메뉴 건너뛰기




Volumn 56, Issue 6, 2010, Pages 507-515

Complete mitochondrial genome sequence of the yeast Pichia farinosa and comparative analysis of closely related species

Author keywords

CTG group; Mitochondrial genome; Phylogeny; Pichia farinosa

Indexed keywords

MITOCHONDRIAL DNA; RIBOSOME RNA; TRANSFER RNA;

EID: 78649318096     PISSN: 01728083     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00294-010-0318-y     Document Type: Article
Times cited : (23)

References (41)
  • 2
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • DOI 10.1093/nar/25.17.3389
    • SF Altschul TL Madden AA Schäffer J Zhang Z Zhang W Miller DJ Lipman 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res 25 3389 3402 9254694 1:CAS:528:DyaK2sXlvFyhu7w%3D 10.1093/nar/25.17.3389 (Pubitemid 27359211)
    • (1997) Nucleic Acids Research , vol.25 , Issue.17 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5    Miller, W.6    Lipman, D.J.7
  • 3
    • 0035156156 scopus 로고    scopus 로고
    • Infrequent genetic exchange and recombination in the mitochondrial genome of Candida albicans
    • DOI 10.1128/JB.183.3.865-872.2001
    • JB Anderson C Wickens M Khan LE Cowen N Federspiel T Jones LM Kohn 2001 Infrequent genetic exchange and recombination in the mitochondrial genome of Candida albicans J Bacteriol 183 865 872 11208783 1:CAS:528: DC%2BD3MXmsVOisA%3D%3D 10.1128/JB.183.3.865-872.2001 (Pubitemid 32095295)
    • (2001) Journal of Bacteriology , vol.183 , Issue.3 , pp. 865-872
    • Anderson, J.B.1    Wickens, C.2    Khan, M.3    Cowen, L.E.4    Federspiel, N.5    Jones, T.6    Kohn, L.M.7
  • 6
    • 0035883706 scopus 로고    scopus 로고
    • Homing endonucleases: Structural and functional insight into the catalysts of intron/intein mobility
    • 11557808 1:CAS:528:DC%2BD3MXot1eku74%3D 10.1093/nar/29.18.3757
    • BS Chevalier BL Stoddard 2001 Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility Nucleic Acids Res 29 3757 3774 11557808 1:CAS:528:DC%2BD3MXot1eku74%3D 10.1093/nar/29.18.3757
    • (2001) Nucleic Acids Res , vol.29 , pp. 3757-3774
    • Chevalier, B.S.1    Stoddard, B.L.2
  • 8
    • 77953754620 scopus 로고    scopus 로고
    • Yeast evolutionary genomics
    • 20559329 1:CAS:528:DC%2BC3cXnsFGks7o%3D 10.1038/nrg2811
    • B Dujon 2010 Yeast evolutionary genomics Nat Rev Genet 11 512 524 20559329 1:CAS:528:DC%2BC3cXnsFGks7o%3D 10.1038/nrg2811
    • (2010) Nat Rev Genet , vol.11 , pp. 512-524
    • Dujon, B.1
  • 9
    • 13244255415 scopus 로고    scopus 로고
    • MUSCLE: A multiple sequence alignment method with reduced time and space complexity
    • DOI 10.1186/1471-2105-5-113
    • RC Edgar 2004 MUSCLE: a multiple sequence alignment method with reduced time and space complexity BMC Bioinformatics 5 113 15318951 10.1186/1471-2105-5- 113 (Pubitemid 40195393)
    • (2004) BMC Bioinformatics , vol.5 , pp. 113
    • Edgar, R.C.1
  • 10
    • 33845452848 scopus 로고    scopus 로고
    • A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis
    • DOI 10.1186/1471-2148-6-99
    • DA Fitzpatrick ME Logue JE Stajich G Butler 2006 A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis BMC Evol Biol 6 99 17121679 10.1186/1471-2148-6-99 (Pubitemid 44903742)
    • (2006) BMC Evolutionary Biology , vol.6 , pp. 99
    • Fitzpatrick, D.A.1    Logue, M.E.2    Stajich, J.E.3    Butler, G.4
  • 11
    • 0032426882 scopus 로고    scopus 로고
    • The complete sequence of the mitochondrial genome of Saccharomyces cerevisiae
    • DOI 10.1016/S0014-5793(98)01467-7, PII S0014579398014677
    • F Foury T Roganti N Lecrenier B Purnelle 1998 The complete sequence of the mitochondrial genome of Saccharomyces cerevisiae FEBS Lett 440 325 331 9872396 1:CAS:528:DyaK1cXnvVSqsrg%3D 10.1016/S0014-5793(98)01467-7 (Pubitemid 29052308)
    • (1998) FEBS Letters , vol.440 , Issue.3 , pp. 325-331
    • Foury, F.1    Roganti, T.2    Lecrenier, N.3    Purnelle, B.4
  • 12
    • 0242578620 scopus 로고    scopus 로고
    • A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
    • DOI 10.1080/10635150390235520
    • S Guindon O Gascuel 2003 A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood Syst Biol 52 696 704 14530136 10.1080/10635150390235520 (Pubitemid 37365050)
    • (2003) Systematic Biology , vol.52 , Issue.5 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 13
    • 12344329187 scopus 로고    scopus 로고
    • The natural history of group I introns
    • DOI 10.1016/j.tig.2004.12.007, PII S016895250400335X
    • P Haugen DM Simon D Bhattacharya 2005 The natural history of group I introns Trends Genet 21 111 119 15661357 1:CAS:528:DC%2BD2MXmslKgtA%3D%3D 10.1016/j.tig.2004.12.007 (Pubitemid 40127355)
    • (2005) Trends in Genetics , vol.21 , Issue.2 , pp. 111-119
    • Haugen, P.1    Simon, D.M.2    Bhattacharya, D.3
  • 14
    • 0021022518 scopus 로고
    • The intron of the mitochondrial 21S rRNA gene: Distribution in different yeast species and sequence comparison between Kluyveromyces thermotolerans and Saccharomyces cerevisiae
    • 6361491 1:CAS:528:DyaL2cXks1Wrtg%3D%3D 10.1007/BF00392195
    • A Jacquier B Dujon 1983 The intron of the mitochondrial 21S rRNA gene: distribution in different yeast species and sequence comparison between Kluyveromyces thermotolerans and Saccharomyces cerevisiae Mol Gen Genet 192 487 499 6361491 1:CAS:528:DyaL2cXks1Wrtg%3D%3D 10.1007/BF00392195
    • (1983) Mol Gen Genet , vol.192 , pp. 487-499
    • Jacquier, A.1    Dujon, B.2
  • 15
    • 33744914986 scopus 로고    scopus 로고
    • Engineering yeasts for xylose metabolism
    • Jeffries TW (2006) Engineering yeasts for xylose metabolism. Curr Opin Biotechnol 17:320-326
    • (2006) Curr Opin Biotechnol , vol.17 , pp. 320-326
    • Jeffries, T.W.1
  • 17
    • 68849111626 scopus 로고    scopus 로고
    • The complete mitochondrial genome of the yeast Pichia sorbitophila
    • 19594828 1:CAS:528:DC%2BD1MXhtFChsbjN 10.1111/j.1567-1364.2009.00540.x
    • PP Jung J Schacherer JL Souciet S Potier P Wincker J de Montigny 2009 The complete mitochondrial genome of the yeast Pichia sorbitophila FEMS Yeast Res 9 903 910 19594828 1:CAS:528:DC%2BD1MXhtFChsbjN 10.1111/j.1567-1364.2009.00540.x
    • (2009) FEMS Yeast Res , vol.9 , pp. 903-910
    • Jung, P.P.1    Schacherer, J.2    Souciet, J.L.3    Potier, S.4    Wincker, P.5    De Montigny, J.6
  • 19
    • 0034835968 scopus 로고    scopus 로고
    • How mitochondria redefine the code
    • DOI 10.1007/s002390010220
    • RD Knight LF Landweber M Yarus 2001 How mitochondria redefine the code J Mol Evol 53 299 313 11675590 1:CAS:528:DC%2BD3MXotVaiurc%3D 10.1007/ s002390010220 (Pubitemid 32889538)
    • (2001) Journal of Molecular Evolution , vol.53 , Issue.4-5 , pp. 299-313
    • Knight, R.D.1    Landweber, L.F.2    Yarus, M.3
  • 20
    • 33646710847 scopus 로고    scopus 로고
    • Complete DNA sequences of the mitochondrial genomes of the pathogenic yeasts Candida orthopsilosis and Candida metapsilosis: Insight into the evolution of linear DNA genomes from mitochondrial telomere mutants
    • DOI 10.1093/nar/gkl327
    • P Kosa M Valach L Tomaska KH Wolfe J Nosek 2006 Complete DNA sequences of the mitochondrial genomes of the pathogenic yeasts Candida orthopsilosis and Candida metapsilosis: insight into the evolution of linear DNA genomes from mitochondrial telomere mutants Nucleic Acids Res 34 2472 2481 16684995 1:CAS:528:DC%2BD28Xks1Sls78%3D 10.1093/nar/gkl327 (Pubitemid 43985685)
    • (2006) Nucleic Acids Research , vol.34 , Issue.8 , pp. 2472-2481
    • Kosa, P.1    Valach, M.2    Tomaska, L.3    Wolfe, K.H.4    Nosek, J.5
  • 21
    • 12244310145 scopus 로고    scopus 로고
    • The complete mitochondrial genome sequence of the pathogenic yeast Candida (Torulopsis) glabrata
    • DOI 10.1016/S0014-5793(02)03749-3
    • R Koszul A Malpertuy L Frangeul C Bouchier P Wincker A Thierry S Duthoy S Ferris C Hennequin B Dujon 2003 The complete mitochondrial genome sequence of the pathogenic yeast Candida (Torulopsis) glabrata FEBS Lett 534 39 48 12527359 1:CAS:528:DC%2BD3sXjt1Sksw%3D%3D 10.1016/S0014-5793(02)03749-3 (Pubitemid 36084516)
    • (2003) FEBS Letters , vol.534 , Issue.1-3 , pp. 39-48
    • Koszul, R.1    Malpertuy, A.2    Frangeul, L.3    Bouchier, C.4    Wincker, P.5    Thierry, A.6    Duthoy, S.7    Ferris, S.8    Hennequin, C.9    Dujon, B.10
  • 23
    • 0037540048 scopus 로고    scopus 로고
    • Phylogenetic relationships among yeasts of the 'Saccharomyces complex' determined from multigene sequence analyses
    • DOI 10.1016/S1567-1356(03)00012-6
    • CP Kurtzman CJ Robnett 2003 Phylogenetic relationships among yeasts of the 'Saccharomyces complex' determined from multigene sequence analyses FEMS Yeast Res 3 417 432 12748053 1:CAS:528:DC%2BD3sXjs1eksLs%3D 10.1016/S1567- 1356(03)00012-6 (Pubitemid 36570320)
    • (2003) FEMS Yeast Research , vol.3 , Issue.4 , pp. 417-432
    • Kurtzman, C.P.1    Robnett, C.J.2
  • 24
    • 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
    • 1:CAS:528:DC%2BC3cXitVKnsr8%3D 10.1007/s10267-009-0011-5
    • CP Kurtzman M Suzuki 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 1:CAS:528:DC%2BC3cXitVKnsr8%3D 10.1007/s10267-009-0011-5
    • (2010) Mycoscience , vol.51 , pp. 2-14
    • Kurtzman, C.P.1    Suzuki, M.2
  • 25
    • 33847192548 scopus 로고    scopus 로고
    • Mitochondrial introns: A critical view
    • 17280737 1:CAS:528:DC%2BD2sXitFOisLs%3D 10.1016/j.tig.2007.01.006
    • BF Lang M Laforest G Burger 2007 Mitochondrial introns: a critical view Trends Genet 23 119 125 17280737 1:CAS:528:DC%2BD2sXitFOisLs%3D 10.1016/j.tig.2007.01.006
    • (2007) Trends Genet , vol.23 , pp. 119-125
    • Lang, B.F.1    Laforest, M.2    Burger, G.3
  • 26
    • 38349180130 scopus 로고    scopus 로고
    • ARWEN: A program to detect tRNA genes in metazoan mitochondrial nucleotide sequences
    • 18033792 1:CAS:528:DC%2BD1cXptlWgtw%3D%3D 10.1093/bioinformatics/btm573
    • D Laslett B Canbäck 2008 ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences Bioinformatics 24 172 175 18033792 1:CAS:528:DC%2BD1cXptlWgtw%3D%3D 10.1093/bioinformatics/btm573
    • (2008) Bioinformatics , vol.24 , pp. 172-175
    • Laslett, D.1    Canbäck, B.2
  • 27
    • 33646252240 scopus 로고    scopus 로고
    • Two glucose/xylose transporter genes from the yeast Candida intermedia: First molecular characterization of a yeast xylose-H+ symporter
    • 16402921 1:CAS:528:DC%2BD28XjtlCgsbo%3D 10.1042/BJ20051465
    • MJ Leandro P Gonçalves I Spencer-Martins 2006 Two glucose/xylose transporter genes from the yeast Candida intermedia: first molecular characterization of a yeast xylose-H+ symporter Biochem J 395 543 549 16402921 1:CAS:528:DC%2BD28XjtlCgsbo%3D 10.1042/BJ20051465
    • (2006) Biochem J , vol.395 , pp. 543-549
    • Leandro, M.J.1    Gonçalves, P.2    Spencer-Martins, I.3
  • 28
    • 67650711615 scopus 로고    scopus 로고
    • SOAP2: An improved ultrafast tool for short read alignment
    • 19497933 1:CAS:528:DC%2BD1MXovVeku7w%3D 10.1093/bioinformatics/btp336
    • R Li C Yu Y Li T Lam S Yiu K Kristiansen J Wang 2009 SOAP2: an improved ultrafast tool for short read alignment Bioinformatics 25 1966 1967 19497933 1:CAS:528:DC%2BD1MXovVeku7w%3D 10.1093/bioinformatics/btp336
    • (2009) Bioinformatics , vol.25 , pp. 1966-1967
    • Li, R.1    Yu, C.2    Li, Y.3    Lam, T.4    Yiu, S.5    Kristiansen, K.6    Wang, J.7
  • 29
    • 0030854739 scopus 로고    scopus 로고
    • tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
    • DOI 10.1093/nar/25.5.955
    • TM Lowe SR Eddy 1997 tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence Nucleic Acids Res 25 955 964 9023104 1:CAS:528:DyaK2sXhvVahtrk%3D 10.1093/nar/25.5.955 (Pubitemid 27298263)
    • (1997) Nucleic Acids Research , vol.25 , Issue.5 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 30
    • 0042887624 scopus 로고    scopus 로고
    • Physiological characterization of osmotolerant yeast Pichia sorbitophila and comparison with a putative synonym Pichia farinosa
    • 10.1007/BF02930958
    • L Maresová H Sychrová 2003 Physiological characterization of osmotolerant yeast Pichia sorbitophila and comparison with a putative synonym Pichia farinosa Folia Microbiol 48 211 217 10.1007/BF02930958
    • (2003) Folia Microbiol , vol.48 , pp. 211-217
    • Maresová, L.1    Sychrová, H.2
  • 31
    • 0032795245 scopus 로고    scopus 로고
    • Transport and utilization of hexoses and pentoses in the halotolerant yeast Debaryomyces hansenii
    • 10427054 1:CAS:528:DyaK1MXltVOltrk%3D
    • A Nobre C Lucas C Leão 1999 Transport and utilization of hexoses and pentoses in the halotolerant yeast Debaryomyces hansenii Appl Environ Microbiol 65 3594 3598 10427054 1:CAS:528:DyaK1MXltVOltrk%3D
    • (1999) Appl Environ Microbiol , vol.65 , pp. 3594-3598
    • Nobre, A.1    Lucas, C.2    Leão, C.3
  • 32
    • 5644249499 scopus 로고    scopus 로고
    • Complete DNA sequence of the linear mitochondrial genome of the pathogenic yeast Candida parapsilosis
    • DOI 10.1007/s00438-004-1046-0
    • J Nosek M Novotna Z Hlavatovicova DW Ussery J Fajkus L Tomaska 2004 Complete DNA sequence of the linear mitochondrial genome of the pathogenic yeast Candida parapsilosis Mol Genet Genomics 272 173 180 15449175 1:CAS:528:DC%2BD2cXns1eqsL8%3D 10.1007/s00438-004-1046-0 (Pubitemid 39371519)
    • (2004) Molecular Genetics and Genomics , vol.272 , Issue.2 , pp. 173-180
    • Nosek, J.1    Novotna, M.2    Hlavatovicova, Z.3    Ussery, D.W.4    Fajkus, J.5    Tomaska, L.6
  • 33
    • 0027260944 scopus 로고
    • Non-universal decoding of the leucine codon CUG in several Candida species
    • 8371978 1:CAS:528:DyaK2cXitlOhsLk%3D 10.1093/nar/21.17.4039
    • T Ohama T Suzuki M Mori S Osawa T Ueda K Watanabe T Nakase 1993 Non-universal decoding of the leucine codon CUG in several Candida species Nucleic Acids Res 21 4039 4045 8371978 1:CAS:528:DyaK2cXitlOhsLk%3D 10.1093/nar/21.17.4039
    • (1993) Nucleic Acids Res , vol.21 , pp. 4039-4045
    • Ohama, T.1    Suzuki, T.2    Mori, M.3    Osawa, S.4    Ueda, T.5    Watanabe, K.6    Nakase, T.7
  • 34
    • 0019287046 scopus 로고
    • Pichia sorbitophila sp. nov.
    • 7436402 1:STN:280:DyaL3M%2FmtFSgtQ%3D%3D 10.1007/BF00444070
    • L Rodriques de Miranda KR Appel H Seyfarth 1980 Pichia sorbitophila sp. nov. Antonie Van Leeuwenhoek 46 157 159 7436402 1:STN:280:DyaL3M%2FmtFSgtQ%3D%3D 10.1007/BF00444070
    • (1980) Antonie Van Leeuwenhoek , vol.46 , pp. 157-159
    • Rodriques De Miranda, L.1    Appel, K.R.2    Seyfarth, H.3
  • 35
    • 49749135547 scopus 로고    scopus 로고
    • Promiscuous DNA in the nuclear genomes of hemiascomycetous yeasts
    • 18673395 1:CAS:528:DC%2BD1cXhtVyltLvE 10.1111/j.1567-1364.2008.00409.x
    • C Sacerdot S Casaregola I Lafontaine F Tekaia B Dujon O Ozier-Kalogeropoulos 2008 Promiscuous DNA in the nuclear genomes of hemiascomycetous yeasts FEMS Yeast Res 8 846 857 18673395 1:CAS:528: DC%2BD1cXhtVyltLvE 10.1111/j.1567-1364.2008.00409.x
    • (2008) FEMS Yeast Res , vol.8 , pp. 846-857
    • Sacerdot, C.1    Casaregola, S.2    Lafontaine, I.3    Tekaia, F.4    Dujon, B.5    Ozier-Kalogeropoulos, O.6
  • 36
    • 0029045375 scopus 로고
    • The CUG codon is decoded in vivo as serine and not leucine in Candida albicans
    • 7784200 1:CAS:528:DyaK2MXlvFalu78%3D 10.1093/nar/23.9.1481
    • MA Santos MF Tuite 1995 The CUG codon is decoded in vivo as serine and not leucine in Candida albicans Nucleic Acids Res 23 1481 1486 7784200 1:CAS:528:DyaK2MXlvFalu78%3D 10.1093/nar/23.9.1481
    • (1995) Nucleic Acids Res , vol.23 , pp. 1481-1486
    • Santos, M.A.1    Tuite, M.F.2
  • 37
    • 23644440813 scopus 로고    scopus 로고
    • RNA maturation in mitochondria of S. cerevisiae and S. pombe
    • DOI 10.1016/j.gene.2005.03.032, PII S037811190500168X
    • B Schäfer 2005 RNA maturation in mitochondria of S. pombe Gene 354 80 85 15913924 10.1016/j.gene.2005.03.032 (Pubitemid 41116685)
    • (2005) Gene , vol.354 , Issue.1-2 SPEC. ISS. , pp. 80-85
    • Schafer, B.1
  • 38
    • 0029015813 scopus 로고
    • The complete mitochondrial DNA sequence of Hansenula wingei reveals new characteristics of yeast mitochondria
    • 8536312 1:CAS:528:DyaK2MXnsVajs78%3D 10.1007/BF00311880
    • T Sekito K Okamoto H Kitano K Yoshida 1995 The complete mitochondrial DNA sequence of Hansenula wingei reveals new characteristics of yeast mitochondria Curr Genet 28 39 53 8536312 1:CAS:528:DyaK2MXnsVajs78%3D 10.1007/BF00311880
    • (1995) Curr Genet , vol.28 , pp. 39-53
    • Sekito, T.1    Okamoto, K.2    Kitano, H.3    Yoshida, K.4
  • 39
    • 11144353440 scopus 로고    scopus 로고
    • The complete mitochondrial genome of the yeast Kluyveromyces thermotolerans
    • DOI 10.1016/j.febslet.2004.10.106, PII S0014579304014206
    • E Talla V Anthouard C Bouchier L Frangeul B Dujon 2005 The complete mitochondrial genome of the yeast Kluyveromyces thermotolerans FEBS Lett 579 30 40 15620687 1:CAS:528:DC%2BD2cXhtFGht7rP 10.1016/j.febslet.2004.10.106 (Pubitemid 40023370)
    • (2005) FEBS Letters , vol.579 , Issue.1 , pp. 30-40
    • Talla, E.1    Anthouard, V.2    Bouchier, C.3    Frangeul, L.4    Dujon, B.5
  • 40
    • 43549090929 scopus 로고    scopus 로고
    • Re-examining the phylogeny of clinically relevant Candida species and allied genera based on multigene analyses
    • DOI 10.1111/j.1567-1364.2007.00342.x
    • CKM Tsui H Daniel V Robert W Meyer 2008 Re-examining the phylogeny of clinically relevant Candida species and allied genera based on multigene analyses FEMS Yeast Res 8 651 659 18248416 1:CAS:528:DC%2BD1cXntFWmtb4%3D 10.1111/j.1567-1364.2007.00342.x (Pubitemid 351678644)
    • (2008) FEMS Yeast Research , vol.8 , Issue.4 , pp. 651-659
    • Tsui, C.K.M.1    Daniel, H.-M.2    Robert, V.3    Meyer, W.4
  • 41
    • 48749105850 scopus 로고    scopus 로고
    • Preparation of yeast mitochondrial DNA for direct sequence analysis
    • 18568348 1:CAS:528:DC%2BD1cXptFOrsrY%3D 10.1007/s00294-008-0200-3
    • M Valach L Tomaska J Nosek 2008 Preparation of yeast mitochondrial DNA for direct sequence analysis Curr Genet 54 105 109 18568348 1:CAS:528: DC%2BD1cXptFOrsrY%3D 10.1007/s00294-008-0200-3
    • (2008) Curr Genet , vol.54 , pp. 105-109
    • Valach, M.1    Tomaska, L.2    Nosek, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.