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Volumn 13, Issue 6, 2013, Pages 574-584

Primers for fourteen protein-coding genes and the deep phylogeny of the true yeasts

Author keywords

PCR primers; Phylogenetics; Saccharomycetales

Indexed keywords

RIBOSOME DNA;

EID: 84881546150     PISSN: 15671356     EISSN: 15671364     Source Type: Journal    
DOI: 10.1111/1567-1364.12059     Document Type: Article
Times cited : (2)

References (42)
  • 1
    • 0033950267 scopus 로고    scopus 로고
    • Phylogeny of the genus Kluyveromyces inferred from the mitochondrial cytochrome c oxidase II gene
    • Belloch C, Querol A, Garcia MD & Barrio E (2000) Phylogeny of the genus Kluyveromyces inferred from the mitochondrial cytochrome c oxidase II gene. Int J Syst Evol Microbiol 50: 405-416.
    • (2000) Int J Syst Evol Microbiol , vol.50 , pp. 405-416
    • Belloch, C.1    Querol, A.2    Garcia, M.D.3    Barrio, E.4
  • 2
    • 44449161646 scopus 로고    scopus 로고
    • Rapid evolution of yeast centromeres in the absence of drive
    • Bensasson D, Zarowiecki M, Burt A & Koufopanou V (2008) Rapid evolution of yeast centromeres in the absence of drive. Genetics 178: 2161-2167.
    • (2008) Genetics , vol.178 , pp. 2161-2167
    • Bensasson, D.1    Zarowiecki, M.2    Burt, A.3    Koufopanou, V.4
  • 3
    • 66649105285 scopus 로고    scopus 로고
    • Evolution of pathogenicity and sexual reproduction in eight Candida genomes
    • Butler G, Rasmussen MD, Lin MF et al. (2009) Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature 459: 657-662.
    • (2009) Nature , vol.459 , pp. 657-662
    • Butler, G.1    Rasmussen, M.D.2    Lin, M.F.3
  • 4
    • 84884840399 scopus 로고    scopus 로고
    • Yeasts pathogenic to humans
    • 5th edn (Kurtzman CP, Fell JW & Boekhout T, eds). Elsevier, Amsterdam.
    • Cooper CRJ (2011) Yeasts pathogenic to humans. The Yeasts, a Taxonomic Study, 5th edn (Kurtzman CP, Fell JW & Boekhout T, eds), pp. 9-19. Elsevier, Amsterdam.
    • (2011) The Yeasts, a Taxonomic Study , pp. 9-19
    • Cooper, C.R.J.1
  • 5
    • 77953754620 scopus 로고    scopus 로고
    • Yeast evolutionary genomics
    • Dujon B (2010) Yeast evolutionary genomics. Nat Rev Genet 11: 512-524.
    • (2010) Nat Rev Genet , vol.11 , pp. 512-524
    • Dujon, B.1
  • 6
    • 84871959613 scopus 로고    scopus 로고
    • Yeast spoilage of foods and beverages
    • 5th edn (Kurtzman CP, Fell JW & Boekhout T, eds). Elsevier, Amsterdam.
    • Fleet GH (2011) Yeast spoilage of foods and beverages. The Yeasts, a Taxonomic Study, 5th edn (Kurtzman CP, Fell JW & Boekhout T, eds), pp. 53-63. Elsevier, Amsterdam.
    • (2011) The Yeasts, a Taxonomic Study , pp. 53-63
    • Fleet, G.H.1
  • 7
    • 78650459424 scopus 로고    scopus 로고
    • Biased gene conversion affects patterns of codon usage and amino acid usage in the Saccharomyces sensu stricto group of yeasts
    • Harrison RL & Charlesworth B (2011) Biased gene conversion affects patterns of codon usage and amino acid usage in the Saccharomyces sensu stricto group of yeasts. Mol Biol Evol 28: 117-129.
    • (2011) Mol Biol Evol , vol.28 , pp. 117-129
    • Harrison, R.L.1    Charlesworth, B.2
  • 8
    • 79961133759 scopus 로고    scopus 로고
    • Addressing inter-gene heterogeneity in maximum likelihood phylogenomic analysis: yeasts revisited
    • Hess J & Goldman N (2011) Addressing inter-gene heterogeneity in maximum likelihood phylogenomic analysis: yeasts revisited. PLoS ONE 6: e22783.
    • (2011) PLoS ONE , vol.6
    • Hess, J.1    Goldman, N.2
  • 9
    • 84867703157 scopus 로고    scopus 로고
    • Yeast biotechnology
    • 5th edn (Kurtzman CP, Fell JW & Boekhout T, eds). Elsevier, Amsterdam.
    • Johnson EA & Echavarri-Erasun C (2011) Yeast biotechnology. The Yeasts, a Taxonomic Study, 5th edn (Kurtzman CP, Fell JW & Boekhout T, eds), pp. 21-44. Elsevier, Amsterdam.
    • (2011) The Yeasts, a Taxonomic Study , pp. 21-44
    • Johnson, E.A.1    Echavarri-Erasun, C.2
  • 10
    • 0030995435 scopus 로고    scopus 로고
    • Concordance of gene genealogies reveals reproductive isolation in the pathogenic fungus Coccidioides immitis
    • Koufopanou V, Burt A & Taylor JW (1997) Concordance of gene genealogies reveals reproductive isolation in the pathogenic fungus Coccidioides immitis. P Natl Acad Sci USA 94: 5478-5482.
    • (1997) P Natl Acad Sci USA , vol.94 , pp. 5478-5482
    • Koufopanou, V.1    Burt, A.2    Taylor, J.W.3
  • 11
    • 33751235592 scopus 로고    scopus 로고
    • The spatial scale of genetic differentiation in a model organism: the wild yeast Saccharomyces paradoxus
    • Koufopanou V, Hughes J, Bell G & Burt A (2006) The spatial scale of genetic differentiation in a model organism: the wild yeast Saccharomyces paradoxus. Philos Trans R Soc Lond B Biol Sci 361: 1941-1946.
    • (2006) Philos Trans R Soc Lond B Biol Sci , vol.361 , pp. 1941-1946
    • Koufopanou, V.1    Hughes, J.2    Bell, G.3    Burt, A.4
  • 12
    • 84884893949 scopus 로고    scopus 로고
    • Discussion of teleomorphic and anamorphic ascomycetous yeasts and yeast-like taxa
    • 5th edn (Kurtzman CP, Fell JW & Boekhout T, eds). Elsevier, Amsterdam.
    • Kurtzman CP (2011) Discussion of teleomorphic and anamorphic ascomycetous yeasts and yeast-like taxa. The Yeasts, a Taxonomic Study, 5th edn (Kurtzman CP, Fell JW & Boekhout T, eds), pp. 293-307. Elsevier, Amsterdam.
    • (2011) The Yeasts, a Taxonomic Study , pp. 293-307
    • Kurtzman, C.P.1
  • 13
    • 0031792246 scopus 로고    scopus 로고
    • Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences
    • Kurtzman CP & Robnett CJ (1998) Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences. Antonie Van Leeuwenhoek (Int J Gen Mol Microbiol) 73: 331-371.
    • (1998) Antonie Van Leeuwenhoek (Int J Gen Mol Microbiol) , vol.73 , pp. 331-371
    • Kurtzman, C.P.1    Robnett, C.J.2
  • 14
    • 0037540048 scopus 로고    scopus 로고
    • Phylogenetic relationships among yeasts of the 'Saccharomyces complex' determined from multigene sequence analyses
    • Kurtzman CP & Robnett CJ (2003) Phylogenetic relationships among yeasts of the 'Saccharomyces complex' determined from multigene sequence analyses. FEMS Yeast Res 3: 417-432.
    • (2003) FEMS Yeast Res , vol.3 , pp. 417-432
    • Kurtzman, C.P.1    Robnett, C.J.2
  • 15
    • 84872388076 scopus 로고    scopus 로고
    • Relationships among genera of the Saccharomycotina (Ascomycota) from multigene phylogenetic analysis of type species
    • Kurtzman CP & Robnett CJ (2013) Relationships among genera of the Saccharomycotina (Ascomycota) from multigene phylogenetic analysis of type species. FEMS Yeast Res 13: 23-33.
    • (2013) FEMS Yeast Res , vol.13 , pp. 23-33
    • Kurtzman, C.P.1    Robnett, C.J.2
  • 16
    • 84875279015 scopus 로고    scopus 로고
    • Saccaromycopsis Schiönning (1903)
    • 5th edn (Kurtzman CP, Fell JW & Boekhout T, eds). Elsevier, Amsterdam.
    • Kurtzman CP & Smith MT (2011) Saccaromycopsis Schiönning (1903). The Yeast, a Taxonomic Study, 5th edn (Kurtzman CP, Fell JW & Boekhout T, eds), pp. 751-764. Elsevier, Amsterdam.
    • (2011) The Yeast, a Taxonomic Study , pp. 751-764
    • Kurtzman, C.P.1    Smith, M.T.2
  • 17
    • 76649127721 scopus 로고    scopus 로고
    • Phylogenetic analysis of ascomycete yeasts that form coenzyme Q-9 and the proposal of the new genera Babjeviella, Meyerozyma, Millerozyma, Priceomyces, and Scheffersomyces
    • Kurtzman CP & Suzuki M (2010) Phylogenetic analysis of ascomycete yeasts that form coenzyme Q-9 and the proposal of the new genera Babjeviella, Meyerozyma, Millerozyma, Priceomyces, and Scheffersomyces. Mycoscience 51: 2-14.
    • (2010) Mycoscience , vol.51 , pp. 2-14
    • Kurtzman, C.P.1    Suzuki, M.2
  • 18
    • 34547860863 scopus 로고    scopus 로고
    • Multigene phylogenetic analysis of the Lipomycetaceae and the proposed transfer of Zygozyma species to Lipomyces and Babjevia anomala to Dipodascopsis
    • Kurtzman CP, Albertyn J & Basehoar-Powers E (2007) Multigene phylogenetic analysis of the Lipomycetaceae and the proposed transfer of Zygozyma species to Lipomyces and Babjevia anomala to Dipodascopsis. FEMS Yeast Res 7: 1027-1034.
    • (2007) FEMS Yeast Res , vol.7 , pp. 1027-1034
    • Kurtzman, C.P.1    Albertyn, J.2    Basehoar-Powers, E.3
  • 19
    • 49749124650 scopus 로고    scopus 로고
    • Phylogenetic relationships among species of Pichia, Issatchenkia and Williopsis determined from multigene sequence analysis, and the proposal of Barnettozyma gen. nov., Lindnera gen. nov and Wickerhamomyces gen. nov
    • Kurtzman CP, Robnett CJ & Basehoar-Powers E (2008) Phylogenetic relationships among species of Pichia, Issatchenkia and Williopsis determined from multigene sequence analysis, and the proposal of Barnettozyma gen. nov., Lindnera gen. nov and Wickerhamomyces gen. nov. FEMS Yeast Res 8: 939-954.
    • (2008) FEMS Yeast Res , vol.8 , pp. 939-954
    • Kurtzman, C.P.1    Robnett, C.J.2    Basehoar-Powers, E.3
  • 20
    • 84884867971 scopus 로고    scopus 로고
    • Definition, classification and nomenclature of the yeasts
    • 5th edn (Kurtzman CP, Fell JW & Boekhout T, eds). Elsevier, Amsterdam.
    • Kurtzman CP, Fell JW & Boekhout T (2011a) Definition, classification and nomenclature of the yeasts. The Yeasts, a Taxonomic Study, 5th edn (Kurtzman CP, Fell JW & Boekhout T, eds), pp. 3-5. Elsevier, Amsterdam.
    • (2011) The Yeasts, a Taxonomic Study , pp. 3-5
    • Kurtzman, C.P.1    Fell, J.W.2    Boekhout, T.3
  • 21
    • 84884866407 scopus 로고    scopus 로고
    • Gene sequence analyses and other DNA-based methods for yeast species recognition
    • 5th edn (Kurtzman CP, Fell JW & Boekhout T, eds). Elsevier, Amsterdam.
    • Kurtzman CP, Fell JW & Boekhout T (2011b) Gene sequence analyses and other DNA-based methods for yeast species recognition. The Yeasts, a Taxonomic Study, 5th edn (Kurtzman CP, Fell JW & Boekhout T, eds), pp. 137-144. Elsevier, Amsterdam.
    • (2011) The Yeasts, a Taxonomic Study , pp. 137-144
    • Kurtzman, C.P.1    Fell, J.W.2    Boekhout, T.3
  • 24
    • 45849154166 scopus 로고    scopus 로고
    • An improved general amino acid replacement matrix
    • Le SQ & Gascuel O (2008) An improved general amino acid replacement matrix. Mol Biol Evol 25: 1307-1320.
    • (2008) Mol Biol Evol , vol.25 , pp. 1307-1320
    • Le, S.Q.1    Gascuel, O.2
  • 25
    • 62649089109 scopus 로고    scopus 로고
    • Population genomics of domestic and wild yeasts
    • Liti G, Carter DM, Moses AM et al. (2009) Population genomics of domestic and wild yeasts. Nature 458: 337-341.
    • (2009) Nature , vol.458 , pp. 337-341
    • Liti, G.1    Carter, D.M.2    Moses, A.M.3
  • 26
    • 0026709809 scopus 로고
    • Evolution of codon usage patterns - the extent and nature of divergence between Candida albicans and Saccharomyces cerevisiae
    • Lloyd AT & Sharp PM (1992) Evolution of codon usage patterns - the extent and nature of divergence between Candida albicans and Saccharomyces cerevisiae. Nucleic Acids Res 20: 5289-5295.
    • (1992) Nucleic Acids Res , vol.20 , pp. 5289-5295
    • Lloyd, A.T.1    Sharp, P.M.2
  • 28
    • 84856350965 scopus 로고    scopus 로고
    • Reconstructing the fungal tree of life using phylogenomics and a preliminary investigation of the distribution of yeast prion-like proteins in the fungal kingdom
    • Medina EM, Jones GW & Fitzpatrick DA (2011) Reconstructing the fungal tree of life using phylogenomics and a preliminary investigation of the distribution of yeast prion-like proteins in the fungal kingdom. J Mol Evol 73: 116-133.
    • (2011) J Mol Evol , vol.73 , pp. 116-133
    • Medina, E.M.1    Jones, G.W.2    Fitzpatrick, D.A.3
  • 29
    • 0033990061 scopus 로고    scopus 로고
    • Flexible sequence similarity searching with the FASTA3 program package
    • Pearson WR (2000) Flexible sequence similarity searching with the FASTA3 program package. Methods Mol Biol 132: 185-219.
    • (2000) Methods Mol Biol , vol.132 , pp. 185-219
    • Pearson, W.R.1
  • 30
    • 77953147755 scopus 로고    scopus 로고
    • Nuclear ribosomal spacer regions in plant phylogenetics: problems and prospects
    • Poczai P & Hyvönen J (2010) Nuclear ribosomal spacer regions in plant phylogenetics: problems and prospects. Mol Biol Rep 37: 1897-1912.
    • (2010) Mol Biol Rep , vol.37 , pp. 1897-1912
    • Poczai, P.1    Hyvönen, J.2
  • 31
    • 0242365676 scopus 로고    scopus 로고
    • Genome-scale approaches to resolving incongruence in molecular phylogenies
    • Rokas A, Williams BL, King N & Carroll SB (2003) Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425: 798-804.
    • (2003) Nature , vol.425 , pp. 798-804
    • Rokas, A.1    Williams, B.L.2    King, N.3    Carroll, S.B.4
  • 34
    • 75149170450 scopus 로고    scopus 로고
    • New primers for promising single-copy genes in fungal phylogenetics and systematics
    • Schmitt I, Crespo A, Divakar PK et al. (2009) New primers for promising single-copy genes in fungal phylogenetics and systematics. Persoonia 23: 35-40.
    • (2009) Persoonia , vol.23 , pp. 35-40
    • Schmitt, I.1    Crespo, A.2    Divakar, P.K.3
  • 35
    • 0025978949 scopus 로고
    • Getting started with yeast
    • Guthrie C & Fink GR, eds). Academic Press, San Diego, CA.
    • Sherman F (1991) Getting started with yeast. Guide to Yeast Genetics and Molecular Biology, (Guthrie C & Fink GR, eds), pp. 3-21. Academic Press, San Diego, CA.
    • (1991) Guide to Yeast Genetics and Molecular Biology , pp. 3-21
    • Sherman, F.1
  • 36
    • 83655167077 scopus 로고    scopus 로고
    • Radical instability and spurious branch support by likelihood when applied to matrices with non-random distributions of missing data
    • Simmons MP (2012) Radical instability and spurious branch support by likelihood when applied to matrices with non-random distributions of missing data. Mol Phylogenet Evol 62: 472-484.
    • (2012) Mol Phylogenet Evol , vol.62 , pp. 472-484
    • Simmons, M.P.1
  • 37
    • 34248157233 scopus 로고    scopus 로고
    • Selection on synthesis cost affects interprotein amino acid usage in all three domains of life
    • Swire J (2007) Selection on synthesis cost affects interprotein amino acid usage in all three domains of life. J Mol Evol 64: 558-571.
    • (2007) J Mol Evol , vol.64 , pp. 558-571
    • Swire, J.1
  • 39
    • 0041694475 scopus 로고    scopus 로고
    • Fungal multilocus sequence typing - it's not just for bacteria
    • Taylor JW & Fisher MC (2003) Fungal multilocus sequence typing - it's not just for bacteria. Curr Opin Microbiol 6: 351-356.
    • (2003) Curr Opin Microbiol , vol.6 , pp. 351-356
    • Taylor, J.W.1    Fisher, M.C.2
  • 40
    • 0027968068 scopus 로고
    • CLUSTAL-W - Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • 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.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 41
    • 42449128411 scopus 로고    scopus 로고
    • Population genomics of the wild yeast Saccharomyces paradoxus: quantifying the life cycle
    • Tsai IJ, Bensasson D, Burt A & Koufopanou V (2008) Population genomics of the wild yeast Saccharomyces paradoxus: quantifying the life cycle. P Natl Acad Sci USA 105: 4957-4962.
    • (2008) P Natl Acad Sci USA , vol.105 , pp. 4957-4962
    • Tsai, I.J.1    Bensasson, D.2    Burt, A.3    Koufopanou, V.4
  • 42
    • 43549090929 scopus 로고    scopus 로고
    • Re-examining the phylogeny of clinically relevant Candida species and allied genera based on multigene analyses
    • Tsui CKM, Daniel H-M, Robert V & Meyer W (2008) Re-examining the phylogeny of clinically relevant Candida species and allied genera based on multigene analyses. FEMS Yeast Res 8: 651-659.
    • (2008) FEMS Yeast Res , vol.8 , pp. 651-659
    • Tsui, C.K.M.1    Daniel, H.-M.2    Robert, V.3    Meyer, W.4


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