메뉴 건너뛰기




Volumn 9, Issue 9, 2013, Pages

The Genome and Development-Dependent Transcriptomes of Pyronema confluens: A Window into Fungal Evolution

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ASCOMYCETES; CONTROLLED STUDY; FUNGAL GENE; FUNGAL GENOME; FUNGAL STRUCTURES; GENE DELETION; GENE EXPRESSION; GENE SEQUENCE; GENETIC COMPLEMENTATION; GENETIC CONSERVATION; NONHUMAN; NUCLEOTIDE SEQUENCE; ORPHAN GENE; PHOTORECEPTOR GENE; PRO44 GENE; PYRONEMA CONFLUENS; RNA SEQUENCE; SEQUENCE ANALYSIS; SEXUAL DEVELOPMENT; SORDARIA MACROSPORA; TRANSCRIPTOMICS; UPREGULATION;

EID: 84884682760     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1003820     Document Type: Article
Times cited : (74)

References (209)
  • 2
    • 0035712954 scopus 로고    scopus 로고
    • The magnitude of fungal diversity: the 1.5 million species estimate revisited
    • Hawksworth DL, (2001) The magnitude of fungal diversity: the 1.5 million species estimate revisited. Mycol Res 105: 1422-1432.
    • (2001) Mycol Res , vol.105 , pp. 1422-1432
    • Hawksworth, D.L.1
  • 5
    • 1842532972 scopus 로고    scopus 로고
    • Body plan evolution of ascomycetes, as inferred from an RNA polymerase II phylogeny
    • Liu YJ, Hall BD, (2004) Body plan evolution of ascomycetes, as inferred from an RNA polymerase II phylogeny. Proc Nat Acad Sci USA 101: 4507-4512.
    • (2004) Proc Nat Acad Sci USA , vol.101 , pp. 4507-4512
    • Liu, Y.J.1    Hall, B.D.2
  • 6
    • 33645220604 scopus 로고    scopus 로고
    • Comparative gene expression analysis of fruiting body development in two filamentous fungi
    • Nowrousian M, Kück U, (2006) Comparative gene expression analysis of fruiting body development in two filamentous fungi. FEMS Microbiol Lett 257: 328-335.
    • (2006) FEMS Microbiol Lett , vol.257 , pp. 328-335
    • Nowrousian, M.1    Kück, U.2
  • 7
    • 84868131349 scopus 로고    scopus 로고
    • What an rRNA secondary structure tells about phylogeny of fungi in ascomycota with emphasis on evolution of major types of ascus
    • Zhuang WY, Liu CY, (2012) What an rRNA secondary structure tells about phylogeny of fungi in ascomycota with emphasis on evolution of major types of ascus. PLoS One 7: e47546.
    • (2012) PLoS One , vol.7
    • Zhuang, W.Y.1    Liu, C.Y.2
  • 9
    • 77951144839 scopus 로고    scopus 로고
    • Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis
    • Martin F, Kohler A, Murat C, Balestrini R, Coutinho PM, et al. (2010) Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. Nature 464: 1033-1039.
    • (2010) Nature , vol.464 , pp. 1033-1039
    • Martin, F.1    Kohler, A.2    Murat, C.3    Balestrini, R.4    Coutinho, P.M.5
  • 10
    • 80053445520 scopus 로고    scopus 로고
    • Genomic and proteomic analyses of the fungus Arthrobotrys oligospora provide insights into nematode-trap formation
    • Yang J, Wang L, Ji X, Feng Y, Li X, et al. (2011) Genomic and proteomic analyses of the fungus Arthrobotrys oligospora provide insights into nematode-trap formation. PLoS Pathog 7: e1002179.
    • (2011) PLoS Pathog , vol.7
    • Yang, J.1    Wang, L.2    Ji, X.3    Feng, Y.4    Li, X.5
  • 11
    • 0009198331 scopus 로고
    • Two Arthrobotrys anamorphs from Orbilia auricolor
    • Pfister DH, Liftik ME, (1995) Two Arthrobotrys anamorphs from Orbilia auricolor. Mycologia 87: 684-688.
    • (1995) Mycologia , vol.87 , pp. 684-688
    • Pfister, D.H.1    Liftik, M.E.2
  • 12
    • 84861182813 scopus 로고    scopus 로고
    • Genome evolution in filamentous platn pathogens: why bigger can be better
    • Raffaele S, Kamoun S, (2012) Genome evolution in filamentous platn pathogens: why bigger can be better. Nat Rev Microbiol 10: 417-430.
    • (2012) Nat Rev Microbiol , vol.10 , pp. 417-430
    • Raffaele, S.1    Kamoun, S.2
  • 13
    • 33645225729 scopus 로고
    • Zur Entwicklungsgeschichte der Ascomyceten. Pyronema confluens
    • Claussen P, (1912) Zur Entwicklungsgeschichte der Ascomyceten. Pyronema confluens. Zeitschr f Bot 4: 1-63.
    • (1912) Zeitschr F Bot , vol.4 , pp. 1-63
    • Claussen, P.1
  • 14
    • 0344184419 scopus 로고
    • Contributions to the study of Pyronema confluens
    • Gwynne-Vaughan HCI, Williamson HS, (1931) Contributions to the study of Pyronema confluens. Ann Bot 45: 355-371.
    • (1931) Ann Bot , vol.45 , pp. 355-371
    • Gwynne-Vaughan, H.C.I.1    Williamson, H.S.2
  • 15
    • 33645210938 scopus 로고
    • Über Regenerationsversuche an Fruchtkörpern und andere entwicklungsphysiologische Untersuchungen bei Pyronema confluens
    • Kerl I, (1937) Über Regenerationsversuche an Fruchtkörpern und andere entwicklungsphysiologische Untersuchungen bei Pyronema confluens. Zeitschr f Bot 31: 9-174.
    • (1937) Zeitschr F Bot , vol.31 , pp. 9-174
    • Kerl, I.1
  • 17
    • 77954383980 scopus 로고
    • The ascogenous hyphae of Pyronema confluens
    • Wilson IM, (1952) The ascogenous hyphae of Pyronema confluens. Ann Bot 56: 321-338.
    • (1952) Ann Bot , vol.56 , pp. 321-338
    • Wilson, I.M.1
  • 18
    • 84860565364 scopus 로고    scopus 로고
    • The histone chaperone ASF1 is essential for sexual development in the filamentous fungus Sordaria macrospora
    • Gesing S, Schindler D, Fränzel B, Wolters D, Nowrousian M, (2012) The histone chaperone ASF1 is essential for sexual development in the filamentous fungus Sordaria macrospora. Mol Microbiol 84: 748-765.
    • (2012) Mol Microbiol , vol.84 , pp. 748-765
    • Gesing, S.1    Schindler, D.2    Fränzel, B.3    Wolters, D.4    Nowrousian, M.5
  • 19
    • 84883609525 scopus 로고    scopus 로고
    • Suppression subtractive hybridization and comparative expression analysis to identify developmentally regulated genes in filamentous fungi
    • doi: 10.1002/jobm.201200223
    • Gesing S, Schindler D, Nowrousian M, (2012) Suppression subtractive hybridization and comparative expression analysis to identify developmentally regulated genes in filamentous fungi. J Basic Microbiol doi: 10.1002/jobm.201200223.
    • (2012) J Basic Microbiol
    • Gesing, S.1    Schindler, D.2    Nowrousian, M.3
  • 20
    • 0009068130 scopus 로고
    • Studies in pyrophilous fungi - I. The occurence and cultivation of Pyronema
    • Seaver FJ, (1909) Studies in pyrophilous fungi- I. The occurence and cultivation of Pyronema. Mycologia 1: 131-139.
    • (1909) Mycologia , vol.1 , pp. 131-139
    • Seaver, F.J.1
  • 21
    • 0010350296 scopus 로고
    • The conditions of growth and development of Pyronema confluens, Tul. (P. omphaloides, (Bull.) Fuckel)
    • Robinson W, (1926) The conditions of growth and development of Pyronema confluens, Tul. (P. omphaloides, (Bull.) Fuckel). Ann Bot 40: 245-272.
    • (1926) Ann Bot , vol.40 , pp. 245-272
    • Robinson, W.1
  • 22
    • 77952337288 scopus 로고    scopus 로고
    • De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis
    • Nowrousian M, Stajich JE, Chu M, Engh I, Espagne E, et al. (2010) De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis. PLoS Genet 6: e1000891.
    • (2010) PLoS Genet , vol.6
    • Nowrousian, M.1    Stajich, J.E.2    Chu, M.3    Engh, I.4    Espagne, E.5
  • 23
    • 79960422847 scopus 로고    scopus 로고
    • Genome sequence and analysis of the tuber crop potato
    • The Potato Genome Sequencing Consortium
    • The Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475: 189-195.
    • (2011) Nature , vol.475 , pp. 189-195
  • 24
    • 84866637856 scopus 로고    scopus 로고
    • Combining laser microdissection and RNA-seq to chart the transcriptional landscape of fungal development
    • Teichert I, Wolff G, Kück U, Nowrousian M, (2012) Combining laser microdissection and RNA-seq to chart the transcriptional landscape of fungal development. BMC Genomics 13: 511.
    • (2012) BMC Genomics , vol.13 , pp. 511
    • Teichert, I.1    Wolff, G.2    Kück, U.3    Nowrousian, M.4
  • 25
    • 38049057159 scopus 로고    scopus 로고
    • MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes
    • Cantarel BL, Korf I, Robb SMC, Parra G, Ross E, et al. (2008) MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res 18: 188-196.
    • (2008) Genome Res , vol.18 , pp. 188-196
    • Cantarel, B.L.1    Korf, I.2    Robb, S.M.C.3    Parra, G.4    Ross, E.5
  • 27
    • 78651282093 scopus 로고    scopus 로고
    • Deep RNA sequencing improved the structural annotation of the Tuber melanosporum transcriptome
    • Tisserant E, Da Silva C, Kohler A, Morin E, Wincker P, et al. (2011) Deep RNA sequencing improved the structural annotation of the Tuber melanosporum transcriptome. New Phytol 189: 883-891.
    • (2011) New Phytol , vol.189 , pp. 883-891
    • Tisserant, E.1    Da Silva, C.2    Kohler, A.3    Morin, E.4    Wincker, P.5
  • 28
    • 77956107299 scopus 로고    scopus 로고
    • Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing
    • Wang B, Guo G, Wang C, Lin Y, Wang X, et al. (2010) Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing. Nucl Acids Res 38: 5075-5087.
    • (2010) Nucl Acids Res , vol.38 , pp. 5075-5087
    • Wang, B.1    Guo, G.2    Wang, C.3    Lin, Y.4    Wang, X.5
  • 30
    • 84864076971 scopus 로고    scopus 로고
    • Natural antisense transcripts in fungi
    • Donaldson ME, Saville BJ, (2012) Natural antisense transcripts in fungi. Mol Microbiol 83: 405-417.
    • (2012) Mol Microbiol , vol.83 , pp. 405-417
    • Donaldson, M.E.1    Saville, B.J.2
  • 31
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: discovering splice junctions with RNA-Seq
    • Trapnell C, Pachter L, Salzberg SL, (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinf 25: 1105-1111.
    • (2009) Bioinf , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 32
    • 84866145069 scopus 로고    scopus 로고
    • Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing
    • Delmas S, Pullan ST, Gaddipati S, Kokolski M, Malla S, et al. (2012) Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing. PLoS Genet 8: e1002875.
    • (2012) PLoS Genet , vol.8
    • Delmas, S.1    Pullan, S.T.2    Gaddipati, S.3    Kokolski, M.4    Malla, S.5
  • 33
    • 33846617381 scopus 로고    scopus 로고
    • Deep and comparative analysis of the mycelium and appressorium transcriptomes of Magnaporthe grisea using MPSS, RL-SAGE, and oligoarray methods
    • Gowda M, Venu RC, Raghupathy MB, Nobuta K, Li H, et al. (2006) Deep and comparative analysis of the mycelium and appressorium transcriptomes of Magnaporthe grisea using MPSS, RL-SAGE, and oligoarray methods. BMC Genomics 7: 310.
    • (2006) BMC Genomics , vol.7 , pp. 310
    • Gowda, M.1    Venu, R.C.2    Raghupathy, M.B.3    Nobuta, K.4    Li, H.5
  • 34
    • 55349096760 scopus 로고    scopus 로고
    • The effect of temperature on natural antisense transcript (NAT) expression in Aspergillus flavus
    • Smith CA, Robertson D, Yates B, Nielsen DM, Brown D, et al. (2008) The effect of temperature on natural antisense transcript (NAT) expression in Aspergillus flavus. Curr Genet 54: 241-269.
    • (2008) Curr Genet , vol.54 , pp. 241-269
    • Smith, C.A.1    Robertson, D.2    Yates, B.3    Nielsen, D.M.4    Brown, D.5
  • 35
    • 84875074474 scopus 로고    scopus 로고
    • 5′-Serial analysis of gene expression studies reveal a transcriptomic switch during fruiting body development in Coprinopsis cinerea
    • Cheng CK, Au CH, Wilke SK, Stajich JE, Zolan ME, et al. (2013) 5′-Serial analysis of gene expression studies reveal a transcriptomic switch during fruiting body development in Coprinopsis cinerea. BMC Genomics 14: 195.
    • (2013) BMC Genomics , vol.14 , pp. 195
    • Cheng, C.K.1    Au, C.H.2    Wilke, S.K.3    Stajich, J.E.4    Zolan, M.E.5
  • 36
    • 80053095672 scopus 로고    scopus 로고
    • Ustilago maydis transcript features identified through full-length cDNA analysis
    • Doyle EE, Donaldson ME, Morrison EN, Saville BJ, (2011) Ustilago maydis transcript features identified through full-length cDNA analysis. Mol Genet Genomics 286: 143-159.
    • (2011) Mol Genet Genomics , vol.286 , pp. 143-159
    • Doyle, E.E.1    Donaldson, M.E.2    Morrison, E.N.3    Saville, B.J.4
  • 37
  • 38
    • 84883177540 scopus 로고    scopus 로고
    • Comparative genomics of a plant-pathogenic fungus, Pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence
    • Manning VA, Pandelova I, Dhillon B, Wilhelm LJ, Goodwin SB, et al. (2013) Comparative genomics of a plant-pathogenic fungus, Pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence. G3 (Bethesda) 3: 41-63.
    • (2013) G3 (Bethesda) , vol.3 , pp. 41-63
    • Manning, V.A.1    Pandelova, I.2    Dhillon, B.3    Wilhelm, L.J.4    Goodwin, S.B.5
  • 40
    • 70149110707 scopus 로고    scopus 로고
    • The genome of Nectria haematococca: Contribution of supernumerary chromosomes to gene expansion
    • Coleman JJ, Rounsley SD, Rodriguez-Carres M, Kuo A, Wasmann CC, et al. (2009) The genome of Nectria haematococca: Contribution of supernumerary chromosomes to gene expansion. PLoS Genet 5: e1000618.
    • (2009) PLoS Genet , vol.5
    • Coleman, J.J.1    Rounsley, S.D.2    Rodriguez-Carres, M.3    Kuo, A.4    Wasmann, C.C.5
  • 41
    • 0037172977 scopus 로고    scopus 로고
    • A cytosine methyltransferase homologue is essential for repeat-induced point mutation in Neurospora crassa
    • Freitag M, Williams RL, Kothe GO, Selker EU, (2002) A cytosine methyltransferase homologue is essential for repeat-induced point mutation in Neurospora crassa. Proc Nat Acad Sci USA 99: 8802-8807.
    • (2002) Proc Nat Acad Sci USA , vol.99 , pp. 8802-8807
    • Freitag, M.1    Williams, R.L.2    Kothe, G.O.3    Selker, E.U.4
  • 42
    • 0023644245 scopus 로고
    • Rearrangement of duplicated DNA in specialized cells of Neurospora
    • Selker EU, Cambareri EB, Jensen BC, Haack KR, (1987) Rearrangement of duplicated DNA in specialized cells of Neurospora. Cell 51: 741-752.
    • (1987) Cell , vol.51 , pp. 741-752
    • Selker, E.U.1    Cambareri, E.B.2    Jensen, B.C.3    Haack, K.R.4
  • 44
    • 4143050271 scopus 로고    scopus 로고
    • RIP: the evolutionary cost of genome defense
    • Galagan JE, Selker EU, (2004) RIP: the evolutionary cost of genome defense. Trends Genet 20: 417-423.
    • (2004) Trends Genet , vol.20 , pp. 417-423
    • Galagan, J.E.1    Selker, E.U.2
  • 45
    • 42949174108 scopus 로고    scopus 로고
    • Comparative genomic analysis of fungal genomes reveals intron-rich ancestors
    • Stajich JE, Dietrich FS, Roy SW, (2007) Comparative genomic analysis of fungal genomes reveals intron-rich ancestors. Genome Biol 8: R223.
    • (2007) Genome Biol , vol.8
    • Stajich, J.E.1    Dietrich, F.S.2    Roy, S.W.3
  • 46
    • 79958724665 scopus 로고    scopus 로고
    • RNA sequencing reveals two major classes of gene expression levels in metazoan cells
    • Hebenstreit D, Fang M, Gu M, Charoensawan V, van Oudenaarden A, et al. (2011) RNA sequencing reveals two major classes of gene expression levels in metazoan cells. Mol Syst Biol 7: 497.
    • (2011) Mol Syst Biol , vol.7 , pp. 497
    • Hebenstreit, D.1    Fang, M.2    Gu, M.3    Charoensawan, V.4    van Oudenaarden, A.5
  • 48
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5
  • 49
    • 0037314098 scopus 로고    scopus 로고
    • r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock
    • Sanderson MJ, (2003) r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinf 19: 301-302.
    • (2003) Bioinf , vol.19 , pp. 301-302
    • Sanderson, M.J.1
  • 50
    • 84871781177 scopus 로고    scopus 로고
    • Historical biogeography and diversification of truffles in the Tuberaceae and their newly identified southern hemisphere sister lineage
    • Bonito G, Smith ME, Nowak M, Healy RA, Guevara G, et al. (2013) Historical biogeography and diversification of truffles in the Tuberaceae and their newly identified southern hemisphere sister lineage. PLoS One 8: e52765.
    • (2013) PLoS One , vol.8
    • Bonito, G.1    Smith, M.E.2    Nowak, M.3    Healy, R.A.4    Guevara, G.5
  • 51
    • 0034513749 scopus 로고    scopus 로고
    • Proposed nomenclature for mating type genes of filamentous ascomycetes
    • Turgeon G, Yoder OC, (2000) Proposed nomenclature for mating type genes of filamentous ascomycetes. Fungal Genet Biol 31: 1-5.
    • (2000) Fungal Genet Biol , vol.31 , pp. 1-5
    • Turgeon, G.1    Yoder, O.C.2
  • 52
    • 0034847382 scopus 로고    scopus 로고
    • Mating-type genes for classical strain improvements of ascomycetes
    • Pöggeler S, (2001) Mating-type genes for classical strain improvements of ascomycetes. Appl Microbiol Biotechnol 56: 589-601.
    • (2001) Appl Microbiol Biotechnol , vol.56 , pp. 589-601
    • Pöggeler, S.1
  • 53
    • 0030846843 scopus 로고    scopus 로고
    • Mating-type genes from the homothallic fungus Sordaria macrospora are functionally expressed in a heterothallic ascomycete
    • Pöggeler S, Risch S, Kück U, Osiewacz HD, (1997) Mating-type genes from the homothallic fungus Sordaria macrospora are functionally expressed in a heterothallic ascomycete. Genetics 147: 567-580.
    • (1997) Genetics , vol.147 , pp. 567-580
    • Pöggeler, S.1    Risch, S.2    Kück, U.3    Osiewacz, H.D.4
  • 54
    • 79959898334 scopus 로고    scopus 로고
    • Molecular organization of the mating-type loci in the homothallic ascomycete Eupenicillium crustaceum
    • Pöggeler S, O'Gorman CM, Hoff B, Kück U, (2011) Molecular organization of the mating-type loci in the homothallic ascomycete Eupenicillium crustaceum. Fungal Biol 115: 615-624.
    • (2011) Fungal Biol , vol.115 , pp. 615-624
    • Pöggeler, S.1    O'Gorman, C.M.2    Hoff, B.3    Kück, U.4
  • 55
    • 77953748116 scopus 로고    scopus 로고
    • Mating systems and sexual morphogenesis in ascomycetes
    • In: Borkovich KA, Ebbole DJ, editors, Washington, DC: ASM Press
    • Debuchy R, Berteaux-Leceleir V, Silar P (2010) Mating systems and sexual morphogenesis in ascomycetes. In: Borkovich KA, Ebbole DJ, editors. Cellular and molecular biology of filamentous fungi. Washington, DC: ASM Press. pp. 501-535.
    • (2010) Cellular and molecular biology of filamentous fungi , pp. 501-535
    • Debuchy, R.1    Berteaux-Leceleir, V.2    Silar, P.3
  • 56
    • 34547905019 scopus 로고    scopus 로고
    • Mating type and the genetic basis of self-fertility in the model fungus Aspergillus nidulans
    • Paoletti M, Seymour FA, Alcocer MJC, Kaur N, Calvo AM, et al. (2007) Mating type and the genetic basis of self-fertility in the model fungus Aspergillus nidulans. Curr Biol 17: 1384-1389.
    • (2007) Curr Biol , vol.17 , pp. 1384-1389
    • Paoletti, M.1    Seymour, F.A.2    Alcocer, M.J.C.3    Kaur, N.4    Calvo, A.M.5
  • 57
    • 34249682649 scopus 로고    scopus 로고
    • DNA sequence characterization and molecular evolution of MAT1 and MAT2 mating-type loci of the self-compatible ascomycete mold Neosartorya fischeri
    • Rydholm C, Dyer PS, Lutzoni F, (2007) DNA sequence characterization and molecular evolution of MAT1 and MAT2 mating-type loci of the self-compatible ascomycete mold Neosartorya fischeri. Eukaryot Cell 6: 868-874.
    • (2007) Eukaryot Cell , vol.6 , pp. 868-874
    • Rydholm, C.1    Dyer, P.S.2    Lutzoni, F.3
  • 58
    • 78651337617 scopus 로고    scopus 로고
    • Isolation and characterization of MAT genes in the symbiotic ascomycete Tuber melanosporum
    • Rubini A, Belfiori B, Riccioni C, Tisserant E, Arcioni S, et al. (2011) Isolation and characterization of MAT genes in the symbiotic ascomycete Tuber melanosporum. New Phytol 183: 710-722.
    • (2011) New Phytol , vol.183 , pp. 710-722
    • Rubini, A.1    Belfiori, B.2    Riccioni, C.3    Tisserant, E.4    Arcioni, S.5
  • 59
    • 33846084519 scopus 로고    scopus 로고
    • Mating-type structure, evolution, and function in Euascomycetes
    • In: Kües U, Fischer R, editors, Berlin, Heidelberg: Springer-Verlag
    • Debuchy R, Turgeon BG (2006) Mating-type structure, evolution, and function in Euascomycetes. In: Kües U, Fischer R, editors. The Mycota I: Growth, differentiation and sexuality. Berlin, Heidelberg: Springer-Verlag. pp. 293-323.
    • (2006) The Mycota I: Growth, differentiation and sexuality , pp. 293-323
    • Debuchy, R.1    Turgeon, B.G.2
  • 61
    • 46949101573 scopus 로고    scopus 로고
    • Sexual reproduction and significance of MAT in the Aspergilli
    • In: Heitman J, Kronstad JW, Taylor JW, Casselton LA, editors, Washington, DC: ASM Press
    • Dyer PS (2007) Sexual reproduction and significance of MAT in the Aspergilli. In: Heitman J, Kronstad JW, Taylor JW, Casselton LA, editors. Sex in fungi. Washington, DC: ASM Press. pp. 123-142.
    • (2007) Sex in fungi , pp. 123-142
    • Dyer, P.S.1
  • 62
    • 40949097281 scopus 로고    scopus 로고
    • Eighty years after its discovery, Fleming's Penicillium strain discloses the secret of its sex
    • Hoff B, Pöggeler S, Kück U, (2008) Eighty years after its discovery, Fleming's Penicillium strain discloses the secret of its sex. Eukaryot Cell 7: 465-470.
    • (2008) Eukaryot Cell , vol.7 , pp. 465-470
    • Hoff, B.1    Pöggeler, S.2    Kück, U.3
  • 64
    • 85047700164 scopus 로고    scopus 로고
    • The rapid evolution of reproductive proteins
    • Swanson WJ, Vacquier VD, (2002) The rapid evolution of reproductive proteins. Nat Rev Genet 3: 137-144.
    • (2002) Nat Rev Genet , vol.3 , pp. 137-144
    • Swanson, W.J.1    Vacquier, V.D.2
  • 65
    • 32544445408 scopus 로고    scopus 로고
    • Evolution of reproductive proteins from animals and plants
    • Clark NL, Aagarard JE, Swanson WJ, (2006) Evolution of reproductive proteins from animals and plants. Reproduction 131: 11-22.
    • (2006) Reproduction , vol.131 , pp. 11-22
    • Clark, N.L.1    Aagarard, J.E.2    Swanson, W.J.3
  • 66
    • 80054976678 scopus 로고    scopus 로고
    • The evolution of gene expression levels in mammalian organs
    • Brawand D, Soumillon M, Necsulea A, Julien P, Csardi G, et al. (2011) The evolution of gene expression levels in mammalian organs. Nature 478: 343-348.
    • (2011) Nature , vol.478 , pp. 343-348
    • Brawand, D.1    Soumillon, M.2    Necsulea, A.3    Julien, P.4    Csardi, G.5
  • 67
    • 66649105285 scopus 로고    scopus 로고
    • Evolution of pathogenicity and sexual reproduction in eight Candida genomes
    • Butler G, Rasmussen MD, Lin MF, Santos MAS, Sakthikumar S, 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    Santos, M.A.S.4    Sakthikumar, S.5
  • 68
    • 0032878010 scopus 로고    scopus 로고
    • Phylogenetic relationships between mating-type sequences from homothallic and heterothallic ascomycetes
    • Pöggeler S, (1999) Phylogenetic relationships between mating-type sequences from homothallic and heterothallic ascomycetes. Curr Genet 36: 222-231.
    • (1999) Curr Genet , vol.36 , pp. 222-231
    • Pöggeler, S.1
  • 69
    • 38349137174 scopus 로고    scopus 로고
    • The evolution of the pheromonal signal system and its potential role for reproductive isolation in heterothallic Neurospora
    • Karlsson M, Nygren K, Johannesson H, (2008) The evolution of the pheromonal signal system and its potential role for reproductive isolation in heterothallic Neurospora. Mol Biol Evol 25: 168-178.
    • (2008) Mol Biol Evol , vol.25 , pp. 168-178
    • Karlsson, M.1    Nygren, K.2    Johannesson, H.3
  • 70
    • 84869869378 scopus 로고    scopus 로고
    • Analyses of expressed sequence tags in Neurospora reveal rapid evolution of genes associated with the early stages of sexual reproduction in fungi
    • Nygren K, Wallberg A, Samils N, Stajich JE, Townsend JP, et al. (2012) Analyses of expressed sequence tags in Neurospora reveal rapid evolution of genes associated with the early stages of sexual reproduction in fungi. BMC Evol Biol 12: 229.
    • (2012) BMC Evol Biol , vol.12 , pp. 229
    • Nygren, K.1    Wallberg, A.2    Samils, N.3    Stajich, J.E.4    Townsend, J.P.5
  • 72
    • 0034978556 scopus 로고    scopus 로고
    • Highly expressed genes in yeast evolve slowly
    • Pál C, Papp B, Hurst LD, (2001) Highly expressed genes in yeast evolve slowly. Genetics 158: 927-931.
    • (2001) Genetics , vol.158 , pp. 927-931
    • Pál, C.1    Papp, B.2    Hurst, L.D.3
  • 73
    • 5044252972 scopus 로고    scopus 로고
    • Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome
    • Subramanian S, Kumar S, (2004) Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome. Genetics 168: 373-381.
    • (2004) Genetics , vol.168 , pp. 373-381
    • Subramanian, S.1    Kumar, S.2
  • 74
    • 33745616793 scopus 로고    scopus 로고
    • Accelerated evoutionary rate may be responsible for the emergence of lineage-specific genes in ascomycota
    • Cai JJ, Woo PCY, Lau SKP, Smith DK, Yuen KY, (2006) Accelerated evoutionary rate may be responsible for the emergence of lineage-specific genes in ascomycota. J Mol Evol 63: 1-11.
    • (2006) J Mol Evol , vol.63 , pp. 1-11
    • Cai, J.J.1    Woo, P.C.Y.2    Lau, S.K.P.3    Smith, D.K.4    Yuen, K.Y.5
  • 76
    • 80052969570 scopus 로고    scopus 로고
    • The evolutionary origin of orphan genes
    • Tautz D, Domazet-Lošo T, (2011) The evolutionary origin of orphan genes. Nat Rev Genet 12: 692-702.
    • (2011) Nat Rev Genet , vol.12 , pp. 692-702
    • Tautz, D.1    Domazet-Lošo, T.2
  • 77
    • 51649109165 scopus 로고    scopus 로고
    • Dissecting colony development of Neurospora crassa using mRNA profiling and comparative genomics approaches
    • Kasuga T, Glass NL, (2008) Dissecting colony development of Neurospora crassa using mRNA profiling and comparative genomics approaches. Eukaryot Cell 7: 1549-1564.
    • (2008) Eukaryot Cell , vol.7 , pp. 1549-1564
    • Kasuga, T.1    Glass, N.L.2
  • 79
    • 69549126598 scopus 로고    scopus 로고
    • Sexual development in the industrial workhorse Trichoderma reesei
    • Seidl V, Seibel C, Kubicek CP, Schmoll M, (2009) Sexual development in the industrial workhorse Trichoderma reesei. Proc Nat Acad Sci USA 106: 13909-13914.
    • (2009) Proc Nat Acad Sci USA , vol.106 , pp. 13909-13914
    • Seidl, V.1    Seibel, C.2    Kubicek, C.P.3    Schmoll, M.4
  • 80
    • 84866510169 scopus 로고    scopus 로고
    • Blue light acts as a s double-edged sword in regulating sexual development in Hypocrea jecorina (Trichoderma reesei)
    • Chen CL, Kuo HC, Tung SY, Hsu PWC, Wang CL, et al. (2012) Blue light acts as a s double-edged sword in regulating sexual development in Hypocrea jecorina (Trichoderma reesei). PLoS One 7: e44969.
    • (2012) PLoS One , vol.7
    • Chen, C.L.1    Kuo, H.C.2    Tung, S.Y.3    Hsu, P.W.C.4    Wang, C.L.5
  • 81
    • 0014643741 scopus 로고
    • Morphogenesis in Schizophyllum commune. I. Effects of white light
    • Perkins JH, (1969) Morphogenesis in Schizophyllum commune. I. Effects of white light. Plant Physiol 44: 1706-1711.
    • (1969) Plant Physiol , vol.44 , pp. 1706-1711
    • Perkins, J.H.1
  • 82
    • 18844476379 scopus 로고    scopus 로고
    • Life history and developmental processes in the basidiomycete Coprinus cinereus
    • Kües U, (2000) Life history and developmental processes in the basidiomycete Coprinus cinereus. Microbiol Mol Biol Rev 64: 316-353.
    • (2000) Microbiol Mol Biol Rev , vol.64 , pp. 316-353
    • Kües, U.1
  • 83
    • 0014632660 scopus 로고
    • Morphogenesis in Schizophyllum commune. II. Effects of monochromatic light
    • Perkins JH, Gordon SA, (1969) Morphogenesis in Schizophyllum commune. II. Effects of monochromatic light. Plant Physiol 44: 1712-1716.
    • (1969) Plant Physiol , vol.44 , pp. 1712-1716
    • Perkins, J.H.1    Gordon, S.A.2
  • 84
    • 0037008528 scopus 로고    scopus 로고
    • White Collar-1, a circadian blue light photoreceptor, binding to the frequency promoter
    • Froehlich AC, Liu Y, Loros JJ, Dunlap JC, (2002) White Collar-1, a circadian blue light photoreceptor, binding to the frequency promoter. Science 297: 815-819.
    • (2002) Science , vol.297 , pp. 815-819
    • Froehlich, A.C.1    Liu, Y.2    Loros, J.J.3    Dunlap, J.C.4
  • 85
    • 0029879678 scopus 로고    scopus 로고
    • White collar-1, a central regulator of blue-light responses in Neurospora, is a zinc finger protein
    • Ballario P, Vittorioso P, Magrelli A, Talora C, Cabibbo A, et al. (1996) White collar-1, a central regulator of blue-light responses in Neurospora, is a zinc finger protein. EMBO J 15: 1650-1657.
    • (1996) EMBO J , vol.15 , pp. 1650-1657
    • Ballario, P.1    Vittorioso, P.2    Magrelli, A.3    Talora, C.4    Cabibbo, A.5
  • 86
    • 0030982250 scopus 로고    scopus 로고
    • Neurospora wc-1 and wc-2: Transcription, photoresponses, and the origins of circadian rhythmicity
    • Crosthwaite SC, Dunlap JC, Loros JJ, (1997) Neurospora wc-1 and wc-2: Transcription, photoresponses, and the origins of circadian rhythmicity. Science 276: 763-769.
    • (1997) Science , vol.276 , pp. 763-769
    • Crosthwaite, S.C.1    Dunlap, J.C.2    Loros, J.J.3
  • 87
    • 0031014876 scopus 로고    scopus 로고
    • White collar 2, a partner in blue-light signal transduction, controlling expression of light-regulated genes in Neurospora crassa
    • Linden H, Macino G, (1997) White collar 2, a partner in blue-light signal transduction, controlling expression of light-regulated genes in Neurospora crassa. EMBO J 16: 98-109.
    • (1997) EMBO J , vol.16 , pp. 98-109
    • Linden, H.1    Macino, G.2
  • 88
    • 0033568490 scopus 로고    scopus 로고
    • Role of a white collar-1-white collar-2 complex in blue-light signal transduction
    • Talora C, Franchi L, Linden H, Ballario P, Macino G, (1999) Role of a white collar-1-white collar-2 complex in blue-light signal transduction. EMBO J 18: 4961-4968.
    • (1999) EMBO J , vol.18 , pp. 4961-4968
    • Talora, C.1    Franchi, L.2    Linden, H.3    Ballario, P.4    Macino, G.5
  • 89
    • 0035830504 scopus 로고    scopus 로고
    • The PAS protein VIVID defines a clock-associated feedback loop that represses light input, modulates gating, and regulates clock resetting
    • Heintzen C, Loros JJ, Dunlap JC, (2001) The PAS protein VIVID defines a clock-associated feedback loop that represses light input, modulates gating, and regulates clock resetting. Cell 104: 453-464.
    • (2001) Cell , vol.104 , pp. 453-464
    • Heintzen, C.1    Loros, J.J.2    Dunlap, J.C.3
  • 90
    • 0141848660 scopus 로고    scopus 로고
    • VIVID is a flavoprotein and serves as a fungal blue light photoreceptor for photoadaptation
    • Schwerdtfeger C, Linden H, (2003) VIVID is a flavoprotein and serves as a fungal blue light photoreceptor for photoadaptation. EMBO J 22: 4846-4855.
    • (2003) EMBO J , vol.22 , pp. 4846-4855
    • Schwerdtfeger, C.1    Linden, H.2
  • 91
    • 27144432820 scopus 로고    scopus 로고
    • The Aspergillus nidulans phytochrome FphA represses sexual development in red light
    • Blumenstein A, Vienken K, Tasler R, Purschwitz J, Veith D, et al. (2005) The Aspergillus nidulans phytochrome FphA represses sexual development in red light. Curr Biol 15: 1833-1838.
    • (2005) Curr Biol , vol.15 , pp. 1833-1838
    • Blumenstein, A.1    Vienken, K.2    Tasler, R.3    Purschwitz, J.4    Veith, D.5
  • 92
    • 0033607149 scopus 로고    scopus 로고
    • A eukaryotic protein, NOP-1, binds retinal to form an archaeal rhodopsin-like photochemically reactive pigment
    • Bieszke JA, Spudich EN, Scott KL, Borkovich KA, Spudich JL, (1999) A eukaryotic protein, NOP-1, binds retinal to form an archaeal rhodopsin-like photochemically reactive pigment. Biochemistry 38: 14138-14145.
    • (1999) Biochemistry , vol.38 , pp. 14138-14145
    • Bieszke, J.A.1    Spudich, E.N.2    Scott, K.L.3    Borkovich, K.A.4    Spudich, J.L.5
  • 93
    • 0033529279 scopus 로고    scopus 로고
    • The nop-1 gene of Neurospora crassa encodes a seven transmembrane helix retinal-binding protein homologous to archaeal rhodopsins
    • Bieszke JA, Braun EL, Bean LE, Kang S, Natvig DO, et al. (1999) The nop-1 gene of Neurospora crassa encodes a seven transmembrane helix retinal-binding protein homologous to archaeal rhodopsins. Proc Nat Acad Sci USA 96: 8034-8039.
    • (1999) Proc Nat Acad Sci USA , vol.96 , pp. 8034-8039
    • Bieszke, J.A.1    Braun, E.L.2    Bean, L.E.3    Kang, S.4    Natvig, D.O.5
  • 94
    • 3242797479 scopus 로고    scopus 로고
    • Fungal rhodopsins and opsin-related proteins: eukaryotic homologues of bacteriorhodopsin with unknown functions
    • Brown LS, (2004) Fungal rhodopsins and opsin-related proteins: eukaryotic homologues of bacteriorhodopsin with unknown functions. Photochem Photobiol Sci 3: 555-565.
    • (2004) Photochem Photobiol Sci , vol.3 , pp. 555-565
    • Brown, L.S.1
  • 95
    • 33751251331 scopus 로고    scopus 로고
    • How fungi keep time: circadian system in Neurospora and other fungi
    • Dunlap JC, Loros JJ, (2006) How fungi keep time: circadian system in Neurospora and other fungi. Curr Opin Microbiol 9: 579-587.
    • (2006) Curr Opin Microbiol , vol.9 , pp. 579-587
    • Dunlap, J.C.1    Loros, J.J.2
  • 96
    • 77951887222 scopus 로고    scopus 로고
    • The diversity and evolution of circadian clock proteins in fungi
    • Salichos L, Rokas A, (2010) The diversity and evolution of circadian clock proteins in fungi. Mycologia 102: 269-278.
    • (2010) Mycologia , vol.102 , pp. 269-278
    • Salichos, L.1    Rokas, A.2
  • 97
    • 0029047917 scopus 로고
    • Light-Induced resetting of a circadian clock is mediated by a rapid increase in frequency transcript
    • Crosthwaite SC, Loros JJ, Dunlap JC, (1995) Light-Induced resetting of a circadian clock is mediated by a rapid increase in frequency transcript. Cell 81: 1003-1012.
    • (1995) Cell , vol.81 , pp. 1003-1012
    • Crosthwaite, S.C.1    Loros, J.J.2    Dunlap, J.C.3
  • 98
    • 0242669950 scopus 로고    scopus 로고
    • Role for antisense RNA in regulating circadian clock function in Neurospora crassa
    • Kramer C, Loros JJ, Dunlap JC, Crosthwaite SK, (2003) Role for antisense RNA in regulating circadian clock function in Neurospora crassa. Nature 421: 948-952.
    • (2003) Nature , vol.421 , pp. 948-952
    • Kramer, C.1    Loros, J.J.2    Dunlap, J.C.3    Crosthwaite, S.K.4
  • 99
    • 24344437155 scopus 로고    scopus 로고
    • Molecular mechanism of temperature sensing by the circadian clock of Neurospora crassa
    • Diernfellner ACR, Schafmeier T, Merrow MW, Brunner M, (2005) Molecular mechanism of temperature sensing by the circadian clock of Neurospora crassa. Genes Dev 19: 1968-1973.
    • (2005) Genes Dev , vol.19 , pp. 1968-1973
    • Diernfellner, A.C.R.1    Schafmeier, T.2    Merrow, M.W.3    Brunner, M.4
  • 100
    • 28644441707 scopus 로고    scopus 로고
    • Temperature-modulated alternative splicing and promoter use in the circadian clock gene frequency
    • Colot HV, Loros JJ, Dunlap JC, (2005) Temperature-modulated alternative splicing and promoter use in the circadian clock gene frequency. Mol Biol Cell 16: 5563-5571.
    • (2005) Mol Biol Cell , vol.16 , pp. 5563-5571
    • Colot, H.V.1    Loros, J.J.2    Dunlap, J.C.3
  • 101
    • 67349203997 scopus 로고    scopus 로고
    • Genome-wide analysis of light-inducible responses reveals hierarchical light signalling in Neurospora
    • Chen CH, Ringelberg CS, Gross RH, Dunlap JC, Loros JJ, (2009) Genome-wide analysis of light-inducible responses reveals hierarchical light signalling in Neurospora. EMBO J 28: 1029-1042.
    • (2009) EMBO J , vol.28 , pp. 1029-1042
    • Chen, C.H.1    Ringelberg, C.S.2    Gross, R.H.3    Dunlap, J.C.4    Loros, J.J.5
  • 102
    • 33745924142 scopus 로고    scopus 로고
    • A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors
    • Colot HV, Park G, Turner GE, Ringelberg C, Crew CM, et al. (2006) A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors. Proc Nat Acad Sci USA 103: 10352-10357.
    • (2006) Proc Nat Acad Sci USA , vol.103 , pp. 10352-10357
    • Colot, H.V.1    Park, G.2    Turner, G.E.3    Ringelberg, C.4    Crew, C.M.5
  • 103
    • 0034897976 scopus 로고    scopus 로고
    • The nsdD gene encodes a putative GATA-type transcription factor necessary for sexual development of Aspergillus nidulans
    • Han KH, Han KY, Yu JH, Chae KS, Jahng KY, et al. (2001) The nsdD gene encodes a putative GATA-type transcription factor necessary for sexual development of Aspergillus nidulans. Mol Microbiol 41: 299-309.
    • (2001) Mol Microbiol , vol.41 , pp. 299-309
    • Han, K.H.1    Han, K.Y.2    Yu, J.H.3    Chae, K.S.4    Jahng, K.Y.5
  • 104
    • 84860557378 scopus 로고    scopus 로고
    • Whole-genome sequencing of Sordaria macrospora mutants identifies developmental genes
    • Nowrousian M, Teichert I, Masloff S, Kück U, (2012) Whole-genome sequencing of Sordaria macrospora mutants identifies developmental genes. G3 (Bethesda) 2: 261-270.
    • (2012) G3 (Bethesda) , vol.2 , pp. 261-270
    • Nowrousian, M.1    Teichert, I.2    Masloff, S.3    Kück, U.4
  • 105
    • 77953515722 scopus 로고    scopus 로고
    • Conserved regulators of mating are essential for Aspergillus fumigatus cleistothecium formation
    • Szewczyk E, Krappmann S, (2010) Conserved regulators of mating are essential for Aspergillus fumigatus cleistothecium formation. Eukaryot Cell 9: 774-783.
    • (2010) Eukaryot Cell , vol.9 , pp. 774-783
    • Szewczyk, E.1    Krappmann, S.2
  • 106
    • 77957233305 scopus 로고    scopus 로고
    • Photobiology in the Zygomycota: multiple photoreceptor genes for complex responses to light
    • Corrochano LM, Garre V, (2010) Photobiology in the Zygomycota: multiple photoreceptor genes for complex responses to light. Fungal Genet Biol 47: 893-899.
    • (2010) Fungal Genet Biol , vol.47 , pp. 893-899
    • Corrochano, L.M.1    Garre, V.2
  • 107
    • 76649085202 scopus 로고    scopus 로고
    • Light regulation of metabolic pathways in fungi
    • Tisch D, Schmoll M, (2010) Light regulation of metabolic pathways in fungi. Appl Microbiol Biotechnol 85: 1259-1277.
    • (2010) Appl Microbiol Biotechnol , vol.85 , pp. 1259-1277
    • Tisch, D.1    Schmoll, M.2
  • 108
    • 0001036895 scopus 로고
    • Photoregulation of the carotenoid biosynthetic pathway in albino and white collar mutants of Neurospora crassa
    • Harding RW, Turner RV, (1981) Photoregulation of the carotenoid biosynthetic pathway in albino and white collar mutants of Neurospora crassa. Plant Physiol 68: 745-749.
    • (1981) Plant Physiol , vol.68 , pp. 745-749
    • Harding, R.W.1    Turner, R.V.2
  • 109
    • 0025006934 scopus 로고
    • Cloning, sequence, and photoregulation of al-1, a carotenoid biosynthetic gene of Neurospora crassa
    • Schmidhauser TJ, Lauter FR, Russo VE, Yanofsky C, (1990) Cloning, sequence, and photoregulation of al-1, a carotenoid biosynthetic gene of Neurospora crassa. Mol Cell Biol 10: 5064-5070.
    • (1990) Mol Cell Biol , vol.10 , pp. 5064-5070
    • Schmidhauser, T.J.1    Lauter, F.R.2    Russo, V.E.3    Yanofsky, C.4
  • 110
    • 0028291805 scopus 로고
    • Characterization of al-2, the phytoene synthase gene of Neurospora crassa. Cloning, sequence analysis, and photoregulation
    • Schmidhauser TJ, Lauter FR, Schumacher M, Zhou W, Russo VE, et al. (1994) Characterization of al-2, the phytoene synthase gene of Neurospora crassa. Cloning, sequence analysis, and photoregulation. J Biol Chem 269: 12060-12066.
    • (1994) J Biol Chem , vol.269 , pp. 12060-12066
    • Schmidhauser, T.J.1    Lauter, F.R.2    Schumacher, M.3    Zhou, W.4    Russo, V.E.5
  • 111
    • 0024634005 scopus 로고
    • Molecular cloning of a Neurospora crassa carotenoid biosynthetic gene (albino-3) regulated by blue light and the products of the white collar locus
    • Nelson MA, Morelli G, Carattoli A, Romano N, Macino G, (1989) Molecular cloning of a Neurospora crassa carotenoid biosynthetic gene (albino-3) regulated by blue light and the products of the white collar locus. Mol Cell Biol 9: 1271-1276.
    • (1989) Mol Cell Biol , vol.9 , pp. 1271-1276
    • Nelson, M.A.1    Morelli, G.2    Carattoli, A.3    Romano, N.4    Macino, G.5
  • 112
    • 36949070663 scopus 로고
    • Carotenoids and reproduction in Pyronema confluens
    • Carlile MJ, Friend J, (1956) Carotenoids and reproduction in Pyronema confluens. Nature 178: 369-370.
    • (1956) Nature , vol.178 , pp. 369-370
    • Carlile, M.J.1    Friend, J.2
  • 113
    • 77649190125 scopus 로고    scopus 로고
    • A complex photoreceptor system mediates the regulation by light of the conidiation genes con-10 and con-6 in Neurospora crassa
    • Olmedo M, Ruger-Herreros C, Luque EM, Corrochano LM, (2010) A complex photoreceptor system mediates the regulation by light of the conidiation genes con-10 and con-6 in Neurospora crassa. Fungal Genet Biol 47: 352-363.
    • (2010) Fungal Genet Biol , vol.47 , pp. 352-363
    • Olmedo, M.1    Ruger-Herreros, C.2    Luque, E.M.3    Corrochano, L.M.4
  • 114
    • 0042848482 scopus 로고    scopus 로고
    • Natural disulfide bond-disrupted mutants of AVR4 of the tomato pathogen Cladosporium fulvum are sensitive to proteolysis, circumvent Cf-4-mediated resistance, but retain their chitin binding ability
    • van den Burg HA, Westerink N, Francoijs KJ, Roth R, Woestenenk E, et al. (2003) Natural disulfide bond-disrupted mutants of AVR4 of the tomato pathogen Cladosporium fulvum are sensitive to proteolysis, circumvent Cf-4-mediated resistance, but retain their chitin binding ability. J Biol Chem 278: 27340-27346.
    • (2003) J Biol Chem , vol.278 , pp. 27340-27346
    • van den Burg, H.A.1    Westerink, N.2    Francoijs, K.J.3    Roth, R.4    Woestenenk, E.5
  • 115
    • 33751578407 scopus 로고    scopus 로고
    • Cladosporium fulvum Avr4 protects fungal cell walls against hydrolysis by plant chitinases accumulating during infection
    • van den Burg HA, Harrison SJ, Joosten MHAJ, Vervoort J, de Wit PJ, (2006) Cladosporium fulvum Avr4 protects fungal cell walls against hydrolysis by plant chitinases accumulating during infection. Mol Plant Microbe Interact 19: 1420-1430.
    • (2006) Mol Plant Microbe Interact , vol.19 , pp. 1420-1430
    • van den Burg, H.A.1    Harrison, S.J.2    Joosten, M.H.A.J.3    Vervoort, J.4    de Wit, P.J.5
  • 116
    • 0025311318 scopus 로고
    • A potent antibacterial protein in royal jelly. Purification and determination of the primary structure of royalisin
    • Fujiwara S, Imai J, Fujiwara M, Yaeshima T, Kawashima T, et al. (1990) A potent antibacterial protein in royal jelly. Purification and determination of the primary structure of royalisin. J Biol Chem 265: 11333-11337.
    • (1990) J Biol Chem , vol.265 , pp. 11333-11337
    • Fujiwara, S.1    Imai, J.2    Fujiwara, M.3    Yaeshima, T.4    Kawashima, T.5
  • 117
    • 0033022730 scopus 로고    scopus 로고
    • Antimicrobial peptides in insects; structure and function
    • Bulet P, Hetru C, Dimarcq JL, Hoffmann D, (1999) Antimicrobial peptides in insects; structure and function. Dev Comp Immunol 23: 329-344.
    • (1999) Dev Comp Immunol , vol.23 , pp. 329-344
    • Bulet, P.1    Hetru, C.2    Dimarcq, J.L.3    Hoffmann, D.4
  • 118
    • 27144504220 scopus 로고    scopus 로고
    • Plectasin is a peptide antibiotic with therapeutic potential from a saprophytic fungus
    • Mygind PH, Fischer RL, Schnorr KM, Hansen MT, Sonksen CP, et al. (2005) Plectasin is a peptide antibiotic with therapeutic potential from a saprophytic fungus. Nature 437: 975-980.
    • (2005) Nature , vol.437 , pp. 975-980
    • Mygind, P.H.1    Fischer, R.L.2    Schnorr, K.M.3    Hansen, M.T.4    Sonksen, C.P.5
  • 119
    • 77952976637 scopus 로고    scopus 로고
    • Plectasin, a fungal defensin, targets the bacterial cell wall precursor lipid II
    • Schneider T, Kruse T, Wimmer R, Wiedemann I, Sass V, et al. (2010) Plectasin, a fungal defensin, targets the bacterial cell wall precursor lipid II. Science 328: 1168-1172.
    • (2010) Science , vol.328 , pp. 1168-1172
    • Schneider, T.1    Kruse, T.2    Wimmer, R.3    Wiedemann, I.4    Sass, V.5
  • 121
    • 33748507381 scopus 로고    scopus 로고
    • Secondary metabolic gene cluster silencing in Aspergillus nidulans
    • Bok JW, Noordermeer D, Kale SP, Keller NP, (2006) Secondary metabolic gene cluster silencing in Aspergillus nidulans. Mol Microbiol 61: 1636-1645.
    • (2006) Mol Microbiol , vol.61 , pp. 1636-1645
    • Bok, J.W.1    Noordermeer, D.2    Kale, S.P.3    Keller, N.P.4
  • 123
    • 77951831492 scopus 로고    scopus 로고
    • Lateral transfer of genes from fungi underlies carotenoid production in aphids
    • Moran NA, Jarvik T, (2010) Lateral transfer of genes from fungi underlies carotenoid production in aphids. Science 328: 624-627.
    • (2010) Science , vol.328 , pp. 624-627
    • Moran, N.A.1    Jarvik, T.2
  • 124
    • 84856331791 scopus 로고    scopus 로고
    • Self/nonself recognition in Tuber melanosporum is not mediated by a heterokaryon incompatibility system
    • Iotti M, Rubini A, Tisserant E, Kholer A, Paolocci F, et al. (2012) Self/nonself recognition in Tuber melanosporum is not mediated by a heterokaryon incompatibility system. Fungal Biol 116: 261-275.
    • (2012) Fungal Biol , vol.116 , pp. 261-275
    • Iotti, M.1    Rubini, A.2    Tisserant, E.3    Kholer, A.4    Paolocci, F.5
  • 125
    • 0027234098 scopus 로고
    • A single amino acid difference is sufficient to elicit vegetative incompatibility in the fungus Podospora anserina
    • Deleu C, Clavé C, Bégueret J, (1993) A single amino acid difference is sufficient to elicit vegetative incompatibility in the fungus Podospora anserina. Genetics 135: 45-52.
    • (1993) Genetics , vol.135 , pp. 45-52
    • Deleu, C.1    Clavé, C.2    Bégueret, J.3
  • 126
    • 0029817633 scopus 로고    scopus 로고
    • The product of the het-C heterokaryon incompatibility gene of Neurospora crassa has characteristics of a glycine-rich cell wall protein
    • Saupe SJ, Kuldau GA, Smith ML, Glass NL, (1996) The product of the het-C heterokaryon incompatibility gene of Neurospora crassa has characteristics of a glycine-rich cell wall protein. Genetics 143: 1589-1600.
    • (1996) Genetics , vol.143 , pp. 1589-1600
    • Saupe, S.J.1    Kuldau, G.A.2    Smith, M.L.3    Glass, N.L.4
  • 127
    • 0037524441 scopus 로고    scopus 로고
    • Fatal attraction: nonself recognition and heterokaryon incompatibility in filamentous fungi
    • Glass NL, Kaneko I, (2003) Fatal attraction: nonself recognition and heterokaryon incompatibility in filamentous fungi. Eukaryot Cell 2: 1-8.
    • (2003) Eukaryot Cell , vol.2 , pp. 1-8
    • Glass, N.L.1    Kaneko, I.2
  • 128
    • 0347994901 scopus 로고    scopus 로고
    • Phylogenomic analyis of type I polyketide synthase genes in pathogenic and saprobic ascomycetes
    • Kroken S, Glass NL, Taylor JW, Yoder OC, Turgeon BG, (2003) Phylogenomic analyis of type I polyketide synthase genes in pathogenic and saprobic ascomycetes. Proc Nat Acad Sci USA 100: 15670-15675.
    • (2003) Proc Nat Acad Sci USA , vol.100 , pp. 15670-15675
    • Kroken, S.1    Glass, N.L.2    Taylor, J.W.3    Yoder, O.C.4    Turgeon, B.G.5
  • 129
    • 77149168140 scopus 로고    scopus 로고
    • Phylogenomics reveals subfamilies of fungal nonribosomal peptide synthetases and their evolutionary relationships
    • Bushley KE, Turgeon BG, (2010) Phylogenomics reveals subfamilies of fungal nonribosomal peptide synthetases and their evolutionary relationships. BMC Evol Biol 10: 26.
    • (2010) BMC Evol Biol , vol.10 , pp. 26
    • Bushley, K.E.1    Turgeon, B.G.2
  • 130
    • 84874019033 scopus 로고    scopus 로고
    • Evolution of genes for secondary metabolism in fungi
    • In: Pöggeler S, Wöstemeyer J, editors, Berlin, Heidelberg: Springer-Verlag
    • Teichert I, Nowrousian M (2011) Evolution of genes for secondary metabolism in fungi. In: Pöggeler S, Wöstemeyer J, editors. Evolution of fungi and fungal-like organisms, The Mycota XIV. Berlin, Heidelberg: Springer-Verlag. pp. 231-255.
    • (2011) Evolution of fungi and fungal-like organisms, The Mycota XIV , pp. 231-255
    • Teichert, I.1    Nowrousian, M.2
  • 131
    • 60649096983 scopus 로고    scopus 로고
    • Module evolution and substrate specificity of fungal nonribosomal peptide synthetases involved in siderophore biosynthesis
    • Bushley KE, Ripoll DR, Turgeon BG, (2008) Module evolution and substrate specificity of fungal nonribosomal peptide synthetases involved in siderophore biosynthesis. BMC Evol Biol 8: 328.
    • (2008) BMC Evol Biol , vol.8 , pp. 328
    • Bushley, K.E.1    Ripoll, D.R.2    Turgeon, B.G.3
  • 132
  • 133
    • 45149124021 scopus 로고    scopus 로고
    • Molecular genetic mining of the Aspergillus secondary metabolome: discovery of the Emericellamide biosynthetic pathway
    • Chiang Y-M, Szewczyk E, Nayak T, Davidson AD, Sanchez JF, et al. (2008) Molecular genetic mining of the Aspergillus secondary metabolome: discovery of the Emericellamide biosynthetic pathway. Chem Biol 15: 527-532.
    • (2008) Chem Biol , vol.15 , pp. 527-532
    • Chiang, Y.-M.1    Szewczyk, E.2    Nayak, T.3    Davidson, A.D.4    Sanchez, J.F.5
  • 134
    • 79960082560 scopus 로고    scopus 로고
    • Fungal defences against animal antagonists - lectins & more
    • Kempken F, (2011) Fungal defences against animal antagonists- lectins & more. Mol Ecol 20: 2876-2877.
    • (2011) Mol Ecol , vol.20 , pp. 2876-2877
    • Kempken, F.1
  • 135
    • 77955585447 scopus 로고    scopus 로고
    • Fungal secondary metabolite biosynthesis - a chemical defense strategy against antagonistic animals?
    • Kempken F, Rohlfs M, (2010) Fungal secondary metabolite biosynthesis- a chemical defense strategy against antagonistic animals? Fungal Ecol 3: 107-114.
    • (2010) Fungal Ecol , vol.3 , pp. 107-114
    • Kempken, F.1    Rohlfs, M.2
  • 136
    • 12144287318 scopus 로고    scopus 로고
    • Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism
    • Borkovich KA, Alex LA, Yarden O, Freitag M, Turner GE, et al. (2004) Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism. Microbiol Mol Biol Rev 68: 1-108.
    • (2004) Microbiol Mol Biol Rev , vol.68 , pp. 1-108
    • Borkovich, K.A.1    Alex, L.A.2    Yarden, O.3    Freitag, M.4    Turner, G.E.5
  • 137
    • 80055103105 scopus 로고    scopus 로고
    • A phenome-based functional analysis of transcription factors in the cereal head blight fungus, Fusarium graminearum
    • Son H, Seo YS, Min K, Park AR, Lee J, et al. (2011) A phenome-based functional analysis of transcription factors in the cereal head blight fungus, Fusarium graminearum. PLoS Pathog 7: e1002310.
    • (2011) PLoS Pathog , vol.7
    • Son, H.1    Seo, Y.S.2    Min, K.3    Park, A.R.4    Lee, J.5
  • 138
    • 34548669353 scopus 로고    scopus 로고
    • The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization
    • Cuomo CA, Güldener U, Xu JR, Trail F, Turgeon BG, et al. (2007) The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization. Science 317: 1400-1402.
    • (2007) Science , vol.317 , pp. 1400-1402
    • Cuomo, C.A.1    Güldener, U.2    Xu, J.R.3    Trail, F.4    Turgeon, B.G.5
  • 139
    • 78651294508 scopus 로고    scopus 로고
    • Genome-wide search and functional identification of transcription factors in the mycorrhizal fungus Tuber melanosporum
    • Montanini B, Levati E, Bolchi A, Kohler A, Morin E, et al. (2011) Genome-wide search and functional identification of transcription factors in the mycorrhizal fungus Tuber melanosporum. New Phytol 189: 736-750.
    • (2011) New Phytol , vol.189 , pp. 736-750
    • Montanini, B.1    Levati, E.2    Bolchi, A.3    Kohler, A.4    Morin, E.5
  • 140
    • 0029154633 scopus 로고
    • Molecular mechanisms of cell-type determination in budding yeast
    • Johnson AD, (1995) Molecular mechanisms of cell-type determination in budding yeast. Curr Opin Genet Dev 5: 552-558.
    • (1995) Curr Opin Genet Dev , vol.5 , pp. 552-558
    • Johnson, A.D.1
  • 141
    • 33750002506 scopus 로고    scopus 로고
    • A STE12 homologue of the homothallic ascomycete Sordaria macrospora interacts with the MADS box protein MCM1 and is required for ascosporogenesis
    • Nolting N, Pöggeler S, (2006) A STE12 homologue of the homothallic ascomycete Sordaria macrospora interacts with the MADS box protein MCM1 and is required for ascosporogenesis. Mol Microbiol 62: 853-868.
    • (2006) Mol Microbiol , vol.62 , pp. 853-868
    • Nolting, N.1    Pöggeler, S.2
  • 142
    • 23344437797 scopus 로고    scopus 로고
    • A mitogen-activated protein kinase pathway essential for mating and contributing to vegetative growth in Neurospora crassa
    • Li D, Bobrowicz P, Wilkinson HH, Ebbole DJ, (2005) A mitogen-activated protein kinase pathway essential for mating and contributing to vegetative growth in Neurospora crassa. Genetics 170: 1091-1104.
    • (2005) Genetics , vol.170 , pp. 1091-1104
    • Li, D.1    Bobrowicz, P.2    Wilkinson, H.H.3    Ebbole, D.J.4
  • 143
    • 0034098572 scopus 로고    scopus 로고
    • Aspergillus SteA (sterile12-like) is a homeodomain-C2/H2-Zn+2 finger transcription factor required for sexual reproduction
    • Vallim MA, Miller KY, Miller BL, (2000) Aspergillus SteA (sterile12-like) is a homeodomain-C2/H2-Zn+2 finger transcription factor required for sexual reproduction. Mol Microbiol 36: 290-301.
    • (2000) Mol Microbiol , vol.36 , pp. 290-301
    • Vallim, M.A.1    Miller, K.Y.2    Miller, B.L.3
  • 144
    • 0141993704 scopus 로고    scopus 로고
    • A gene-coexpression network for global discovery of conserved genetic modules
    • Stuart JM, Segal E, Koller D, Kim SK, (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science 302: 249-255.
    • (2003) Science , vol.302 , pp. 249-255
    • Stuart, J.M.1    Segal, E.2    Koller, D.3    Kim, S.K.4
  • 145
    • 84863885448 scopus 로고    scopus 로고
    • Comparative studies of gene expression and the evolution of gene regulation
    • Romero IG, Ruvinsky I, Gilad Y, (2012) Comparative studies of gene expression and the evolution of gene regulation. Nat Rev Genet 13: 505-516.
    • (2012) Nat Rev Genet , vol.13 , pp. 505-516
    • Romero, I.G.1    Ruvinsky, I.2    Gilad, Y.3
  • 146
    • 34247604389 scopus 로고    scopus 로고
    • Systematics of the Pezizomycetes - the operculate discomycetes
    • Hansen K, Pfister DH, (2006) Systematics of the Pezizomycetes- the operculate discomycetes. Mycologia 98: 1029-1040.
    • (2006) Mycologia , vol.98 , pp. 1029-1040
    • Hansen, K.1    Pfister, D.H.2
  • 147
    • 0030700379 scopus 로고    scopus 로고
    • Towards a subordinal classification of the Pezizales (Ascomycota): phylogenetic analyses of SSU rDNA sequences
    • Landvik S, Egger KN, Schumacher T, (1997) Towards a subordinal classification of the Pezizales (Ascomycota): phylogenetic analyses of SSU rDNA sequences. Nord J Bot 17: 403-418.
    • (1997) Nord J Bot , vol.17 , pp. 403-418
    • Landvik, S.1    Egger, K.N.2    Schumacher, T.3
  • 150
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino DR, Birney E, (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821-829.
    • (2008) Genome Res , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 151
    • 0032849859 scopus 로고    scopus 로고
    • CAP3: A DNA sequence assembly program
    • Huang X, Madan A, (1999) CAP3: A DNA sequence assembly program. Genome Res 9: 868-877.
    • (1999) Genome Res , vol.9 , pp. 868-877
    • Huang, X.1    Madan, A.2
  • 152
    • 18744366950 scopus 로고    scopus 로고
    • Cross-species microarray hybridization to identify developmentally regulated genes in the filamentous fungus Sordaria macrospora
    • Nowrousian M, Ringelberg C, Dunlap JC, Loros JJ, Kück U, (2005) Cross-species microarray hybridization to identify developmentally regulated genes in the filamentous fungus Sordaria macrospora. Mol Genet Genomics 273: 137-149.
    • (2005) Mol Genet Genomics , vol.273 , pp. 137-149
    • Nowrousian, M.1    Ringelberg, C.2    Dunlap, J.C.3    Loros, J.J.4    Kück, U.5
  • 153
    • 79960264362 scopus 로고    scopus 로고
    • Full-length transcriptome assembly from RNA-Seq data without a reference genome
    • Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotech 29: 644-652.
    • (2011) Nat Biotech , vol.29 , pp. 644-652
    • Grabherr, M.G.1    Haas, B.J.2    Yassour, M.3    Levin, J.Z.4    Thompson, D.A.5
  • 154
    • 0141905891 scopus 로고    scopus 로고
    • Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
    • Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK Jr, et al. (2003) Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucl Acids Res 31: 5654-5666.
    • (2003) Nucl Acids Res , vol.31 , pp. 5654-5666
    • Haas, B.J.1    Delcher, A.L.2    Mount, S.M.3    Wortman, J.R.4    Smith Jr., R.K.5
  • 155
    • 2942544417 scopus 로고    scopus 로고
    • Gene finding in novel genomes
    • Korf I, (2004) Gene finding in novel genomes. BMC Bioinformatics 5: 59.
    • (2004) BMC Bioinformatics , vol.5 , pp. 59
    • Korf, I.1
  • 156
    • 33645161645 scopus 로고    scopus 로고
    • Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources
    • Stanke M, Schöffmann O, Morgenstern B, Waack S, (2006) Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics 7: 62.
    • (2006) BMC Bioinformatics , vol.7 , pp. 62
    • Stanke, M.1    Schöffmann, O.2    Morgenstern, B.3    Waack, S.4
  • 157
    • 2942527473 scopus 로고    scopus 로고
    • Gene prediction with a hidden Markov model and a new intron submodel
    • Stanke M, Waack S, (2003) Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 19 (suppl. 2) (): ii215-225.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 2
    • Stanke, M.1    Waack, S.2
  • 158
    • 23144452801 scopus 로고    scopus 로고
    • GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses
    • Besemer J, Borodovsky M, (2005) GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucl Acids Res 33: W451-454.
    • (2005) Nucl Acids Res , vol.33
    • Besemer, J.1    Borodovsky, M.2
  • 161
    • 80055082271 scopus 로고    scopus 로고
    • Accelerated profile HMM searches
    • Eddy SR, (2011) Accelerated profile HMM searches. PLoS Comp Biol 7: e1002195.
    • (2011) PLoS Comp Biol , vol.7
    • Eddy, S.R.1
  • 162
    • 1242297827 scopus 로고    scopus 로고
    • ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences
    • Laslett D, Canback B, (2004) ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucl Acids Res 32: 11-16.
    • (2004) Nucl Acids Res , vol.32 , pp. 11-16
    • Laslett, D.1    Canback, B.2
  • 163
    • 65549111754 scopus 로고    scopus 로고
    • Infernal 1.0: inference of RNA alignments
    • Nawrocki EP, Kolbe DL, Eddy SR, (2009) Infernal 1.0: inference of RNA alignments. Bioinformatics 25: 1335-1337.
    • (2009) Bioinformatics , vol.25 , pp. 1335-1337
    • Nawrocki, E.P.1    Kolbe, D.L.2    Eddy, S.R.3
  • 164
    • 34547558775 scopus 로고    scopus 로고
    • TFAM 1.0: an online tRNA function classifier
    • Taquist H, Cui Y, Ardell DH, (2007) TFAM 1.0: an online tRNA function classifier. Nucl Acids Res 35: W350-353.
    • (2007) Nucl Acids Res , vol.35
    • Taquist, H.1    Cui, Y.2    Ardell, D.H.3
  • 165
    • 0030854739 scopus 로고    scopus 로고
    • tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
    • Lowe TM, Eddy SR, (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucl Acids Res 25: 955-964.
    • (1997) Nucl Acids Res , vol.25 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 167
    • 61949250367 scopus 로고    scopus 로고
    • Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassa
    • Lewis ZA, Honda S, Khlafallah TK, Jeffress JK, Freitag M, et al. (2009) Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassa. Genome Res 19: 427-437.
    • (2009) Genome Res , vol.19 , pp. 427-437
    • Lewis, Z.A.1    Honda, S.2    Khlafallah, T.K.3    Jeffress, J.K.4    Freitag, M.5
  • 168
    • 0031927613 scopus 로고    scopus 로고
    • A methylated Neurospora 5S rRNA pseudogene contains a transposable element inactivated by repeat-induced point mutation
    • Margolin BS, Garrett-Engele PW, Stevens JN, Fritz DY, Garrett-Engele C, et al. (1998) A methylated Neurospora 5S rRNA pseudogene contains a transposable element inactivated by repeat-induced point mutation. Genetics 149: 1787-1797.
    • (1998) Genetics , vol.149 , pp. 1787-1797
    • Margolin, B.S.1    Garrett-Engele, P.W.2    Stevens, J.N.3    Fritz, D.Y.4    Garrett-Engele, C.5
  • 171
    • 84867919345 scopus 로고    scopus 로고
    • Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche
    • Morin E, Kohler A, Baker AR, Foulongne-Oriol M, Lombard V, et al. (2012) Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche. Proc Nat Acad Sci USA 109: 17501-17506.
    • (2012) Proc Nat Acad Sci USA , vol.109 , pp. 17501-17506
    • Morin, E.1    Kohler, A.2    Baker, A.R.3    Foulongne-Oriol, M.4    Lombard, V.5
  • 172
    • 78650122420 scopus 로고    scopus 로고
    • Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism
    • Spanu PD, Abbott J, C., Amselem J, Burgis TA, Soanes DM, et al. (2010) Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism. Science 330: 1543-1546.
    • (2010) Science , vol.330 , pp. 1543-1546
    • Spanu, P.D.1    Abbott, J.C.2    Amselem, J.3    Burgis, T.A.4    Soanes, D.M.5
  • 173
    • 70349645483 scopus 로고    scopus 로고
    • Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives
    • Sharpton TJ, Stajich JE, Rounsley SD, Gardner MJ, Wortman JR, et al. (2009) Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Res 19: 1722-1731.
    • (2009) Genome Res , vol.19 , pp. 1722-1731
    • Sharpton, T.J.1    Stajich, J.E.2    Rounsley, S.D.3    Gardner, M.J.4    Wortman, J.R.5
  • 174
    • 28844461287 scopus 로고    scopus 로고
    • Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae
    • Galagan JE, Calvo SE, Cuomo C, Ma L-J, Wortman JR, et al. (2005) Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 438: 1105-1115.
    • (2005) Nature , vol.438 , pp. 1105-1115
    • Galagan, J.E.1    Calvo, S.E.2    Cuomo, C.3    Ma, L.-J.4    Wortman, J.R.5
  • 175
    • 40449120632 scopus 로고    scopus 로고
    • The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis
    • Martin F, Aerts A, Ahren D, Brun A, Danchin EGJ, et al. (2008) The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 452: 88-92.
    • (2008) Nature , vol.452 , pp. 88-92
    • Martin, F.1    Aerts, A.2    Ahren, D.3    Brun, A.4    Danchin, E.G.J.5
  • 176
    • 79959834134 scopus 로고    scopus 로고
    • Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis
    • Goodwin SB, M'barek SB, Dhillon B, Wittenberg AH, Crane CF, et al. (2011) Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis. PLoS Genet 7: e1002070.
    • (2011) PLoS Genet , vol.7
    • Goodwin, S.B.1    M'barek, S.B.2    Dhillon, B.3    Wittenberg, A.H.4    Crane, C.F.5
  • 177
    • 43249118838 scopus 로고    scopus 로고
    • Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus
    • Fedorova ND, Khaldi N, Joardar VS, Maiti R, Amedeo P, et al. (2008) Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. PLOS Genet 4: e1000046.
    • (2008) PLOS Genet , vol.4
    • Fedorova, N.D.1    Khaldi, N.2    Joardar, V.S.3    Maiti, R.4    Amedeo, P.5
  • 178
  • 179
    • 37848998569 scopus 로고    scopus 로고
    • Dothideomycete plant interactions illuminated by genome sequencing and EST analysis of the wheat pathogen Stagonospora nodorum
    • Hane JK, Lowe RGT, Solomon PS, Tan K-C, Schoch CL, et al. (2007) Dothideomycete plant interactions illuminated by genome sequencing and EST analysis of the wheat pathogen Stagonospora nodorum. Plant Cell 19: 3347-3368.
    • (2007) Plant Cell , vol.19 , pp. 3347-3368
    • Hane, J.K.1    Lowe, R.G.T.2    Solomon, P.S.3    Tan, K.-C.4    Schoch, C.L.5
  • 181
  • 182
    • 80052319576 scopus 로고    scopus 로고
    • Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea
    • Amselem J, Cuomo CA, van Kan JAL, Viaud M, Benito EP, et al. (2011) Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet 7: e1002230.
    • (2011) PLoS Genet , vol.7
    • Amselem, J.1    Cuomo, C.A.2    van Kan, J.A.L.3    Viaud, M.4    Benito, E.P.5
  • 184
    • 78651300216 scopus 로고    scopus 로고
    • PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions
    • Huerta-Cepas J, Capella-Gutierrez S, Pryszcz LP, Denisov I, Kormes D, et al. (2011) PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions. Nucl Acids Res 39: D556-560.
    • (2011) Nucl Acids Res , vol.39
    • Huerta-Cepas, J.1    Capella-Gutierrez, S.2    Pryszcz, L.P.3    Denisov, I.4    Kormes, D.5
  • 185
    • 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. Nucl Acids Res 32: 1792-1797.
    • (2004) Nucl Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 186
    • 13744252890 scopus 로고    scopus 로고
    • MAFFT version 5: improvement in accuracy of multiple sequence alignment
    • Katoh K, Kuma K, Toh H, Miyata T, (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucl Acids Res 33: 511-518.
    • (2005) Nucl Acids Res , vol.33 , pp. 511-518
    • Katoh, K.1    Kuma, K.2    Toh, H.3    Miyata, T.4
  • 187
    • 45949105543 scopus 로고    scopus 로고
    • DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment
    • Subramanian AR, Kaufmann M, Morgenstern B, (2008) DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment. Algorithms Mol Biol 3: 6.
    • (2008) Algorithms Mol Biol , vol.3 , pp. 6
    • Subramanian, A.R.1    Kaufmann, M.2    Morgenstern, B.3
  • 188
    • 34548088457 scopus 로고    scopus 로고
    • Heads or tails: a simple reliability check for multiple sequence alignments
    • Landan G, Graur D, (2007) Heads or tails: a simple reliability check for multiple sequence alignments. Mol Biol Evol 24: 1380-1383.
    • (2007) Mol Biol Evol , vol.24 , pp. 1380-1383
    • Landan, G.1    Graur, D.2
  • 189
    • 33645507429 scopus 로고    scopus 로고
    • M-Coffee: combining multiple sequence alignment methods with T-Coffee
    • Wallace IM, O'Sullivan O, Higgins DG, Notredame C, (2006) M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucl Acids Res 34: 1692-1699.
    • (2006) Nucl Acids Res , vol.34 , pp. 1692-1699
    • Wallace, I.M.1    O'Sullivan, O.2    Higgins, D.G.3    Notredame, C.4
  • 190
    • 67650757433 scopus 로고    scopus 로고
    • trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
    • Capella-Gutierrez S, Silla-Martinez JM, Gabaldón T, (2009) trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinf 25: 1972-1973.
    • (2009) Bioinf , vol.25 , pp. 1972-1973
    • Capella-Gutierrez, S.1    Silla-Martinez, J.M.2    Gabaldón, T.3
  • 191
    • 77950806408 scopus 로고    scopus 로고
    • New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0
    • Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, et al. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59: 307-321.
    • (2010) Syst Biol , vol.59 , pp. 307-321
    • Guindon, S.1    Dufayard, J.F.2    Lefort, V.3    Anisimova, M.4    Hordijk, W.5
  • 192
    • 0030807655 scopus 로고    scopus 로고
    • BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data
    • Gascuel O, (1997) BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol 14: 685-695.
    • (1997) Mol Biol Evol , vol.14 , pp. 685-695
    • Gascuel, O.1
  • 193
    • 76749100709 scopus 로고    scopus 로고
    • ETE: a python Environment for Tree Exploration
    • Huerta-Cepas J, Dopazo J, Gabaldón T, (2010) ETE: a python Environment for Tree Exploration. Bioinf 11: 24.
    • (2010) Bioinf , vol.11 , pp. 24
    • Huerta-Cepas, J.1    Dopazo, J.2    Gabaldón, T.3
  • 194
    • 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
  • 195
    • 46249126320 scopus 로고    scopus 로고
    • DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony
    • Wehe A, Bansal MS, Burleigh JG, Eulenstein O, (2008) DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony. Bioinf 24: 1540-1541.
    • (2008) Bioinf , vol.24 , pp. 1540-1541
    • Wehe, A.1    Bansal, M.S.2    Burleigh, J.G.3    Eulenstein, O.4
  • 196
    • 33751381461 scopus 로고    scopus 로고
    • TimeTree: a public knowledge-base of divergence times among organisms
    • Hedges SB, Dudley J, Kumar S, (2006) TimeTree: a public knowledge-base of divergence times among organisms. Bioinf 22: 2971-2972.
    • (2006) Bioinf , vol.22 , pp. 2971-2972
    • Hedges, S.B.1    Dudley, J.2    Kumar, S.3
  • 197
    • 0035839062 scopus 로고    scopus 로고
    • Molecular evidence for the early colonization of land by fungi and plants
    • Heckman DS, Geiser DM, Eidell BR, Stauffer RL, Kardos NL, et al. (2001) Molecular evidence for the early colonization of land by fungi and plants. Science 293: 1129-1133.
    • (2001) Science , vol.293 , pp. 1129-1133
    • Heckman, D.S.1    Geiser, D.M.2    Eidell, B.R.3    Stauffer, R.L.4    Kardos, N.L.5
  • 198
    • 77955016107 scopus 로고    scopus 로고
    • LOX: inferring Level Of eXpression from diverse methods of census sequencing
    • Zhang Z, López-Giráldez F, Townsend JP, (2010) LOX: inferring Level Of eXpression from diverse methods of census sequencing. Bioinf 26: 1918-1919.
    • (2010) Bioinf , vol.26 , pp. 1918-1919
    • Zhang, Z.1    López-Giráldez, F.2    Townsend, J.P.3
  • 199
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders S, Huber W, (2010) Differential expression analysis for sequence count data. Genome Biol 11: R106.
    • (2010) Genome Biol , vol.11
    • Anders, S.1    Huber, W.2
  • 200
    • 77955298482 scopus 로고    scopus 로고
    • baySeq: empirical Bayesian methods for identifying differential expression in sequence count data
    • Hardcastle TJ, Kelly KA, (2010) baySeq: empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinf 11: 422.
    • (2010) BMC Bioinf , vol.11 , pp. 422
    • Hardcastle, T.J.1    Kelly, K.A.2
  • 201
    • 0035998835 scopus 로고    scopus 로고
    • Model-based clustering, discriminant analysis, and density estimation J Amer Stat Assoc
    • Fraley C, Raftery AE, (2002) Model-based clustering, discriminant analysis, and density estimation J Amer Stat Assoc. 97: 611-631.
    • (2002) , vol.97 , pp. 611-631
    • Fraley, C.1    Raftery, A.E.2
  • 202
    • 77953758862 scopus 로고    scopus 로고
    • Functional characterization of MAT1-1-specific mating-type genes in the homothallic ascomycete Sordaria macrospora provides new insights into essential and non-essential sexual regulators
    • Klix V, Nowrousian M, Ringelberg C, Loros JJ, Dunlap JC, et al. (2010) Functional characterization of MAT1-1-specific mating-type genes in the homothallic ascomycete Sordaria macrospora provides new insights into essential and non-essential sexual regulators. Eukaryot Cell 9: 894-905.
    • (2010) Eukaryot Cell , vol.9 , pp. 894-905
    • Klix, V.1    Nowrousian, M.2    Ringelberg, C.3    Loros, J.J.4    Dunlap, J.C.5
  • 203
    • 0032927876 scopus 로고    scopus 로고
    • Cell differentiation during sexual development of the fungus Sordaria macrospora requires ATP citrate lyase activity
    • Nowrousian M, Masloff S, Pöggeler S, Kück U, (1999) Cell differentiation during sexual development of the fungus Sordaria macrospora requires ATP citrate lyase activity. Mol Cell Biol 19: 450-460.
    • (1999) Mol Cell Biol , vol.19 , pp. 450-460
    • Nowrousian, M.1    Masloff, S.2    Pöggeler, S.3    Kück, U.4
  • 204
    • 0031574072 scopus 로고    scopus 로고
    • The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG, (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24: 4876-4882.
    • (1997) Nucleic Acids Res , vol.24 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 206
    • 0030203863 scopus 로고    scopus 로고
    • TREEVIEW: an application to display phylogenetic trees on personal computers
    • Page R, (1996) TREEVIEW: an application to display phylogenetic trees on personal computers. Appl Biosci 12: 357-358.
    • (1996) Appl Biosci , vol.12 , pp. 357-358
    • Page, R.1
  • 207
    • 68249097196 scopus 로고    scopus 로고
    • Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication
    • Ma L-J, Ibrahim AS, Skory C, Grabherr MG, Burger G, et al. (2009) Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication. PLoS Genet 5: e1000549.
    • (2009) PLoS Genet , vol.5
    • Ma, L.-J.1    Ibrahim, A.S.2    Skory, C.3    Grabherr, M.G.4    Burger, G.5
  • 208
    • 60549116487 scopus 로고    scopus 로고
    • Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion
    • Martinez D, Challacombe J, Morgenstern I, Hibbett D, Schmoll M, et al. (2009) Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion. Proc Nat Acad Sci USA 106: 1954-1959.
    • (2009) Proc Nat Acad Sci USA , vol.106 , pp. 1954-1959
    • Martinez, D.1    Challacombe, J.2    Morgenstern, I.3    Hibbett, D.4    Schmoll, M.5
  • 209
    • 77955350734 scopus 로고    scopus 로고
    • Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)
    • Stajich JE, Wilke SK, Ahrén D, Au CH, Birren BW, et al. (2010) Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). Proc Nat Acad Sci USA 107: 11889-11894.
    • (2010) Proc Nat Acad Sci USA , vol.107 , pp. 11889-11894
    • Stajich, J.E.1    Wilke, S.K.2    Ahrén, D.3    Au, C.H.4    Birren, B.W.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.