Highly variable rates of genome rearrangements between hemiascomycetous yeast lineages

PLoS Genetics

Volumn 2, Issue 3, 2006, Pages 0253-0261

  Fischer, Gilles ^a   Rocha, Eduardo P C ^b,c   Brunet, Frédéric ^d   Vergassola, Massimo ^b   Dujon, Bernard ^a  

^a CNRS   (France)

^b INSTITUT PASTEUR   (France)

^c SORBONNE UNIVERSITÉ   (France)

^d UNIVERSITÉ DE LYON   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ASCOMYCETES; CALCULATION; CANDIDA ALBICANS; CANDIDA GLABRATA; CHROMOSOME MAP; CORRELATION ANALYSIS; EUKARYOTE; EVOLUTION; GENE REARRANGEMENT; GENOMIC INSTABILITY; HEMIASCOMYCETE; NONHUMAN; PHYLOGENETIC TREE; SACCHAROMYCES CEREVISIAE; SPECIES DIFFERENCE; YEAST; BACTERIAL GENOME; CHROMOSOME; FUNGAL GENE; GENETICS; GENOME; MOLECULAR EVOLUTION; PHYLOGENY; STATISTICAL MODEL;

ASCOMYCOTA; CANDIDA ALBICANS; CANDIDA GLABRATA; CHORDATA; EUKARYOTA; SACCHAROMYCES CEREVISIAE;

CANDIDA ALBICANS; CANDIDA GLABRATA; CHROMOSOME MAPPING; CHROMOSOMES, FUNGAL; EVOLUTION, MOLECULAR; GENES, FUNGAL; GENOME, BACTERIAL; GENOME, FUNGAL; MODELS, STATISTICAL; PHYLOGENY; SACCHAROMYCES CEREVISIAE; SPECIES SPECIFICITY;

EID: 33645787782     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.0020032     Document Type: Article

References (32)

1. Pfaller MA, Jones RN, Doern GV, Sader HS, Messer SA, et al. (2000) Bloodstream infections due to Candida species: SENTRY antimicrobial surveillance program in North America and Latin America, 1997-1998. Antimicrob Agents Chemother 44: 747-751.
2. Nishikawa A, Tomomatsu H, Sugita T, Ikeda R, Shinoda T (1996) Taxonomic position of clinical isolates of Candida famata. J Med Vet Mycol 34: 411-419.
3. Wong B, Kiehn TE, Edwards F, Bernard EM, Marcove RC, et al. (1982) Bone infection caused by Debaryomyces hansenii in a normal host: A case report. J Clin Microbiol 16: 545-548.
4. Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, et al. (2004) Genome evolution in yeasts. Nature 430: 35-44.
5. Makalowski W, Boguski MS (1998) Evolutionary parameters of the transcribed mammalian genome: An analysis of 2,820 orthologous rodent and human sequences. Proc Natl Acad Sci U S A 95: 9407-9412.
6. Malpertuy A, Tekaia F, Casaregola S, Aigle M, Artiguenave F, et al. (2000) Genomic exploration of the hemiascomycetous yeasts: 19. Ascomycetes - Specific genes. FEBS Lett 487: 113-121.
7. 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.
8. Llorente B, Malpertuy A, Neuveglise C, de Montigny J, Aigle M, et al. (2000) Genomic exploration of the hemiascomycetous yeasts: 18. Comparative analysis of chromosome maps and synteny with Saccharomyces cerevisiae. FEBS Lett 487: 101-112.
9. Fischer G, Neuveglise 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.
10. Fischer G, James SA, Roberts IN, Oliver SG, Louis EJ (2000) Chromosomal evolution in Saccharomyces. Nature 405: 451-454.
11. Wolfe KH, Shields DC (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387: 708-713.
12. Dietrich FS, Voegeli S, Brachat S, Lerch A, Gates K, et al. (2004) The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science 304: 304-307.
13. Kellis M, Birren BW, Lander ES (2004) Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428: 617-624.
14. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, et al. (1996) Life with 6000 genes. Science 274: 546, 563-567.
15. Jones T, Federspiel NA, Chibana H, Dungan J, Kalman S, et al. (2004) The diploid genome sequence of Candida albicans. Proc Natl Acad Sci U S A 101: 7329-7334.
16. Cliften P, Sudarsanam P, Desikan A, Fulton L, Fulton B, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301: 71-76.
17. Liti G, Louis EJ (2005) Yeast evolution and comparative genomics. Annu Rev Microbiol 59: 135-153.
18. Rocha EP (2003) DNA repeats lead to the accelerated loss of gene order in bacteria. Trends Genet 19: 600-603.
19. Rocha EP (2005) Inference and analysis of the relative stability of bacterial chromosomes. Mol Biol Evol. 23: 513-522.
20. Seoighe C, Federspiel N, Jones T, Hansen N, Bivolarovic V, et al. (2000) Prevalence of small inversions in yeast gene order evolution. Proc Natl Acad Sci U S A 97: 14433-14437.
21. Hurst LD, Pal C, Lercher MJ (2004) The evolutionary dynamics of eukaryotic gene order. Nat Rev Genet 5: 299-310.
22. Pal C, and Hurst LD (2003) Evidence for co-evolution of gene order and recombination rate. Nat Genet 33: 392-395.
23. Wall DP, Hirsh AE, Fraser HB, Kumm J, Giaever G, et al. (2005) Functional genomic analysis of the rates of protein evolution. Proc Natl Acad Sci U S A 102: 5483-5488.
24. Bourque G, Zdobnov EM, Bork P, Pevzner PA, Tesler G (2005) Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. Genome Res 15: 98-110.
25. Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, et al. (2004) Genome duplication in the teleost .sh Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431: 946-957.
26. Pearson WR (1990) Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol 183: 63-98.
27. Schmidt HA, Strimmer K, Vingron M, von Haeseler A (2002) TREEPUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18: 502-504.
28. Felsenstein J (2005) PHYLIP (Phylogeny Inference Package) version 3.6 [computer program]. Distributed by the author. Seattle: Department of Genome Sciences, University of Washington.
29. Blanchette M, Kunisawa T, Sankoff D (1996) Parametric genome rearrangement. Gene 172: GC11-GC17.
30. Pevzner P, Tesler G (2003) Genome rearrangements in mammalian evolution: Lessons from human and mouse genomes. Genome Res 13: 37-45.
31. Bazaraa M, Sherali D, Shetty C (1992) Nonlinear programming: Theory and algorithms. New York: Wiley. 640 p.
32. Murphy WJ, Larkin DM, Everts-van der Wind A, Bourque G, Tesler G, et al. (2005) Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309: 613-617.