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Volumn 26, Issue 8, 2016, Pages 1091-1100

Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME TRANSLOCATION; COLLETOTRICHUM; COLLETOTRICHUM HIGGINSIANUM; CONSENSUS SEQUENCE; DNA STRAND BREAKAGE; FUSARIUM OXYSPORUM; GENE DUPLICATION; GENE LOSS; GENE REARRANGEMENT; GENOME; LAST COMMON ANCESTOR; MOLECULAR EVOLUTION; NONHUMAN; PARALOGY; PRIORITY JOURNAL; RETROPOSON; SEGMENTAL DUPLICATION; SINGLE NUCLEOTIDE POLYMORPHISM; SYNTENY; TRANSPOSON; VERTICILLIUM DAHLIAE; FUNGAL GENOME; GENETICS; GENOMICS; MICROBIOLOGY; PATHOGENICITY; PLANT; PLANT DISEASE; VERTICILLIUM;

EID: 84982953280     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.204974.116     Document Type: Article
Times cited : (215)

References (67)
  • 2
    • 0142059650 scopus 로고    scopus 로고
    • An Alu transposition model for the origin and expansion of human segmental duplications
    • Bailey JA, Liu G, Eichler EE. 2003. An Alu transposition model for the origin and expansion of human segmental duplications. Am J Hum Genet 73: 823-834.
    • (2003) Am J Hum Genet , vol.73 , pp. 823-834
    • Bailey, J.A.1    Liu, G.2    Eichler, E.E.3
  • 3
    • 84866266717 scopus 로고    scopus 로고
    • Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): Application and theory
    • Chaisson MJ, Tesler G. 2012. Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): Application and theory. BMC Bioinformatics 13: 238.
    • (2012) BMC Bioinformatics , vol.13 , pp. 238
    • Chaisson, M.J.1    Tesler, G.2
  • 4
    • 84897933810 scopus 로고    scopus 로고
    • Histone H3K9 and H3K27 methylation regulates fungal alkaloid biosynthesis in a fungal endophyte-plant symbiosis
    • Chujo T, Scott B. 2014. Histone H3K9 and H3K27 methylation regulates fungal alkaloid biosynthesis in a fungal endophyte-plant symbiosis. Mol Microbiol 92: 413-434.
    • (2014) Mol Microbiol , vol.92 , pp. 413-434
    • Chujo, T.1    Scott, B.2
  • 6
    • 84887305892 scopus 로고    scopus 로고
    • The Fusarium graminearum histone H3K27 methyltransferase KMT6 regulates development and expression of secondary metabolite gene clusters
    • Connolly LR, Smith KM, Freitag M. 2013. The Fusarium graminearum histone H3K27 methyltransferase KMT6 regulates development and expression of secondary metabolite gene clusters. PLoS Genet 9: E1003916.
    • (2013) PLoS Genet , vol.9 , pp. e1003916
    • Connolly, L.R.1    Smith, K.M.2    Freitag, M.3
  • 7
    • 84938699156 scopus 로고    scopus 로고
    • Understanding plant immunity as a surveillance system to detect invasion
    • Cook DE, Mesarich CH, Thomma BP. 2015. Understanding plant immunity as a surveillance system to detect invasion. Annu Rev Phytopathol 53: 541-563.
    • (2015) Annu Rev Phytopathol , vol.53 , pp. 541-563
    • Cook, D.E.1    Mesarich, C.H.2    Thomma, B.P.3
  • 8
    • 70349318211 scopus 로고    scopus 로고
    • The impact of retrotransposons on human genome evolution
    • Cordaux R, Batzer MA. 2009. The impact of retrotransposons on human genome evolution. Nat Rev Genet 10: 691-703.
    • (2009) Nat Rev Genet , vol.10 , pp. 691-703
    • Cordaux, R.1    Batzer, M.A.2
  • 13
    • 84943519161 scopus 로고    scopus 로고
    • The two-speed genomes of filamentous pathogens: Waltz with plants
    • Dong S, Raffaele S, Kamoun S. 2015. The two-speed genomes of filamentous pathogens: waltz with plants. Curr Opin Genet Dev 35: 57-65.
    • (2015) Curr Opin Genet Dev , vol.35 , pp. 57-65
    • Dong, S.1    Raffaele, S.2    Kamoun, S.3
  • 14
    • 84940872323 scopus 로고    scopus 로고
    • Single-Molecule Real-Time sequencing combined with optical mapping yields completely finished fungal genomes
    • Faino L, Seidl MF, Datema E, van den Berg GC, Janssen A, Wittenberg AH, Thomma BP. 2015. Single-Molecule Real-Time sequencing combined with optical mapping yields completely finished fungal genomes. MBio 6: Pe00936-15.
    • (2015) MBio , vol.6 , pp. pe00936-pe001015
    • Faino, L.1    Seidl, M.F.2    Datema, E.3    Van Den Berg, G.C.4    Janssen, A.5    Wittenberg, A.H.6    Thomma, B.P.7
  • 16
    • 37549029474 scopus 로고    scopus 로고
    • DNA transposons and the evolution of eukaryotic genomes
    • Feschotte C, Pritham EJ. 2007. DNA transposons and the evolution of eukaryotic genomes. Annu Rev Genet 41: 331.
    • (2007) Annu Rev Genet , vol.41 , pp. 331
    • Feschotte, C.1    Pritham, E.J.2
  • 19
    • 33645127793 scopus 로고    scopus 로고
    • Physiology and molecular aspects of Verticillium wilt diseases caused by V. Dahliae and V. Albo-atrum
    • Fradin EF, Thomma BP. 2006. Physiology and molecular aspects of Verticillium wilt diseases caused by V. dahliae and V. albo-atrum. Mol Plant Pathol 7: 71-86.
    • (2006) Mol Plant Pathol , vol.7 , pp. 71-86
    • Fradin, E.F.1    Thomma, B.P.2
  • 22
    • 84900826142 scopus 로고    scopus 로고
    • Variability of chromosome structure in pathogenic fungi-of 'ends and odds'
    • Galazka JM, Freitag M. 2014. Variability of chromosome structure in pathogenic fungi-of 'ends and odds'. Curr Opin Microbiol 20: 19-26.
    • (2014) Curr Opin Microbiol , vol.20 , pp. 19-26
    • Galazka, J.M.1    Freitag, M.2
  • 23
    • 75349113335 scopus 로고    scopus 로고
    • Runaway repeats force expansion of the Phytophthora infestans genome
    • Gijzen M. 2009. Runaway repeats force expansion of the Phytophthora infestans genome. Genome Biol 10: 241.
    • (2009) Genome Biol , vol.10 , pp. 241
    • Gijzen, M.1
  • 27
    • 33846704345 scopus 로고    scopus 로고
    • Inviting instability: Transposable elements, double-strand breaks, and the maintenance of genome integrity
    • Hedges DJ, Deininger PL. 2007. Inviting instability: Transposable elements, double-strand breaks, and the maintenance of genome integrity. Mutat Res 616: 46-59.
    • (2007) Mutat Res , vol.616 , pp. 46-59
    • Hedges, D.J.1    Deininger, P.L.2
  • 29
    • 84055178433 scopus 로고    scopus 로고
    • MAKER2: An annotation pipeline and genome-database management tool for second-generation genome projects
    • Holt C, Yandell M. 2011. MAKER2: An annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics 12: 491.
    • (2011) BMC Bioinformatics , vol.12 , pp. 491
    • Holt, C.1    Yandell, M.2
  • 30
    • 84902253035 scopus 로고    scopus 로고
    • Verticillium systematics and evolution: How confusion impedes Verticillium wilt management and how to resolve it
    • Inderbitzin P, Subbarao KV. 2014. Verticillium systematics and evolution: How confusion impedes Verticillium wilt management and how to resolve it. Phytopathology 104: 564-574.
    • (2014) Phytopathology , vol.104 , pp. 564-574
    • Inderbitzin, P.1    Subbarao, K.V.2
  • 31
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • Elsevier, Academic Press, New York
    • Jukes TH, Cantor CR. 1969. Evolution of protein molecules. In Mammalian protein metabolism, Vol. 3, pp. 21-132. Elsevier, Academic Press, New York.
    • (1969) Mammalian Protein Metabolism , vol.3 , pp. 21-132
    • Jukes, T.H.1    Cantor, C.R.2
  • 37
    • 78649694079 scopus 로고    scopus 로고
    • DNA methylation and normal chromosome behavior in Neurospora depend on five components of a histone methyltransferase complex, DCDC
    • Lewis ZA, Adhvaryu KK, Honda S, Shiver AL, Knip M, Sack R, Selker EU. 2010. DNA methylation and normal chromosome behavior in Neurospora depend on five components of a histone methyltransferase complex, DCDC. PLoS Genet 6: E1001196.
    • (2010) PLoS Genet , vol.6 , pp. e1001196
    • Lewis, Z.A.1    Adhvaryu, K.K.2    Honda, S.3    Shiver, A.L.4    Knip, M.5    Sack, R.6    Selker, E.U.7
  • 38
    • 77949587649 scopus 로고    scopus 로고
    • Fast and accurate long-read alignment with Burrows- Wheeler transform
    • Li H, Durbin R. 2010. Fast and accurate long-read alignment with Burrows- Wheeler transform. Bioinformatics 26: 589-595.
    • (2010) Bioinformatics , vol.26 , pp. 589-595
    • Li, H.1    Durbin, R.2
  • 39
    • 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, C.J.2    Roos, D.S.3
  • 40
    • 84871329875 scopus 로고    scopus 로고
    • How important are transposons for plant evolution?
    • Lisch D. 2013. How important are transposons for plant evolution? Nat Rev Genet 14: 49-61.
    • (2013) Nat Rev Genet , vol.14 , pp. 49-61
    • Lisch, D.1
  • 42
    • 0036028757 scopus 로고    scopus 로고
    • Pathogen population genetics, evolutionary potential, and durable resistance
    • McDonald BA, Linde C. 2002. Pathogen population genetics, evolutionary potential, and durable resistance. Annu Rev Phytopathol 40: 349-379.
    • (2002) Annu Rev Phytopathol , vol.40 , pp. 349-379
    • McDonald, B.A.1    Linde, C.2
  • 43
    • 0034525256 scopus 로고    scopus 로고
    • A telomeric avirulence gene determines efficacy for the rice blast resistance gene Pi-ta
    • Orbach MJ, Farrall L, Sweigard JA, Chumley FG, Valent B. 2000. A telomeric avirulence gene determines efficacy for the rice blast resistance gene Pi-ta. Plant Cell 12: 2019-2032.
    • (2000) Plant Cell , vol.12 , pp. 2019-2032
    • Orbach, M.J.1    Farrall, L.2    Sweigard, J.A.3    Chumley, F.G.4    Valent, B.5
  • 44
    • 84874026483 scopus 로고    scopus 로고
    • Transgenerational gene silencing causes gain of virulence in a plant pathogen
    • Qutob D, Chapman BP, Gijzen M. 2013. Transgenerational gene silencing causes gain of virulence in a plant pathogen. Nat Commun 4: 1349.
    • (2013) Nat Commun , vol.4 , pp. 1349
    • Qutob, D.1    Chapman, B.P.2    Gijzen, M.3
  • 45
    • 84861182813 scopus 로고    scopus 로고
    • Genome evolution in filamentous plant pathogens: Why bigger can be better
    • Raffaele S, Kamoun S. 2012. Genome evolution in filamentous plant 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
  • 48
    • 84901436127 scopus 로고    scopus 로고
    • Filamentous pathogen effector functions: Of pathogens, hosts and microbiomes
    • Rovenich H, Boshoven JC, Thomma BP. 2014. Filamentous pathogen effector functions: Of pathogens, hosts and microbiomes. Curr Opin Plant Biol 20C: 96-103.
    • (2014) Curr Opin Plant Biol 20C , pp. 96-103
    • Rovenich, H.1    Boshoven, J.C.2    Thomma, B.P.3
  • 50
    • 84896736546 scopus 로고    scopus 로고
    • Sex or no sex: Evolutionary adaptation occurs regardless
    • Seidl MF, Thomma BP. 2014. Sex or no sex: Evolutionary adaptation occurs regardless. Bioessays 36: 335-345.
    • (2014) Bioessays , vol.36 , pp. 335-345
    • Seidl, M.F.1    Thomma, B.P.2
  • 51
    • 84923132280 scopus 로고    scopus 로고
    • The genome of the saprophytic fungus Verticillium tricorpus reveals a complex effector repertoire resembling that of its pathogenic relatives
    • Seidl MF, Faino L, Shi-Kunne X, van den Berg GC, Bolton MD, Thomma BP. 2015. The genome of the saprophytic fungus Verticillium tricorpus reveals a complex effector repertoire resembling that of its pathogenic relatives. Mol Plant Microbe Interact 28: 362-373.
    • (2015) Mol Plant Microbe Interact , vol.28 , pp. 362-373
    • Seidl, M.F.1    Faino, L.2    Shi-Kunne, X.3    Van Den Berg, G.C.4    Bolton, M.D.5    Thomma, B.P.6
  • 52
    • 0025641736 scopus 로고
    • Premeiotic instability of repeated sequences in Neurospora crassa
    • Selker EU. 1990. Premeiotic instability of repeated sequences in Neurospora crassa. Annu Rev Genet 24: 579-613.
    • (1990) Annu Rev Genet , vol.24 , pp. 579-613
    • Selker, E.U.1
  • 53
    • 84977534828 scopus 로고    scopus 로고
    • Broad taxonomic characterization of Verticillium wilt resistance genes reveals ancient origin of the tomato Ve1 immune receptor
    • Song Y, Zhang Z, Seidl MF, Majer A, Jakse J, Javornik B, Thomma BP. 2016. Broad taxonomic characterization of Verticillium wilt resistance genes reveals ancient origin of the tomato Ve1 immune receptor. Mol Plant Pathol doi: 10.1111/mpp.12390.
    • (2016) Mol Plant Pathol
    • Song, Y.1    Zhang, Z.2    Seidl, M.F.3    Majer, A.4    Jakse, J.5    Javornik, B.6    Thomma, B.P.7
  • 55
    • 84934912058 scopus 로고    scopus 로고
    • Chromatin-based control of effector gene expression in plant-associated fungi
    • Soyer JL, Rouxel T, Fudal I. 2015. Chromatin-based control of effector gene expression in plant-associated fungi. Curr Opin Plant Biol 26: 51-56.
    • (2015) Curr Opin Plant Biol , vol.26 , pp. 51-56
    • Soyer, J.L.1    Rouxel, T.2    Fudal, I.3
  • 56
    • 79952302258 scopus 로고    scopus 로고
    • Of PAMPs and effectors: The blurred PTI-ETI dichotomy
    • Thomma BP, Nürnberger T, Joosten MH. 2011. Of PAMPs and effectors: The blurred PTI-ETI dichotomy. Plant Cell 23: 4-15.
    • (2011) Plant Cell , vol.23 , pp. 4-15
    • Thomma, B.P.1    Nürnberger, T.2    Joosten, M.H.3
  • 58
    • 33745033975 scopus 로고    scopus 로고
    • The role of transposable element clusters in genome evolution and loss of synteny in the rice blast fungus Magnaporthe oryzae
    • Thon MR, Pan H, Diener S, Papalas J, Taro A, Mitchell TK, Dean RA. 2006. The role of transposable element clusters in genome evolution and loss of synteny in the rice blast fungus Magnaporthe oryzae. Genome Biol 7: R16.
    • (2006) Genome Biol , vol.7 , pp. R16
    • Thon, M.R.1    Pan, H.2    Diener, S.3    Papalas, J.4    Taro, A.5    Mitchell, T.K.6    Dean, R.A.7
  • 59
    • 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. Bioinformatics 25: 1105-1111.
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 60
    • 84866391549 scopus 로고    scopus 로고
    • An integrated pipeline for de novo assembly of microbial genomes
    • Tritt A, Eisen JA, Facciotti MT, Darling AE. 2012. An integrated pipeline for de novo assembly of microbial genomes. PLoS One 7: E42304.
    • (2012) PLoS One , vol.7 , pp. e42304
    • Tritt, A.1    Eisen, J.A.2    Facciotti, M.T.3    Darling, A.E.4
  • 61
    • 84902957015 scopus 로고    scopus 로고
    • Small homologous blocks in Phytophthora genomes do not point to an ancient whole-genome duplication
    • van Hooff JJ, Snel B, Seidl MF. 2014. Small homologous blocks in Phytophthora genomes do not point to an ancient whole-genome duplication. Genome Biol Evol 6: 1079-1085.
    • (2014) Genome Biol Evol , vol.6 , pp. 1079-1085
    • Van Hooff, J.J.1    Snel, B.2    Seidl, M.F.3
  • 62
    • 77951682635 scopus 로고    scopus 로고
    • KaKs-Calculator 2.0: A toolkit incorporating γ-series methods and sliding window strategies
    • Wang D, Zhang Y, Zhang Z, Zhu J, Yu J. 2010. KaKs-Calculator 2.0: A toolkit incorporating γ-series methods and sliding window strategies. Genomics Proteomics Bioinformatics 8: 77-80.
    • (2010) Genomics Proteomics Bioinformatics , vol.8 , pp. 77-80
    • Wang, D.1    Zhang, Y.2    Zhang, Z.3    Zhu, J.4    Yu, J.5
  • 64
    • 77956284088 scopus 로고    scopus 로고
    • Patching gaps in plant genomes results in gene movement and erosion of colinearity
    • Wicker T, Buchmann JP, Keller B. 2010. Patching gaps in plant genomes results in gene movement and erosion of colinearity. Genome Res 20: 1229-1237.
    • (2010) Genome Res , vol.20 , pp. 1229-1237
    • Wicker, T.1    Buchmann, J.P.2    Keller, B.3
  • 65
    • 84883463113 scopus 로고    scopus 로고
    • The wheat powdery mildew genome shows the unique evolution of an obligate biotroph
    • Wicker T, Oberhaensli S, Parlange F, Buchmann JP, Shatalina M, Roffler S, Ben-David R, Doležel J, Šimková H, Schulze-Lefert P, et al. 2013. The wheat powdery mildew genome shows the unique evolution of an obligate biotroph. Nat Genet 45: 1092-1096.
    • (2013) Nat Genet , vol.45 , pp. 1092-1096
    • Wicker T, O.1
  • 66
    • 69749122557 scopus 로고    scopus 로고
    • Sensitive and accurate detection of copy number variants using read depth of coverage
    • Yoon ST, Xuan ZY, Makarov V, Ye K, Sebat J. 2009. Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res 19: 1586-1592.
    • (2009) Genome Res , vol.19 , pp. 1586-1592
    • Yoon, S.T.1    Xuan, Z.Y.2    Makarov, V.3    Ye, K.4    Sebat, J.5
  • 67
    • 84902687767 scopus 로고    scopus 로고
    • Mutational analysis of the Ve1 immune receptor that mediates Verticillium resistance in tomato
    • Zhang Z, Song Y, Liu CM, Thomma BP. 2014. Mutational analysis of the Ve1 immune receptor that mediates Verticillium resistance in tomato. PLoS One 9: E99511.
    • (2014) PLoS One , vol.9 , pp. e99511
    • Zhang, Z.1    Song, Y.2    Liu, C.M.3    Thomma, B.P.4


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