메뉴 건너뛰기




Volumn 6, Issue 2, 2014, Pages 379-390

Comparative genomics provide insights into evolution of Trichoderma nutrition style

Author keywords

Carbohydrate active enzymes; Cellulolytic enzymes; DN dS; Proteases; Purifying selection; Trichoderma longibrachiatum

Indexed keywords

FUNGAL PROTEIN;

EID: 84902956053     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evu018     Document Type: Article
Times cited : (40)

References (42)
  • 1
    • 84874041895 scopus 로고    scopus 로고
    • Comparative transcriptomics reveals different strategies of Trichoderma mycoparasitism
    • Atanasova L, et al. 2013. Comparative transcriptomics reveals different strategies of Trichoderma mycoparasitism. BMC Genomics 14: 121.
    • (2013) BMC Genomics , vol.14 , pp. 121
    • Atanasova, L.1
  • 2
    • 0034098730 scopus 로고    scopus 로고
    • Using gene wise in the Drosophila annotation experiment
    • Birney E, Durbin R. 2000. Using GeneWise in the Drosophila annotation experiment. Genome Res. 10: 547-548.
    • (2000) Genome Res , vol.10 , pp. 547-548
    • Birney, E.1    Durbin, R.2
  • 4
    • 0034043778 scopus 로고    scopus 로고
    • Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
    • Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 17: 540-552.
    • (2000) Mol Biol Evol , vol.17 , pp. 540-552
    • Castresana, J.1
  • 5
    • 70349245249 scopus 로고    scopus 로고
    • Characterization and gene cloning of a novel serine protease with nematicidal activity from Trichoderma pseudokoningii SMF2
    • Chen LL, et al. 2009. Characterization and gene cloning of a novel serine protease with nematicidal activity from Trichoderma pseudokoningii SMF2. FEMS Microbiol Lett. 299: 135-142.
    • (2009) FEMS Microbiol Lett , vol.299 , pp. 135-142
    • Chen, L.L.1
  • 6
    • 3042631307 scopus 로고    scopus 로고
    • Genome sequence assembly using trace signalsandadditional sequence information
    • 1999 Oct 4-6; Hannover, Germany: Comput. Sci. Biol.: Proc. German Conference on Bioinformatics GCB'99 GCB
    • Chevreux B, Wetter T, Suhai S. 1999. Genome sequence assembly using trace signalsandadditional sequence information.GermanConference on Bioinformatics, GCB '99; 1999 Oct 4-6; Hannover, Germany: Comput. Sci. Biol.: Proc. German Conference on Bioinformatics GCB'99 GCB. p. 45-56.
    • (1999) German Conference on Bioinformatics, GCB '99 , pp. 45-56
    • Chevreux, B.1    Wetter, T.2    Suhai, S.3
  • 7
    • 24944435502 scopus 로고    scopus 로고
    • An oligonucleotide barcode for species identification in Trichoderma and Hypocrea
    • Druzhinina IS, et al. 2005. An oligonucleotide barcode for species identification in Trichoderma and Hypocrea. Fungal Genet Biol. 42: 813-828.
    • (2005) Fungal Genet Biol , vol.42 , pp. 813-828
    • Druzhinina, I.S.1
  • 8
    • 80053023139 scopus 로고    scopus 로고
    • Trichoderma: The genomics of opportunistic success
    • Druzhinina IS, et al. 2011. Trichoderma: the genomics of opportunistic success. Nat Rev Microbiol. 9: 749-759.
    • (2011) Nat Rev Microbiol , vol.9 , pp. 749-759
    • Druzhinina, I.S.1
  • 9
    • 84860377075 scopus 로고    scopus 로고
    • Molecular phylogeny and species delimitation in the section Longibrachiatum of Trichoderma
    • Druzhinina IS, et al. 2012. Molecular phylogeny and species delimitation in the section Longibrachiatum of Trichoderma. Fungal Genet Biol. 49: 358-368.
    • (2012) Fungal Genet Biol , vol.49 , pp. 358-368
    • Druzhinina, I.S.1
  • 10
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32: 1792-1797.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 11
    • 0000365320 scopus 로고
    • Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences
    • Goodman M, Czelusniak J, Moore GW, Romero-Herrera AE, Matsuda G. 1979. Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Syst Zool. 28: 132-168.
    • (1979) Syst Zool , vol.28 , pp. 132-168
    • Goodman, M.1    Czelusniak, J.2    Moore, G.W.3    Romero-Herrera, A.E.4    Matsuda, G.5
  • 12
    • 0002051540 scopus 로고    scopus 로고
    • BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT
    • Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser. 41: 95-98.
    • (1999) Nucl Acids Symp ser , vol.41 , pp. 95-98
    • Hall, T.A.1
  • 14
    • 0037226578 scopus 로고    scopus 로고
    • Mechanisms employed by Trichoderma species in the biological control of plant diseases: The history and evolution of current concepts
    • Howell CR. 2003. Mechanisms employed by Trichoderma species in the biological control of plant diseases: the history and evolution of current concepts. Plant Dis. 87: 4-10.
    • (2003) Plant Dis , vol.87 , pp. 4-10
    • Howell, C.R.1
  • 15
    • 77951266103 scopus 로고    scopus 로고
    • Comparative molecular evolution of trichoderma chitinases in response to mycoparasitic interactions
    • Ihrmark K, et al. 2010. Comparative molecular evolution of trichoderma chitinases in response to mycoparasitic interactions. Evol Bioinform Online. 6: 1-26.
    • (2010) Evol Bioinform Online , vol.6 , pp. 1-26
    • Ihrmark, K.1
  • 17
    • 77955274600 scopus 로고    scopus 로고
    • SMURF: Genomic mapping of fungal secondary metabolite clusters
    • Khaldi N, et al. 2010. SMURF: genomic mapping of fungal secondary metabolite clusters. Fungal Genet Biol. 47: 736-741.
    • (2010) Fungal Genet Biol , vol.47 , pp. 736-741
    • Khaldi, N.1
  • 18
    • 79955115574 scopus 로고    scopus 로고
    • Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma
    • Kubicek CP, et al. 2011. Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma. Genome Biol. 12:R40.
    • (2011) Genome Biol , vol.12
    • Kubicek, C.P.1
  • 19
    • 34250665888 scopus 로고    scopus 로고
    • RNAmmer: Consistent and rapid annotation of ribosomal RNA genes
    • Lagesen K, et al. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35: 3100-3108.
    • (2007) Nucleic Acids Res , vol.35 , pp. 3100-3108
    • Lagesen, K.1
  • 20
    • 34748873304 scopus 로고    scopus 로고
    • The cell wall: A carbohydrate armour for the fungal cell
    • Latge JP. 2007. The cell wall: a carbohydrate armour for the fungal cell. Mol Microbiol. 66: 279-290.
    • (2007) Mol Microbiol , vol.66 , pp. 279-290
    • Latge, J.P.1
  • 21
    • 0141519279 scopus 로고    scopus 로고
    • OrthoMCL: Identification of ortholog groups for eukaryotic genomes
    • Li L, Stoeckert CJ Jr, Roos DS. 2003. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13: 2178-2189.
    • (2003) Genome Res , vol.13 , pp. 2178-2189
    • Li, L.1    Stoeckert Jr., C.J.2    Roos, D.S.3
  • 22
    • 77955594228 scopus 로고    scopus 로고
    • Translational research on Trichoderma: From 'omics to the field
    • Lorito M, Woo SL, Harman GE, Monte E. 2010. Translational research on Trichoderma: from 'omics to the field. Annu Rev Phytopathol. 48: 395-417.
    • (2010) Annu Rev Phytopathol , vol.48 , pp. 395-417
    • Lorito, M.1    Woo, S.L.2    Harman, G.E.3    Monte, E.4
  • 23
    • 78649495976 scopus 로고    scopus 로고
    • Antimicrobial peptaibols induce defense responses and systemic resistance in tobacco against tobacco mosaic virus
    • Luo Y, et al. 2010. Antimicrobial peptaibols induce defense responses and systemic resistance in tobacco against tobacco mosaic virus. FEMS Microbiol Lett. 313: 120-126.
    • (2010) FEMS Microbiol Lett , vol.313 , pp. 120-126
    • Luo, Y.1
  • 24
    • 43449098828 scopus 로고    scopus 로고
    • Genome sequencing and analysis of the biomassdegrading fungus Trichoderma reesei (synHypocrea jecorina)
    • Martinez D, et al. 2008. Genome sequencing and analysis of the biomassdegrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat Biotechnol. 26: 553-560.
    • (2008) Nat Biotechnol , vol.26 , pp. 553-560
    • Martinez, D.1
  • 25
    • 27844524905 scopus 로고    scopus 로고
    • Evolutionary change of the numbers of homeobox genes in bilateral animals
    • Nam J, Nei M. 2005. Evolutionary change of the numbers of homeobox genes in bilateral animals. Mol Biol Evol. 22: 2386-2394.
    • (2005) Mol Biol Evol , vol.22 , pp. 2386-2394
    • Nam, J.1    Nei, M.2
  • 26
    • 40249098860 scopus 로고    scopus 로고
    • Extensive gains and losses of olfactory receptor genes in mammalian evolution
    • Niimura Y, Nei M. 2007. Extensive gains and losses of olfactory receptor genes in mammalian evolution. PLoS One 2:e708.
    • (2007) PLoS One , vol.2
    • Niimura, Y.1    Nei, M.2
  • 27
    • 0031110886 scopus 로고    scopus 로고
    • From gene to organismal phylogeny: Reconciled trees and the gene tree/species tree problem
    • Page RD, Charleston MA. 1997. From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem. Mol Phylogenet Evol. 7: 231-240.
    • (1997) Mol Phylogenet Evol , vol.7 , pp. 231-240
    • Page, R.D.1    Charleston, M.A.2
  • 28
    • 84859426282 scopus 로고    scopus 로고
    • MEROPS: The database of proteolytic enzymes, their substrates and inhibitors
    • Rawlings ND, Barrett AJ, Bateman A. 2012. MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. Nucleic Acids Res. 40:D343-D350.
    • (2012) Nucleic Acids Res , vol.40
    • Rawlings, N.D.1    Barrett, A.J.2    Bateman, A.3
  • 29
    • 84860109324 scopus 로고    scopus 로고
    • MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space
    • Ronquist F, et al. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 61: 539-542.
    • (2012) Syst Biol , vol.61 , pp. 539-542
    • Ronquist, F.1
  • 30
    • 0347487346 scopus 로고    scopus 로고
    • Genera of Bionectriaceae, Hypocreaceae and Nectriaceae (Hypocreales, Ascomycetes)
    • Rossman AY, Samuels GJ, Rogerson CT, Lowen R. 1999. Genera of Bionectriaceae, Hypocreaceae and Nectriaceae (Hypocreales, Ascomycetes). Stud Mycol. 42: 1-83.
    • (1999) Stud Mycol , vol.42 , pp. 1-83
    • Rossman, A.Y.1    Samuels, G.J.2    Rogerson, C.T.3    Lowen, R.4
  • 31
    • 0034065724 scopus 로고    scopus 로고
    • Ab initio gene finding in Drosophila genomic DNA
    • Salamov AA, Solovyev VV. 2000. Ab initio gene finding in Drosophila genomic DNA. Genome Res. 10: 516-522.
    • (2000) Genome Res , vol.10 , pp. 516-522
    • Salamov, A.A.1    Solovyev, V.V.2
  • 32
    • 84864930030 scopus 로고    scopus 로고
    • The Longibrachiatum clade of Trichoderma: A revision with new species
    • Samuels GJ, et al. 2012. The Longibrachiatum clade of Trichoderma: a revision with new species. Fungal Divers. 55: 77-108.
    • (2012) Fungal Divers , vol.55 , pp. 77-108
    • Samuels, G.J.1
  • 33
    • 23144460836 scopus 로고    scopus 로고
    • The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs
    • DOI 10.1093/nar/gki366
    • Schattner P, Brooks AN, Lowe TM. 2005. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 33:W686-W689. (Pubitemid 44530010)
    • (2005) Nucleic Acids Research , vol.33 , Issue.WEB. SERV. ISS
    • Schattner, P.1    Brooks, A.N.2    Lowe, T.M.3
  • 34
    • 44449145113 scopus 로고    scopus 로고
    • Chitinases of filamentous fungi: A large group of diverse proteins with multiple physiological functions
    • Seidl V. 2008. Chitinases of filamentous fungi: a large group of diverse proteins with multiple physiological functions. Fungal Biol Rev. 22: 36-42.
    • (2008) Fungal Biol Rev , vol.22 , pp. 36-42
    • Seidl, V.1
  • 35
    • 84855234390 scopus 로고    scopus 로고
    • Antimicrobial peptaibols from Trichoderma pseudokoningii induce programmed cell death in plant fungal pathogens
    • Shi M, et al. 2010. Antimicrobial peptaibols from Trichoderma pseudokoningii induce programmed cell death in plant fungal pathogens. Microbiology 158: 166-175.
    • (2010) Microbiology , vol.158 , pp. 166-175
    • Shi, M.1
  • 36
    • 41549141861 scopus 로고    scopus 로고
    • Horizontal transfer of a nitrate assimilation gene cluster and ecological transitions in fungi: A phylogenetic study
    • Slot JC, Hibbett DS. 2007. Horizontal transfer of a nitrate assimilation gene cluster and ecological transitions in fungi: a phylogenetic study. PLoS One 2:e1097.
    • (2007) PLoS One , vol.2
    • Slot, J.C.1    Hibbett, D.S.2
  • 37
    • 33745045234 scopus 로고    scopus 로고
    • Broad-spectrum antimicrobial activity and high stability of Trichokonins from Trichoderma koningii SMF2 against plant pathogens
    • Song XY, et al. 2006. Broad-spectrum antimicrobial activity and high stability of Trichokonins from Trichoderma koningii SMF2 against plant pathogens. FEMS Microbiol Lett. 260: 119-125.
    • (2006) FEMS Microbiol Lett , vol.260 , pp. 119-125
    • Song, X.Y.1
  • 38
    • 34547510882 scopus 로고    scopus 로고
    • Solid-state fermentation for Trichokonins production from Trichoderma koningii SMF2 and preparative purification of Trichokonin VI by a simple protocol
    • Song XY, et al. 2007. Solid-state fermentation for Trichokonins production from Trichoderma koningii SMF2 and preparative purification of Trichokonin VI by a simple protocol. J Biotechnol. 131: 209-215.
    • (2007) J Biotechnol , vol.131 , pp. 209-215
    • Song, X.Y.1
  • 39
    • 84866678519 scopus 로고    scopus 로고
    • Antimicrobial peptide trichokonin VI-induced alterations in the morphological and nanomechanical properties of Bacillus subtilis
    • Su HN, et al. 2012. Antimicrobial peptide trichokonin VI-induced alterations in the morphological and nanomechanical properties of Bacillus subtilis. PLoS One 7:e45818.
    • (2012) PLoS One , vol.7
    • Su, H.N.1
  • 40
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • Tamura K, et al. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28: 2731-2739.
    • (2011) Mol Biol Evol , vol.28 , pp. 2731-2739
    • Tamura, K.1
  • 41
    • 0037036464 scopus 로고    scopus 로고
    • Identification of peptaibols from Trichoderma virens and cloning of a peptaibol synthetase
    • Wiest A, et al. 2002. Identification of peptaibols from Trichoderma virens and cloning of a peptaibol synthetase. J Biol Chem. 277: 20862-20868.
    • (2002) J Biol Chem , vol.277 , pp. 20862-20868
    • Wiest, A.1
  • 42
    • 34248669040 scopus 로고    scopus 로고
    • KaKs-Calculator: Calculating Ka and Ks through model selection and model averaging
    • Zhang Z, et al. 2006. KaKs-Calculator: calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics. 4: 259-263.
    • (2006) Genomics Proteomics Bioinformatics , vol.4 , pp. 259-263
    • Zhang, Z.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.