Inferences of evolutionary relationships from a population survey of LTR-retrotransposons and telomeric-associated sequences in the Saccharomyces sensu stricto complex

Yeast

Volumn 22, Issue 3, 2005, Pages 177-192

  Liti, Gianni ^a   Peruffo, Antonella ^a,c   James, Steve A ^b   Roberts, Ian N ^b   Louis, Edward J ^a  

^a UNIVERSITY OF LEICESTER   (United Kingdom)

^b INSTITUTE OF FOOD RESEARCH   (United Kingdom)

^c UNIVERSITY OF PADOVA   (Italy)

Author keywords

Evolution; GCR; Hybrids; ITS1; LTR retrotransposon; Saccharomyces; TAS

Indexed keywords

ARTICLE; CHROMOSOME REARRANGEMENT; CHROMOSOME TRANSLOCATION; CONTROLLED STUDY; CORRELATION ANALYSIS; DNA SEQUENCE; FUNGAL STRAIN; FUNGUS ISOLATION; GEOGRAPHIC DISTRIBUTION; HYBRIDIZATION; LONG TERMINAL REPEAT; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RETROPOSON; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES MIKATAE; SEQUENCE ANALYSIS; SPECIES COMPARISON; STRAIN DIFFERENCE; TELOMERE; WILD TYPE;

BASE SEQUENCE; BLOTTING, SOUTHERN; DNA, FUNGAL; DNA, INTERGENIC; ELECTROPHORESIS, GEL, PULSED-FIELD; EVOLUTION, MOLECULAR; GENES, FUNGAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; RETROELEMENTS; SACCHAROMYCES; SEQUENCE ALIGNMENT; TELOMERE; TERMINAL REPEAT SEQUENCES; VARIATION (GENETICS);

EID: 14544290992     PISSN: 0749503X     EISSN: None     Source Type: Journal    
DOI: 10.1002/yea.1200     Document Type: Article

References (48)

1. Casaregola S, Nguyen HV, Lapathitis G, Kotyk A, Gaillardin C. 2001. Analysis of the constitution of the beer yeast genome by PCR, sequencing and subtelomeric sequence hybridization. Int J Syst Evol Microbiol 51: 1607-1618.
2. Cliften P, Sudarsanam P, Desikan A, et al. 2003. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301: 71-76.
3. Cliften PF, Hillier LW, Fulton L, et al. 2001. Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome Res 11: 1175-1186.
4. de Barros Lopes M, Bellon JR, Shirley N J, Ganter PF. 2002. Evidence for multiple interspecific hybridization in Saccharomyces sensu stricto species. FEMS Yeast Res 1: 323-331.
5. Delneri D, Colson I, Grammenoudi S, et al. 2003. Engineering evolution to study speciation in yeasts. Nature 422 68-72.
6. Fischer G, James SA, Roberts IN, Oliver SG, Louis EJ. 2000. Chromosomal evolution in Saccharomyces. Nature 405: 451-454.
7. Greig D, Louis EJ, Borts RH, Travisano M. 2002. Hybrid speciation in experimental populations of yeast. Science 298: 1773-1775.
8. Greig D, Travisano M, Louis EJ, Borts RH. 2003. A role for the mismatch repair system during incipient speciation in Saccharomyces. J Evol Biol 16: 429-437.
9. Groth C, Hansen J, Piskur J. 1999. A natural chimeric yeast containing genetic material from three species. Int J Syst Bacteriol 49(4): 1933-1938.
10. 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.
11. Jager D, Philippsen P. 1989. Many yeast chromosomes lack the telomere-specific Y′ sequence. Mol Cell Biol 9: 5754-5757.
12. James SA, Collins MD, Roberts IN. 1996. Use of an rRNA internal transcribed spacer region to distinguish phylogenetically closely related species of the genera Zygosaccharomyces and Torulaspora. Int J Syst Bacteriol 46: 189-194.
13. Johnson LJ, Koufopanou V, Goddard MR, et al. 2004. Population genetics of the wild yeast Saccharomyces paradoxus. Genetics 166: 43-52.
14. 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.
15. Louis EJ. 1995. The chromosome ends of Saccharomyces cerevisiae. Yeast 11: 1553-1573.
16. Louis EJ. 1998. Whole chromosome analysis. In Yeast gene analysis, Brown AJP and Tuite MF (eds). Academic Press: New York; 15-31.
17. Louis EJ, Haber JE. 1992. The structure and evolution of subtelomeric Y′ repeats in Saccharomyces cerevisiae. Genetics 131: 559-574.
18. Louis EJ, Naumova ES, Lee A, Naumov G, Haber JE. 1994. The chromosome end in yeast: its mosaic nature and influence on recombinational dynamics. Genetics 136: 789-802.
19. Martini AV, Martini A. 1987. Three newly delimited species of Saccharomyces sensu stricto. Antonie Van Leeuwenhoek 53: 77-84.
20. Masneuf I, Hansen J, Groth C, Piskur J, Dubourdieu D. 1998. New hybrids between Saccharomyces sensu stricto yeast species found among wine and cider production strains. Appl Environ Microbiol 64: 3887-3892.
21. Moore SP, Liti G, Stefanisko KM, et al. 2004. Analysis of a Ty1-less variant of Saccharomyces paradoxus: the gain and loss of Ty1 elements. Yeast 21: (in press).
22. Myung K, Chen C, Kolodner RD. 2001. Multiple pathways cooperate in the suppression of genome instability in Saccharomyces cerevisiae. Nature 411: 1073-1076.
23. Naumov GI. 1987. Genetic basis for classification and identification of the ascomycetous yeasts. Stud Mycol 30: 469-475.
24. Naumov GI, James SA, Naumova ES, Louis EJ, Roberts IN. 2000a. Three new species in the Saccharomyces sensu stricto complex: Saccharomyces cariocanus, Saccharomyces kudriavzevii and Saccharomyces mikatae. Int J Syst Evol Microbiol 50(5): 1931-1942.
25. Naumov GI, Naumova ES, Hagler AN, Mendonca-Hagler LC, Louis EJ. 1995a. A new genetically isolated population of the Saccharomyces sensu stricto complex from Brazil. Antonie Van Leeuwenhoek 67 351-355.
26. Naumov GI, Naumova ES, Lantto RA, Louis EJ, Korhola M. 1992. Genetic homology between Saccharomyces cerevisiae and its sibling species S. paradoxus and S. bayanus: electrophoretic karyotypes. Yeast 8: 599-612.
27. Naumov GI, Naumova ES, Louis EJ. 1995b. Two new genetically isolated populations of the Saccharomyces sensu stricto complex from Japan. J Gen Appl Microbiol 41: 499-505.
28. Naumov GI, Naumova ES, Masneuf I, et al. 2000b. Natural polyploidization of some cultured yeast Saccharomyces sensu stricto auto- and allotetraploidy. Syst Appl Microbiol 23: 442-449.
29. Naumov GI, Naumova ES, Sniegowski PD. 1997. Differentiation of European and Far East Asian populations of Saccharomyces paradoxus by allozyme analysis. Int J Syst Bacteriol 47: 341-344.
30. Naumov GI, Naumova ES, Sniegowski PD. 1998. Saccharomyces paradoxus and Saccharomyces cerevisiae are associated with exudates of North American oaks. Can J Microbiol 44: 1045-1050.
31. Naumov GI, Nikonenko TA, Kondrat'eva VI. 1994. [Taxonomic identification of Saccharomyces from yeast genetic stock centers of the University of California]. Genetika 30: 45-48.
32. Neuveglise C, Feldmann H, Bon E, Gaillardin C, Casaregola S. 2002. Genomic evolution of the long terminal repeat retrotransposons in hemiascomycetous yeasts. Genome Res 12: 930-943.
33. Perez-Ortin JE, Querol A, Puig S, Barrio E. 2002. Molecular characterization of a chromosomal rearrangement involved in the adaptive evolution of yeast strains. Genome Res 12: 1533-1539.
34. Pryde FE, Huckle TC, Louis EJ. 1995. Sequence analysis of the right end of chromosome XV in Saccharomyces cerevisiae: an insight into the structural and functional significance of subtelomeric repeat sequences. Yeast 11: 371-382.
35. Pryde FE, Louis EJ. 1997. Saccharomyces cerevisiae telomeres. A review. Biochemistry (Mosc) 62: 1232-1241.
36. Pryde FE, Louis EJ. 1999. Limitations of silencing at native yeast telomeres. EMBO J 18: 2538-2550.
37. Rachidi N, Barre P, Blondin B. 1999. Multiple Ty-mediated chromosomal translocations lead to karyotype changes in a wine strain of Saccharomyces cerevisiae. Mol Gen Genet 261: 841-850.
38. Rachidi N, Martinez MJ, Barre P, Blondin B. 2000. Saccharomyces cerevisiae PAU genes are induced by anaerobiosis. Mol Microbiol 35: 1421-1430.
39. Sniegowski PD, Dombrowski PG, Fingerman E. 2002. Saccharomyces cerevisiae and Saccharomyces paradoxus coexist in a natural woodland site in North America and display different levels of reproductive isolation from European conspecifics. FEBS Yeast Res 1: 299-306.
40. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
41. Vaughan Martini A. 1989. Saccharomyces paradoxus comb. nov., a newly separated species of the Saccharomyces sensu stricto complex based upon nDNA/nDNA homologies. System Appl Microbiol 12: 179-182.
42. Vaughan-Martini A, Martini A. 1995. Facts, myths and legends on the prime industrial microorganism. J Ind Microbiol 14: 514-522.
43. Viswanathan M, Muthukumar G, Cong YS, Lenard J. 1994. Seripauperins of Saccharomyces cerevisiae: a new multigene family encoding serine-poor relatives of serine-rich proteins. Gene 148 149-153.
44. White TJ, Bruns T, Lee S, Taylor J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR Protocols: A Guide for Methods and Applications, Innis MA, Gelfand DH, Sninsky JJ, Taylor TJ (eds). Academic Press: New York; 315-322.
45. Winzeler EA, Castillo-Davis CI, Oshiro G, et al. 2003. Genetic diversity in yeast assessed with whole-genome oligonucleotide arrays. Genetics 163: 79-89.
46. Yamada M, Hayatsu N, Matsuura A, Ishikawa F. 1998. Y′-Help1, a DNA helicase encoded by the yeast subtelomeric Y′ element, is induced in survivors defective for telomerase. J Biol Chem 273: 33 360-33 366.
47. Zakian VA, Blanton HM. 1988. Distribution of telomere-associated sequences on natural chromosomes in Saccharomyces cerevisiae. Mol Cell Biol 8: 2257-2260.
48. Zou S, Wright DA, Voytas DF. 1995. The Saccharomyces Ty5 retrotransposon family is associated with origins of DNA replication at the telomeres and the silent mating locus HMR. Proc Natl Acad Sci USA 92: 920-924.