). 2000. Prevalence of small inversions in yeast gene order evolution. Proc Natl Acad Sci USA. 97:14433-14437.
27. Singer GAC, Lloyd AT, Huminiecki LB, Wolfe KH. 2005. Clusters of co-expressed genes in mammalian genomes are conserved by natural selection. Mol Biol Evol. 22:767-775.
28. Teichmann SA, Veitia RA. 2004. Genes encoding subunits of stable complexes are clustered on the yeast chromosomes: an interpretation from a dosage balance perspective. Genetics. 167:2121-2125.
29. Umezu K, Hiraoka M, Mori M, Maki H. 2002. Structural analysis of aberrant chromosomes that occur spontaneously in diploid Saccharomyces cerevisiae: retrotransposon Ty1 plays a crucial role in chromosomal rearrangements. Genetics. 160:97-110.
30. Wilke CM, Adams J. 1992. Fitness effects of Ty transposition in Saccharomyces cerevisiae. Genetics. 131:31-42.