메뉴 건너뛰기




Volumn 7, Issue 4, 2017, Pages 1301-1314

Genomic data quality impacts automated detection of lateral gene transfer in fungi

Author keywords

Automated detection methods; Comparative genomics; Eukaryotes fungi; Horizontal gene transfer; Lateral gene transfer

Indexed keywords

FUNGAL GENE; GENOME; GENOMICS; HORIZONTAL GENE TRANSFER; HUMAN; INFORMATION PROCESSING; ORTHOLOGY; PHYLOGENY; PREDICTION; SCIENTIST; SEQUENCE ALIGNMENT; SPECIES; AUTOMATION; EPICHLOE; GENETIC VARIATION; GENETICS; MEASUREMENT ACCURACY; SPECIES DIFFERENCE; STANDARDS; STATISTICS;

EID: 85017228614     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.116.038448     Document Type: Article
Times cited : (18)

References (123)
  • 1
    • 77954843377 scopus 로고    scopus 로고
    • Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests
    • Abby, S. S., E. Tannier, M. Gouy, and V. Daubin, 2010 Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests. BMC Bioinformatics 11: 324.
    • (2010) BMC Bioinformatics , vol.11 , pp. 324
    • Abby, S.S.1    Tannier, E.2    Gouy, M.3    Daubin, V.4
  • 2
    • 65549165405 scopus 로고    scopus 로고
    • Horizontal gene transfer in eukaryotic parasites: a case study of Entamoeba histolytica and Trichomonas vaginalis
    • Alsmark, U. C., T. Sicheritz-Ponten, P. G. Foster, R. P. Hirt, and T. M. Embley, 2009 Horizontal gene transfer in eukaryotic parasites: a case study of Entamoeba histolytica and Trichomonas vaginalis. Methods Mol. Biol. 532: 489-500.
    • (2009) Methods Mol. Biol , vol.532 , pp. 489-500
    • Alsmark, U.C.1    Sicheritz-Ponten, T.2    Foster, P.G.3    Hirt, R.P.4    Embley, T.M.5
  • 3
    • 84903974186 scopus 로고    scopus 로고
    • Horizontal gene transfer of a bacterial insect toxin gene into the Epichloë fungal symbionts of grasses
    • Ambrose, K. V., A. M. Koppenhofer, and F. C. Belanger, 2014 Horizontal gene transfer of a bacterial insect toxin gene into the Epichloë fungal symbionts of grasses. Sci. Rep. 4: 5562.
    • (2014) Sci. Rep , vol.4 , pp. 5562
    • Ambrose, K.V.1    Koppenhofer, A.M.2    Belanger, F.C.3
  • 4
    • 80052319576 scopus 로고    scopus 로고
    • Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea
    • Amselem, J., C. A. Cuomo, J. A. van Kan, M. Viaud, E. P. Benito et al., 2011 Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet. 7(8): e1002230.
    • (2011) PLoS Genet , vol.7 , Issue.8 , pp. 8
    • Amselem, J.1    Cuomo, C.A.2    van Kan, J.A.3    Viaud, M.4    Benito, E.P.5
  • 5
    • 84863524200 scopus 로고    scopus 로고
    • Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss
    • Bansal, M. S., E. J. Alm, and M. Kellis, 2012 Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss. Bioinformatics 28(12): i283-i291.
    • (2012) Bioinformatics , vol.28 , Issue.12 , pp. 12
    • Bansal, M.S.1    Alm, E.J.2    Kellis, M.3
  • 6
    • 65549144119 scopus 로고    scopus 로고
    • Untangling hybrid phylogenetic signals: horizontal gene transfer and artifacts of phylogenetic reconstruction
    • Beiko, R. G., and M. A. Ragan, 2009 Untangling hybrid phylogenetic signals: horizontal gene transfer and artifacts of phylogenetic reconstruction. Methods Mol. Biol. 532: 241-256.
    • (2009) Methods Mol. Biol , vol.532 , pp. 241-256
    • Beiko, R.G.1    Ragan, M.A.2
  • 7
    • 84927784719 scopus 로고    scopus 로고
    • Disparate independent genetic events disrupt the secondary metabolism gene perA in certain symbiotic Epichloë species
    • Berry, D., J. E.Takach, C. L. Schardl, N.D.Charlton, B. Scott et al., 2015 Disparate independent genetic events disrupt the secondary metabolism gene perA in certain symbiotic Epichloë species. Appl. Environ. Microbiol. 81(8): 2797-2807.
    • (2015) Appl. Environ. Microbiol , vol.81 , Issue.8 , pp. 8
    • Berry, D.1    Takach, J.E.2    Schardl, C.L.3    Charlton, N.D.4    Scott, B.5
  • 8
    • 0037306453 scopus 로고    scopus 로고
    • Ancient horizontal gene transfer
    • Brown, J. R., 2003 Ancient horizontal gene transfer. Nat. Rev. Genet. 4(2): 121-132.
    • (2003) Nat. Rev. Genet , vol.4 , Issue.2 , pp. 2
    • Brown, J.R.1
  • 9
    • 0036237727 scopus 로고    scopus 로고
    • Coevolution of roots and mycorrhizas of land plants
    • Brundrett, M. C., 2002 Coevolution of roots and mycorrhizas of land plants. New Phytol. 154(2): 275-304.
    • (2002) New Phytol , vol.154 , Issue.2 , pp. 2
    • Brundrett, M.C.1
  • 10
    • 67650757433 scopus 로고    scopus 로고
    • trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
    • Capella-Gutierrez, S., J. M. Silla-Martinez, and T. Gabaldon, 2009 trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25(15): 1972-1973.
    • (2009) Bioinformatics , vol.25 , Issue.15 , pp. 15
    • Capella-Gutierrez, S.1    Silla-Martinez, J.M.2    Gabaldon, T.3
  • 11
    • 84892149592 scopus 로고    scopus 로고
    • Multiple recent horizontal transfers of a large genomic region in cheese making fungi
    • Cheeseman, K., J. Ropars, P. Renault, J. Dupont, J. Gouzy et al., 2014 Multiple recent horizontal transfers of a large genomic region in cheese making fungi. Nat. Commun. 5: 2876.
    • (2014) Nat. Commun , vol.5 , pp. 2876
    • Cheeseman, K.1    Ropars, J.2    Renault, P.3    Dupont, J.4    Gouzy, J.5
  • 12
    • 0033692378 scopus 로고    scopus 로고
    • NOTUNG: a program for dating gene duplications and optimizing gene family trees
    • Chen, K., D. Durand, and M. Farach-Colton, 2000 NOTUNG: a program for dating gene duplications and optimizing gene family trees. J. Comput. Biol. 7(3-4): 429-447.
    • (2000) J. Comput. Biol , vol.7 , Issue.3-4 , pp. 3-4
    • Chen, K.1    Durand, D.2    Farach-Colton, M.3
  • 13
    • 39149111271 scopus 로고    scopus 로고
    • Epichloë endophytes grow by intercalary hyphal extension in elongating grass leaves
    • Christensen, M. J., R. J. Bennett, H. A. Ansari, H. Koga, R. D. Johnson et al., 2008 Epichloë endophytes grow by intercalary hyphal extension in elongating grass leaves. Fungal Genet. Biol. 45(2): 84-93.
    • (2008) Fungal Genet. Biol , vol.45 , Issue.2 , pp. 2
    • Christensen, M.J.1    Bennett, R.J.2    Ansari, H.A.3    Koga, H.4    Johnson, R.D.5
  • 14
    • 0036565814 scopus 로고    scopus 로고
    • Mean shift: a robust approach toward feature space analysis
    • Comaniciu, D., and P. Meer, 2002 Mean shift: a robust approach toward feature space analysis. IEEET Pattern Anal 24(5): 603-619.
    • (2002) IEEET Pattern Anal , vol.24 , Issue.5 , pp. 5
    • Comaniciu, D.1    Meer, P.2
  • 15
    • 84873498227 scopus 로고    scopus 로고
    • Comparative genome structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens
    • Condon, B. J., Y. Leng, D. Wu, K. E. Bushley, R.A.Ohmet al., 2013 Comparative genome structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens. PLoS Genet. 9(1): e1003233.
    • (2013) PLoS Genet , vol.9 , Issue.1 , pp. 1
    • Condon, B.J.1    Leng, Y.2    Wu, D.3    Bushley, K.E.4    Ohm, R.A.5
  • 16
    • 65549131468 scopus 로고    scopus 로고
    • Composition-based methods to identify horizontal gene transfer
    • Cortez, D., L. Delaye, A. Lazcano, and A. Becerra, 2009 Composition-based methods to identify horizontal gene transfer. Methods Mol. Biol. 532: 215-225.
    • (2009) Methods Mol. Biol , vol.532 , pp. 215-225
    • Cortez, D.1    Delaye, L.2    Lazcano, A.3    Becerra, A.4
  • 17
    • 33244491918 scopus 로고    scopus 로고
    • Comparative analysis of methodologies for the detection of horizontally transferred genes: a reassessment of first-order Markov models
    • Cortez, D. Q., A. Lazcano, and A. Becerra, 2005 Comparative analysis of methodologies for the detection of horizontally transferred genes: a reassessment of first-order Markov models. In Silico Biol. 5(5-6): 581-592.
    • (2005) In Silico Biol , vol.5 , Issue.5-6 , pp. 5-6
    • Cortez, D.Q.1    Lazcano, A.2    Becerra, A.3
  • 18
    • 34548669353 scopus 로고    scopus 로고
    • The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization
    • Cuomo, C. A., U. Guldener, J. R. Xu, F. Trail, B. G. Turgeon et al., 2007 The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization. Science 317(5843): 1400-1402.
    • (2007) Science , vol.317 , Issue.5843 , pp. 5843
    • Cuomo, C.A.1    Guldener, U.2    Xu, J.R.3    Trail, F.4    Turgeon, B.G.5
  • 19
    • 84996938696 scopus 로고    scopus 로고
    • Lateral gene transfer in eukaryotes: tip of the iceberg or of the ice cube?
    • Danchin, E. G., 2016 Lateral gene transfer in eukaryotes: tip of the iceberg or of the ice cube? BMC Biol. 14(1): 101.
    • (2016) BMC Biol , vol.14 , Issue.1 , pp. 101
    • Danchin, E.G.1
  • 20
    • 20244366844 scopus 로고    scopus 로고
    • The genome sequence of the rice blast fungus Magnaporthe grisea
    • Dean, R. A., N. J. Talbot, D. J. Ebbole, M. L. Farman, T. K. Mitchell et al., 2005 The genome sequence of the rice blast fungus Magnaporthe grisea. Nature 434(7036): 980-986.
    • (2005) Nature , vol.434 , Issue.7036 , pp. 7036
    • Dean, R.A.1    Talbot, N.J.2    Ebbole, D.J.3    Farman, M.L.4    Mitchell, T.K.5
  • 21
    • 84870667343 scopus 로고    scopus 로고
    • The genomes of the fungal plant pathogens Cladosporium fulvum and Dothistroma septosporum reveal adaptation to different hosts and lifestyles but also signatures of common ancestry
    • de Wit, P. J., A. van der Burgt, B. Okmen, I. Stergiopoulos, K. A. Abd-Elsalam et al., 2012 The genomes of the fungal plant pathogens Cladosporium fulvum and Dothistroma septosporum reveal adaptation to different hosts and lifestyles but also signatures of common ancestry. PLoS Genet. 8(11): e1003088.
    • (2012) PLoS Genet , vol.8 , Issue.11 , pp. 11
    • de Wit, P.J.1    van der Burgt, A.2    Okmen, B.3    Stergiopoulos, I.4    Abd-Elsalam, K.A.5
  • 22
    • 84946024770 scopus 로고    scopus 로고
    • Comparative genomics, proteomics and transcriptomics give new insight into the exoproteome of the basidiomycete Hebeloma cylindrosporum and its involvement in ectomycorrhizal symbiosis
    • Dore, J., M. Perraud, C. Dieryckx, A. Kohler, E. Morin et al., 2015 Comparative genomics, proteomics and transcriptomics give new insight into the exoproteome of the basidiomycete Hebeloma cylindrosporum and its involvement in ectomycorrhizal symbiosis. New Phytol. 208(4): 1169-1187.
    • (2015) New Phytol , vol.208 , Issue.4 , pp. 4
    • Dore, J.1    Perraud, M.2    Dieryckx, C.3    Kohler, A.4    Morin, E.5
  • 23
    • 84946078956 scopus 로고    scopus 로고
    • Fungal endophyte infection of ryegrass reprograms host metabolism and alters development
    • Dupont, P. Y., C. J. Eaton, J. J. Wargent, S. Fechtner, P. Solomon et al., 2015 Fungal endophyte infection of ryegrass reprograms host metabolism and alters development. New Phytol. 208(4): 1227-1240.
    • (2015) New Phytol , vol.208 , Issue.4 , pp. 4
    • Dupont, P.Y.1    Eaton, C.J.2    Wargent, J.J.3    Fechtner, S.4    Solomon, P.5
  • 24
    • 84923177100 scopus 로고    scopus 로고
    • A core gene set describes the molecular basis of mutualism and antagonism in Epichloë spp
    • Eaton, C. J., P. Y. Dupont, P. Solomon, W. Clayton, B. Scott et al., 2015 A core gene set describes the molecular basis of mutualism and antagonism in Epichloë spp. Mol. Plant Microbe Interact. 28(3): 218-231.
    • (2015) Mol. Plant Microbe Interact , vol.28 , Issue.3 , pp. 3
    • Eaton, C.J.1    Dupont, P.Y.2    Solomon, P.3    Clayton, W.4    Scott, B.5
  • 27
    • 84949644520 scopus 로고    scopus 로고
    • Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1
    • Firrincieli, A., R. Otillar, A. Salamov, J. Schmutz, Z. Khan et al., 2015 Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1. Front. Microbiol. 6: 978.
    • (2015) Front. Microbiol , vol.6 , pp. 978
    • Firrincieli, A.1    Otillar, R.2    Salamov, A.3    Schmutz, J.4    Khan, Z.5
  • 28
    • 84857788331 scopus 로고    scopus 로고
    • Horizontal gene transfer in fungi
    • Fitzpatrick, D. A., 2012 Horizontal gene transfer in fungi. FEMS Microbiol. Lett. 329(1): 1-8.
    • (2012) FEMS Microbiol. Lett , vol.329 , Issue.1 , pp. 1
    • Fitzpatrick, D.A.1
  • 29
    • 33845452848 scopus 로고    scopus 로고
    • A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis
    • Fitzpatrick, D. A., M. E. Logue, J. E. Stajich, and G. Butler, 2006 A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol. Biol. 6: 99.
    • (2006) BMC Evol. Biol , vol.6 , pp. 99
    • Fitzpatrick, D.A.1    Logue, M.E.2    Stajich, J.E.3    Butler, G.4
  • 30
    • 47349124015 scopus 로고    scopus 로고
    • Evidence of recent interkingdom horizontal gene transfer between bacteria and Candida parapsilosis
    • Fitzpatrick, D. A., M. E. Logue, and G. Butler, 2008 Evidence of recent interkingdom horizontal gene transfer between bacteria and Candida parapsilosis. BMC Evol. Biol. 8(1): 181.
    • (2008) BMC Evol. Biol , vol.8 , Issue.1 , pp. 1
    • Fitzpatrick, D.A.1    Logue, M.E.2    Butler, G.3
  • 31
    • 84862977387 scopus 로고    scopus 로고
    • The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes
    • Floudas, D., M. Binder, R. Riley, K. Barry, R. A. Blanchette et al., 2012 The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 336(6089): 1715-1719.
    • (2012) Science , vol.336 , Issue.6089 , pp. 6089
    • Floudas, D.1    Binder, M.2    Riley, R.3    Barry, K.4    Blanchette, R.A.5
  • 32
    • 31344459549 scopus 로고    scopus 로고
    • Antimicrobial-resistant bacteria in the community setting
    • Furuya, E. Y., and F. D. Lowy, 2006 Antimicrobial-resistant bacteria in the community setting. Nat. Rev. Microbiol. 4(1): 36-45.
    • (2006) Nat. Rev. Microbiol , vol.4 , Issue.1 , pp. 1
    • Furuya, E.Y.1    Lowy, F.D.2
  • 33
    • 38449096427 scopus 로고    scopus 로고
    • A model of horizontal gene transfer and the bacterial phylogeny problem
    • Galtier, N., 2007 A model of horizontal gene transfer and the bacterial phylogeny problem. Syst. Biol. 56(4): 633-642.
    • (2007) Syst. Biol , vol.56 , Issue.4 , pp. 4
    • Galtier, N.1
  • 34
    • 0033670249 scopus 로고    scopus 로고
    • Horizontal gene transfer in bacterial and archaeal complete genomes
    • Garcia-Vallve, S., A. Romeu, and J. Palau, 2000 Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res. 10(11): 1719-1725.
    • (2000) Genome Res , vol.10 , Issue.11 , pp. 11
    • Garcia-Vallve, S.1    Romeu, A.2    Palau, J.3
  • 35
    • 84955402784 scopus 로고    scopus 로고
    • The genome of Xylona heveae provides a window into fungal endophytism
    • Gazis, R., A. Kuo, R. Riley, K. LaButti, A. Lipzen et al., 2016 The genome of Xylona heveae provides a window into fungal endophytism. Fungal Biol. 120(1): 26-42.
    • (2016) Fungal Biol , vol.120 , Issue.1 , pp. 1
    • Gazis, R.1    Kuo, A.2    Riley, R.3    LaButti, K.4    Lipzen, A.5
  • 36
    • 23944499633 scopus 로고    scopus 로고
    • Horizontal gene transfer, genome innovation and evolution
    • Gogarten, J. P., and J. P. Townsend, 2005 Horizontal gene transfer, genome innovation and evolution. Nat. Rev. Microbiol. 3(9): 679-687.
    • (2005) Nat. Rev. Microbiol , vol.3 , Issue.9 , pp. 9
    • Gogarten, J.P.1    Townsend, J.P.2
  • 37
    • 63449116115 scopus 로고    scopus 로고
    • Reciprocal carbon and nitrogen transfer between an ericaceous dwarf shrub and fungi isolated from Piceirhiza bicolorata ectomycorrhizas
    • Grelet, G. A., D. Johnson, E. Paterson, I. C. Anderson, and I. J. Alexander, 2009 Reciprocal carbon and nitrogen transfer between an ericaceous dwarf shrub and fungi isolated from Piceirhiza bicolorata ectomycorrhizas. New Phytol. 182(2): 359-366.
    • (2009) New Phytol , vol.182 , Issue.2 , pp. 2
    • Grelet, G.A.1    Johnson, D.2    Paterson, E.3    Anderson, I.C.4    Alexander, I.J.5
  • 38
    • 84891752209 scopus 로고    scopus 로고
    • MycoCosm portal: gearing up for 1000 fungal genomes
    • Grigoriev, I. V., R. Nikitin, S. Haridas, A. Kuo, R. Ohm et al., 2014 MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res. 42(Database issue): D699-D704.
    • (2014) Nucleic Acids Res , vol.42 , Issue.DATABASE ISSUE , pp. D699-D704
    • Grigoriev, I.V.1    Nikitin, R.2    Haridas, S.3    Kuo, A.4    Ohm, R.5
  • 39
    • 77950806408 scopus 로고    scopus 로고
    • New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0
    • Guindon, S., J. F. Dufayard, V. Lefort, M. Anisimova, W. Hordijk et al., 2010 New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59(3): 307-321.
    • (2010) Syst. Biol , vol.59 , Issue.3 , pp. 3
    • Guindon, S.1    Dufayard, J.F.2    Lefort, V.3    Anisimova, M.4    Hordijk, W.5
  • 40
    • 84894574409 scopus 로고    scopus 로고
    • Horizontally transferred genetic elements and their role in pathogenesis of bacterial disease
    • Gyles, C., and P. Boerlin, 2014 Horizontally transferred genetic elements and their role in pathogenesis of bacterial disease. Vet. Pathol. 51(2): 328-340.
    • (2014) Vet. Pathol , vol.51 , Issue.2 , pp. 2
    • Gyles, C.1    Boerlin, P.2
  • 41
    • 37848998569 scopus 로고    scopus 로고
    • Dothideomycete plant interactions illuminated by genome sequencing and EST analysis of the wheat pathogen Stagonospora nodorum
    • Hane, J. K., R. G. Lowe, P. S. Solomon, K. C. Tan, C. L. Schoch et al., 2007 Dothideomycete plant interactions illuminated by genome sequencing and EST analysis of the wheat pathogen Stagonospora nodorum. Plant Cell 19(11): 3347-3368.
    • (2007) Plant Cell , vol.19 , Issue.11 , pp. 11
    • Hane, J.K.1    Lowe, R.G.2    Solomon, P.S.3    Tan, K.C.4    Schoch, C.L.5
  • 42
    • 84899489642 scopus 로고    scopus 로고
    • Rapid evolution of avirulence genes in rice blast fungus Magnaporthe oryzae
    • Huang, J., W. Si, Q. Deng, P. Li, and S. Yang, 2014 Rapid evolution of avirulence genes in rice blast fungus Magnaporthe oryzae. BMC Genet. 15: 45.
    • (2014) BMC Genet , vol.15 , pp. 45
    • Huang, J.1    Si, W.2    Deng, Q.3    Li, P.4    Yang, S.5
  • 45
    • 85007247080 scopus 로고    scopus 로고
    • ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony
    • Jacox, E., C. Chauve, G. J. Szöll)osi, Y. Ponty, and C. Scornavacca, 2016 ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony. Bioinformatics 32(13): 2056-2058.
    • (2016) Bioinformatics , vol.32 , Issue.13 , pp. 13
    • Jacox, E.1    Chauve, C.2    Szöllösi, G.J.3    Ponty, Y.4    Scornavacca, C.5
  • 46
    • 33750329972 scopus 로고    scopus 로고
    • Reconstructing the early evolution of fungi using a six-gene phylogeny
    • James, T. Y., F. Kauff, C. L. Schoch, P. B. Matheny, V. Hofstetter et al., 2006 Reconstructing the early evolution of fungi using a six-gene phylogeny. Nature 443(7113): 818-822.
    • (2006) Nature , vol.443 , Issue.7113 , pp. 7113
    • James, T.Y.1    Kauff, F.2    Schoch, C.L.3    Matheny, P.B.4    Hofstetter, V.5
  • 47
    • 84898910228 scopus 로고    scopus 로고
    • SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes
    • Jaron, K. S., J. C. Moravec, and N. Martínková, 2014 SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes. Bioinformatics 30 (8): 1081-1086.
    • (2014) Bioinformatics , vol.30 , Issue.8 , pp. 1081-1086
    • Jaron, K.S.1    Moravec, J.C.2    Martínková, N.3
  • 48
    • 84875619226 scopus 로고    scopus 로고
    • MAFFT multiple sequence alignment software version 7: improvements in performance and usability
    • Katoh, K., and D. M. Standley, 2013 MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30(4): 772-780.
    • (2013) Mol. Biol. Evol , vol.30 , Issue.4 , pp. 4
    • Katoh, K.1    Standley, D.M.2
  • 49
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
    • Katoh, K., K. Misawa, K. Kuma, and T. Miyata, 2002 MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30(14): 3059-3066.
    • (2002) Nucleic Acids Res , vol.30 , Issue.14 , pp. 14
    • Katoh, K.1    Misawa, K.2    Kuma, K.3    Miyata, T.4
  • 50
    • 0036307494 scopus 로고    scopus 로고
    • In situ transfer of antibiotic resistance genes from transgenic (transplastomic) tobacco plants to bacteria
    • Kay, E., T. M. Vogel, F. Bertolla, R. Nalin, and P. Simonet, 2002 In situ transfer of antibiotic resistance genes from transgenic (transplastomic) tobacco plants to bacteria. Appl. Environ. Microbiol. 68(7): 3345-3351.
    • (2002) Appl. Environ. Microbiol , vol.68 , Issue.7 , pp. 7
    • Kay, E.1    Vogel, T.M.2    Bertolla, F.3    Nalin, R.4    Simonet, P.5
  • 51
    • 47649104484 scopus 로고    scopus 로고
    • Horizontal gene transfer in eukaryotic evolution
    • Keeling, P. J., and J. D. Palmer, 2008 Horizontal gene transfer in eukaryotic evolution. Nat. Rev. Genet. 9(8): 605-618.
    • (2008) Nat. Rev. Genet , vol.9 , Issue.8 , pp. 8
    • Keeling, P.J.1    Palmer, J.D.2
  • 52
    • 44649170477 scopus 로고    scopus 로고
    • Evidence for horizontal transfer of a secondary metabolite gene cluster between fungi
    • Khaldi, N., J. Collemare, M.-H. Lebrun, and K. H. Wolfe, 2008 Evidence for horizontal transfer of a secondary metabolite gene cluster between fungi. Genome Biol. 9(1): 1-10.
    • (2008) Genome Biol , vol.9 , Issue.1 , pp. 1
    • Khaldi, N.1    Collemare, J.2    Lebrun, M.-H.3    Wolfe, K.H.4
  • 53
    • 79960934898 scopus 로고    scopus 로고
    • Comparative genomics yields insights into niche adaptation of plant vascular wilt pathogens
    • Klosterman, S. J., K. V. Subbarao, S. Kang, P. Veronese, S. E. Gold et al., 2011 Comparative genomics yields insights into niche adaptation of plant vascular wilt pathogens. PLoS Pathog. 7(7): e1002137.
    • (2011) PLoS Pathog , vol.7 , Issue.7 , pp. 7
    • Klosterman, S.J.1    Subbarao, K.V.2    Kang, S.3    Veronese, P.4    Gold, S.E.5
  • 54
    • 84925005930 scopus 로고    scopus 로고
    • Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists
    • Kohler, A., A. Kuo, L. G. Nagy, E. Morin, K.W. Barry et al., 2015 Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists. Nat. Genet. 47(4): 410-415.
    • (2015) Nat. Genet , vol.47 , Issue.4 , pp. 4
    • Kohler, A.1    Kuo, A.2    Nagy, L.G.3    Morin, E.4    Barry, K.W.5
  • 55
    • 0035099964 scopus 로고    scopus 로고
    • Codon bias and base composition are poor indicators of horizontally transferred genes
    • Koski, L. B., R. A. Morton, and G. B. Golding, 2001 Codon bias and base composition are poor indicators of horizontally transferred genes. Mol. Biol. Evol. 18(3): 404-412.
    • (2001) Mol. Biol. Evol , vol.18 , Issue.3 , pp. 3
    • Koski, L.B.1    Morton, R.A.2    Golding, G.B.3
  • 56
    • 84940488362 scopus 로고    scopus 로고
    • Endosymbiotic origin and differential loss of eukaryotic genes
    • Ku, C., S. Nelson-Sathi, M. Roettger, F. L. Sousa, P. J. Lockhart et al., 2015 Endosymbiotic origin and differential loss of eukaryotic genes. Nature 524(7566): 427-432.
    • (2015) Nature , vol.524 , Issue.7566 , pp. 7566
    • Ku, C.1    Nelson-Sathi, S.2    Roettger, M.3    Sousa, F.L.4    Lockhart, P.J.5
  • 57
    • 0030994798 scopus 로고    scopus 로고
    • Amelioration of bacterial genomes: rates of change and exchange
    • Lawrence, J. G., and H. Ochman, 1997 Amelioration of bacterial genomes: rates of change and exchange. J. Mol. Evol. 44(4): 383-397.
    • (1997) J. Mol. Evol , vol.44 , Issue.4 , pp. 4
    • Lawrence, J.G.1    Ochman, H.2
  • 58
    • 45849154166 scopus 로고    scopus 로고
    • An improved general amino acid replacement matrix
    • Le, S. Q., and O. Gascuel, 2008 An improved general amino acid replacement matrix. Mol. Biol. Evol. 25(7): 1307-1320.
    • (2008) Mol. Biol. Evol , vol.25 , Issue.7 , pp. 7
    • Le, S.Q.1    Gascuel, O.2
  • 59
    • 33645061798 scopus 로고    scopus 로고
    • Screening for rapidly evolving genes in the ectomycorrhizal fungus Paxillus involutus using cDNA microarrays
    • Le Quere, A., K. A. Eriksen, B. Rajashekar, A. Schutzendubel, B. Canback et al., 2006 Screening for rapidly evolving genes in the ectomycorrhizal fungus Paxillus involutus using cDNA microarrays. Mol. Ecol. 15(2): 535-550.
    • (2006) Mol. Ecol , vol.15 , Issue.2 , pp. 2
    • Le Quere, A.1    Eriksen, K.A.2    Rajashekar, B.3    Schutzendubel, A.4    Canback, B.5
  • 60
    • 80053371346 scopus 로고    scopus 로고
    • Widespread horizontal gene transfer from circular single-stranded DNA viruses to eukaryotic genomes
    • Liu, H., Y. Fu, B. Li, X. Yu, J. Xie et al., 2011 Widespread horizontal gene transfer from circular single-stranded DNA viruses to eukaryotic genomes. BMC Evol. Biol. 11: 276.
    • (2011) BMC Evol. Biol , vol.11 , pp. 276
    • Liu, H.1    Fu, Y.2    Li, B.3    Yu, X.4    Xie, J.5
  • 61
    • 33750088189 scopus 로고    scopus 로고
    • Loss of the flagellum happened only once in the fungal lineage: phylogenetic structure of Kingdom Fungi inferred from RNA polymerase II subunit genes
    • Liu, Y. J., M. C. Hodson, and B. D. Hall, 2006 Loss of the flagellum happened only once in the fungal lineage: phylogenetic structure of Kingdom Fungi inferred from RNA polymerase II subunit genes. BMC Evol. Biol. 6: 74.
    • (2006) BMC Evol. Biol , vol.6 , pp. 74
    • Liu, Y.J.1    Hodson, M.C.2    Hall, B.D.3
  • 62
    • 77949714038 scopus 로고    scopus 로고
    • Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium
    • Ma, L.-J., H. C. van der Does, K. A. Borkovich, J. J. Coleman, M.-J. Daboussi et al., 2010 Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 464(7287): 367-373.
    • (2010) Nature , vol.464 , Issue.7287 , pp. 7287
    • Ma, L.-J.1    van der Does, H.C.2    Borkovich, K.A.3    Coleman, J.J.4    Daboussi, M.-J.5
  • 63
    • 0031504952 scopus 로고    scopus 로고
    • Gene trees in species trees
    • Maddison, W. P., 1997 Gene trees in species trees. Syst. Biol. 46(3): 523-536.
    • (1997) Syst. Biol , vol.46 , Issue.3 , pp. 3
    • Maddison, W.P.1
  • 64
    • 77949467943 scopus 로고    scopus 로고
    • Whole genome evaluation of horizontal transfers in the pathogenic fungus Aspergillus fumigatus
    • Mallet, L. V., J. Becq, and P. Deschavanne, 2010 Whole genome evaluation of horizontal transfers in the pathogenic fungus Aspergillus fumigatus. BMC Genomics 11: 171.
    • (2010) BMC Genomics , vol.11 , pp. 171
    • Mallet, L.V.1    Becq, J.2    Deschavanne, P.3
  • 65
    • 72449164089 scopus 로고    scopus 로고
    • Acquisition of prokaryotic genes by fungal genomes
    • Marcet-Houben, M., and T. Gabaldón, 2010 Acquisition of prokaryotic genes by fungal genomes. Trends Genet. 26(1): 5-8.
    • (2010) Trends Genet , vol.26 , Issue.1 , pp. 1
    • Marcet-Houben, M.1    Gabaldón, T.2
  • 66
    • 40449120632 scopus 로고    scopus 로고
    • The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis
    • Martin, F., A. Aerts, D. Ahren, A. Brun, E. G. Danchin et al., 2008 The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 452(7183): 88-92.
    • (2008) Nature , vol.452 , Issue.7183 , pp. 7183
    • Martin, F.1    Aerts, A.2    Ahren, D.3    Brun, A.4    Danchin, E.G.5
  • 67
    • 77951144839 scopus 로고    scopus 로고
    • Perigord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis
    • Martin, F., A. Kohler, C. Murat, R. Balestrini, P. M. Coutinho et al., 2010 Perigord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. Nature 464(7291): 1033-1038.
    • (2010) Nature , vol.464 , Issue.7291 , pp. 7291
    • Martin, F.1    Kohler, A.2    Murat, C.3    Balestrini, R.4    Coutinho, P.M.5
  • 68
    • 47749155981 scopus 로고    scopus 로고
    • Antibiotics and antibiotic resistance genes in natural environments
    • Martínez, J. L., 2008 Antibiotics and antibiotic resistance genes in natural environments. Science 321(5887): 365-367.
    • (2008) Science , vol.321 , Issue.5887 , pp. 5887
    • Martínez, J.L.1
  • 69
    • 84860448420 scopus 로고    scopus 로고
    • GOHTAM: a website for 'genomic origin of horizontal transfers, alignment and metagenomics.'
    • Menigaud, S., L. Mallet, G. Picord, C. Churlaud, A. Borrel et al., 2012 GOHTAM: a website for 'genomic origin of horizontal transfers, alignment and metagenomics.' Bioinformatics 28(9): 1270-1271.
    • (2012) Bioinformatics , vol.28 , Issue.9 , pp. 1270-1271
    • Menigaud, S.1    Mallet, L.2    Picord, G.3    Churlaud, C.4    Borrel, A.5
  • 71
    • 68149139650 scopus 로고    scopus 로고
    • Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus
    • Monier, A., A. Pagarete, C. de Vargas, M. J. Allen, B. Read et al., 2009 Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus. Genome Res. 19(8): 1441-1449.
    • (2009) Genome Res , vol.19 , Issue.8 , pp. 8
    • Monier, A.1    Pagarete, A.2    de Vargas, C.3    Allen, M.J.4    Read, B.5
  • 73
    • 84863806861 scopus 로고    scopus 로고
    • Recurrent horizontal transfer of bacterial toxin genes to eukaryotes
    • Moran, Y., D. Fredman, P. Szczesny, M. Grynberg, and U. Technau, 2012 Recurrent horizontal transfer of bacterial toxin genes to eukaryotes. Mol. Biol. Evol. 29(9): 2223-2230.
    • (2012) Mol. Biol. Evol , vol.29 , Issue.9 , pp. 9
    • Moran, Y.1    Fredman, D.2    Szczesny, P.3    Grynberg, M.4    Technau, U.5
  • 74
    • 84932628455 scopus 로고    scopus 로고
    • Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts
    • Morel, G., L. Sterck, D. Swennen, M. Marcet-Houben, D. Onesime et al., 2015 Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts. Sci. Rep. 5: 11571.
    • (2015) Sci. Rep , vol.5 , pp. 11571
    • Morel, G.1    Sterck, L.2    Swennen, D.3    Marcet-Houben, M.4    Onesime, D.5
  • 75
    • 3042849253 scopus 로고    scopus 로고
    • Biased biological functions of horizontally transferred genes in prokaryotic genomes
    • Nakamura, Y., T. Itoh, H. Matsuda, and T. Gojobori, 2004 Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat. Genet. 36(7): 760-766.
    • (2004) Nat. Genet , vol.36 , Issue.7 , pp. 7
    • Nakamura, Y.1    Itoh, T.2    Matsuda, H.3    Gojobori, T.4
  • 77
    • 84893112532 scopus 로고    scopus 로고
    • Plant expansins in bacteria and fungi: evolution by horizontal gene transfer and independent domain fusion
    • Nikolaidis, N., N. Doran, and D. J. Cosgrove, 2014 Plant expansins in bacteria and fungi: evolution by horizontal gene transfer and independent domain fusion. Mol. Biol. Evol. 31(2): 376-386.
    • (2014) Mol. Biol. Evol , vol.31 , Issue.2 , pp. 2
    • Nikolaidis, N.1    Doran, N.2    Cosgrove, D.J.3
  • 78
    • 84865693932 scopus 로고    scopus 로고
    • Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses
    • O'Connell, R. J., M. R. Thon, S. Hacquard, S. G. Amyotte, J. Kleemann et al., 2012 Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses. Nat. Genet. 44(9): 1060-1065.
    • (2012) Nat. Genet , vol.44 , Issue.9 , pp. 9
    • O'Connell, R.J.1    Thon, M.R.2    Hacquard, S.3    Amyotte, S.G.4    Kleemann, J.5
  • 79
    • 0034682335 scopus 로고    scopus 로고
    • Lateral gene transfer and the nature of bacterial innovation
    • Ochman, H., J. G. Lawrence, and E. A. Groisman, 2000 Lateral gene transfer and the nature of bacterial innovation. Nature 405(6784): 299-304.
    • (2000) Nature , vol.405 , Issue.6784 , pp. 6784
    • Ochman, H.1    Lawrence, J.G.2    Groisman, E.A.3
  • 80
    • 84868159385 scopus 로고    scopus 로고
    • Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi
    • Ohm, R. A., N. Feau, B. Henrissat, C. L. Schoch, B. A. Horwitz et al., 2012 Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi. PLoS Pathog. 8(12): e1003037.
    • (2012) PLoS Pathog , vol.8 , Issue.12 , pp. 12
    • Ohm, R.A.1    Feau, N.2    Henrissat, B.3    Schoch, C.L.4    Horwitz, B.A.5
  • 82
    • 0023822631 scopus 로고
    • Relationships between gene trees and species trees
    • Pamilo, P., and M. Nei, 1988 Relationships between gene trees and species trees. Mol. Biol. Evol. 5(5): 568-583.
    • (1988) Mol. Biol. Evol , vol.5 , Issue.5 , pp. 5
    • Pamilo, P.1    Nei, M.2
  • 84
    • 65549165915 scopus 로고    scopus 로고
    • Testing phylogenetic methods to identify horizontal gene transfer
    • Poptsova, M., 2009 Testing phylogenetic methods to identify horizontal gene transfer. Methods Mol. Biol. 532: 227-240.
    • (2009) Methods Mol. Biol , vol.532 , pp. 227-240
    • Poptsova, M.1
  • 85
    • 34047234772 scopus 로고    scopus 로고
    • The power of phylogenetic approaches to detect horizontally transferred genes
    • Poptsova, M. S., and J. P. Gogarten, 2007 The power of phylogenetic approaches to detect horizontally transferred genes. BMC Evol. Biol. 7: 45.
    • (2007) BMC Evol. Biol , vol.7 , pp. 45
    • Poptsova, M.S.1    Gogarten, J.P.2
  • 86
    • 0035943134 scopus 로고    scopus 로고
    • On surrogate methods for detecting lateral gene transfer
    • Ragan, M. A., 2001 On surrogate methods for detecting lateral gene transfer. FEMS Microbiol. Lett. 201(2): 187-191.
    • (2001) FEMS Microbiol. Lett , vol.201 , Issue.2 , pp. 2
    • Ragan, M.A.1
  • 88
    • 33748857142 scopus 로고    scopus 로고
    • Evolutionary origins of the eukaryotic shikimate pathway: gene fusions, horizontal gene transfer, and endosymbiotic replacements
    • Richards, T. A., J. B. Dacks, S. A. Campbell, J. L. Blanchard, P. G. Foster et al., 2006 Evolutionary origins of the eukaryotic shikimate pathway: gene fusions, horizontal gene transfer, and endosymbiotic replacements. Eukaryot. Cell 5(9): 1517-1531.
    • (2006) Eukaryot. Cell , vol.5 , Issue.9 , pp. 9
    • Richards, T.A.1    Dacks, J.B.2    Campbell, S.A.3    Blanchard, J.L.4    Foster, P.G.5
  • 89
    • 69949175105 scopus 로고    scopus 로고
    • Phylogenomic analysis demonstrates a pattern of rare and ancient horizontal gene transfer between plants and fungi
    • Richards, T. A., D.M. Soanes, P. G. Foster, G. Leonard, C. R. Thornton et al., 2009 Phylogenomic analysis demonstrates a pattern of rare and ancient horizontal gene transfer between plants and fungi. Plant Cell 21(7): 1897-1911.
    • (2009) Plant Cell , vol.21 , Issue.7 , pp. 7
    • Richards, T.A.1    Soanes, D.M.2    Foster, P.G.3    Leonard, G.4    Thornton, C.R.5
  • 90
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • Robinson, D. F., and L. R. Foulds, 1981 Comparison of phylogenetic trees. Math. Biosci. 53(1-2): 131-147.
    • (1981) Math. Biosci , vol.53 , Issue.1-2 , pp. 1-2
    • Robinson, D.F.1    Foulds, L.R.2
  • 91
    • 0013815886 scopus 로고
    • Nucleic acid homologies of selected bacteria, L forms, and Mycoplasma species
    • Rogul, M., Z. McGee, R. Wittler, and S. Falkow, 1965 Nucleic acid homologies of selected bacteria, L forms, and Mycoplasma species. J. Bacteriol. 90(5): 1200-1204.
    • (1965) J. Bacteriol , vol.90 , Issue.5 , pp. 5
    • Rogul, M.1    McGee, Z.2    Wittler, R.3    Falkow, S.4
  • 92
    • 0033738805 scopus 로고    scopus 로고
    • Role of horizontal gene transfer in the evolution of fungi
    • Rosewich, U. L., and H. C. Kistler, 2000 Role of horizontal gene transfer in the evolution of fungi. Annu. Rev. Phytopathol. 38: 325-363.
    • (2000) Annu. Rev. Phytopathol , vol.38 , pp. 325-363
    • Rosewich, U.L.1    Kistler, H.C.2
  • 93
    • 84875420788 scopus 로고    scopus 로고
    • Effector diversification within compartments of the Leptosphaeria maculans genome affected by repeat-induced point mutations
    • Rouxel, T., J. Grandaubert, J. K. Hane, C. Hoede, A. P. van de Wouw et al., 2011 Effector diversification within compartments of the Leptosphaeria maculans genome affected by repeat-induced point mutations. Nat. Commun. 2: 202.
    • (2011) Nat. Commun , vol.2 , pp. 202
    • Rouxel, T.1    Grandaubert, J.2    Hane, J.K.3    Hoede, C.4    van de Wouw, A.P.5
  • 94
    • 79954579960 scopus 로고    scopus 로고
    • Evaluating ortholog prediction algorithms in a yeast model clade
    • Salichos, L., and A. Rokas, 2011 Evaluating ortholog prediction algorithms in a yeast model clade. PLoS One 6(4): e18755.
    • (2011) PLoS One , vol.6 , Issue.4 , pp. 4
    • Salichos, L.1    Rokas, A.2
  • 95
    • 84878113118 scopus 로고    scopus 로고
    • Inferring ancient divergences requires genes with strong phylogenetic signals
    • Salichos, L., and A. Rokas, 2013 Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 497(7449): 327-331.
    • (2013) Nature , vol.497 , Issue.7449 , pp. 7449
    • Salichos, L.1    Rokas, A.2
  • 96
    • 58149200954 scopus 로고    scopus 로고
    • Database resources of the national center for biotechnology information
    • Sayers, E. W., T. Barrett, D. A. Benson, S. H. Bryant, K. Canese et al., 2009 Database resources of the national center for biotechnology information. Nucleic Acids Res. 37(Database issue): D5-D15.
    • (2009) Nucleic Acids Res , vol.37 , Issue.DATABASE ISSUE , pp. D5-D15
    • Sayers, E.W.1    Barrett, T.2    Benson, D.A.3    Bryant, S.H.4    Canese, K.5
  • 97
    • 0035570583 scopus 로고    scopus 로고
    • Epichloë festucae and related mutualistic symbionts of grasses
    • Schardl, C. L., 2001 Epichloë festucae and related mutualistic symbionts of grasses. Fungal Genet. Biol. 33(2): 69-82.
    • (2001) Fungal Genet. Biol , vol.33 , Issue.2 , pp. 2
    • Schardl, C.L.1
  • 98
    • 84874772540 scopus 로고    scopus 로고
    • Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the Clavicipitaceae reveals dynamics of alkaloid loci
    • Schardl, C. L., C. A. Young, U. Hesse, S. G. Amyotte, K. Andreeva et al., 2013 Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the Clavicipitaceae reveals dynamics of alkaloid loci. PLoS Genet. 9(2): e1003323.
    • (2013) PLoS Genet , vol.9 , Issue.2 , pp. 2
    • Schardl, C.L.1    Young, C.A.2    Hesse, U.3    Amyotte, S.G.4    Andreeva, K.5
  • 99
    • 78650100793 scopus 로고    scopus 로고
    • Pathogenicity determinants in smut fungi revealed by genome comparison
    • Schirawski, J., G. Mannhaupt, K. Munch, T. Brefort, K. Schipper et al., 2010 Pathogenicity determinants in smut fungi revealed by genome comparison. Science 330(6010): 1546-1548.
    • (2010) Science , vol.330 , Issue.6010 , pp. 6010
    • Schirawski, J.1    Mannhaupt, G.2    Munch, K.3    Brefort, T.4    Schipper, K.5
  • 100
    • 0014693351 scopus 로고
    • Mutations caused by the insertion of genetic material into the galactose operon of Escherichia coli
    • Shapiro, J. A., 1969 Mutations caused by the insertion of genetic material into the galactose operon of Escherichia coli. J. Mol. Biol. 40(1): 93-105.
    • (1969) J. Mol. Biol , vol.40 , Issue.1 , pp. 1
    • Shapiro, J.A.1
  • 101
    • 0023650543 scopus 로고
    • The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications
    • Sharp, P. M., and W. H. Li, 1987 The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15(3): 1281-1295.
    • (1987) Nucleic Acids Res , vol.15 , Issue.3 , pp. 3
    • Sharp, P.M.1    Li, W.H.2
  • 102
    • 84905465132 scopus 로고    scopus 로고
    • Horizontal gene transfer in eukaryotic plant pathogens
    • Soanes, D., and T. A. Richards, 2014 Horizontal gene transfer in eukaryotic plant pathogens. Annu. Rev. Phytopathol. 52: 583-614.
    • (2014) Annu. Rev. Phytopathol , vol.52 , pp. 583-614
    • Soanes, D.1    Richards, T.A.2
  • 103
    • 84937405121 scopus 로고    scopus 로고
    • Horizontal gene transfer: building the web of life
    • Soucy, S. M., J. Huang, and J. P. Gogarten, 2015 Horizontal gene transfer: building the web of life. Nat. Rev. Genet. 16(8): 472-482.
    • (2015) Nat. Rev. Genet , vol.16 , Issue.8 , pp. 8
    • Soucy, S.M.1    Huang, J.2    Gogarten, J.P.3
  • 104
    • 78650122420 scopus 로고    scopus 로고
    • Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism
    • Spanu, P. D., J. C. Abbott, J. Amselem, T. A. Burgis, D. M. Soanes et al., 2010 Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism. Science 330(6010): 1543-1546.
    • (2010) Science , vol.330 , Issue.6010 , pp. 6010
    • Spanu, P.D.1    Abbott, J.C.2    Amselem, J.3    Burgis, T.A.4    Soanes, D.M.5
  • 105
    • 0026291502 scopus 로고
    • Genetic exchange between kingdoms
    • Sprague, G. F., Jr, 1991 Genetic exchange between kingdoms. Curr. Opin. Genet. Dev. 1(4): 530-533.
    • (1991) Curr. Opin. Genet. Dev , vol.1 , Issue.4 , pp. 4
    • Sprague, G.F.1
  • 106
    • 84868113304 scopus 로고    scopus 로고
    • Genome update of Botrytis cinerea strains B05.10 and T4
    • Staats, M., and J. A. van Kan, 2012 Genome update of Botrytis cinerea strains B05.10 and T4. Eukaryot. Cell 11(11): 1413-1414.
    • (2012) Eukaryot. Cell , vol.11 , Issue.11 , pp. 11
    • Staats, M.1    van Kan, J.A.2
  • 107
    • 84866458802 scopus 로고    scopus 로고
    • Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees
    • Stolzer, M., H. Lai, M. Xu, D. Sathaye, B. Vernot et al., 2012 Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees. Bioinformatics 28(18): i409-i415.
    • (2012) Bioinformatics , vol.28 , Issue.18 , pp. 18
    • Stolzer, M.1    Lai, H.2    Xu, M.3    Sathaye, D.4    Vernot, B.5
  • 108
    • 84871824869 scopus 로고    scopus 로고
    • An improved implementation of effective number of codons (Nc)
    • Sun, X., Q. Yang, and X. Xia, 2013 An improved implementation of effective number of codons (Nc). Mol. Biol. Evol. 30(1): 191-196.
    • (2013) Mol. Biol. Evol , vol.30 , Issue.1 , pp. 1
    • Sun, X.1    Yang, Q.2    Xia, X.3
  • 109
    • 0028606283 scopus 로고
    • Horizontal gene transfer: evidence and possible consequences
    • Syvanen, M., 1994 Horizontal gene transfer: evidence and possible consequences. Annu. Rev. Genet. 28: 237-261.
    • (1994) Annu. Rev. Genet , vol.28 , pp. 237-261
    • Syvanen, M.1
  • 111
    • 33745443572 scopus 로고    scopus 로고
    • Reactive oxygen species play a role in regulating a fungusperennial ryegrass mutualistic interaction
    • Tanaka, A., M. J. Christensen, D. Takemoto, P. Park, and B. Scott, 2006 Reactive oxygen species play a role in regulating a fungusperennial ryegrass mutualistic interaction. Plant Cell 18(4): 1052-1066.
    • (2006) Plant Cell , vol.18 , Issue.4 , pp. 4
    • Tanaka, A.1    Christensen, M.J.2    Takemoto, D.3    Park, P.4    Scott, B.5
  • 112
    • 4043070561 scopus 로고    scopus 로고
    • An analysis of the pea pathogenicity genes of Nectria haematococca MPVI supports the hypothesis of their origin by horizontal transfer and uncovers a potentially new pathogen of garden pea: Neocosmospora boniensis
    • Temporini, E., and H. Van Etten, 2004 An analysis of the pea pathogenicity genes of Nectria haematococca MPVI supports the hypothesis of their origin by horizontal transfer and uncovers a potentially new pathogen of garden pea: Neocosmospora boniensis. Curr. Genet. 46: 29-36.
    • (2004) Curr. Genet , vol.46 , pp. 29-36
    • Temporini, E.1    Van Etten, H.2
  • 113
    • 84899684439 scopus 로고    scopus 로고
    • The relative importance of rapid evolution for plant-microbe interactions depends on ecological context
    • Terhorst, C. P., J. T. Lennon, and J. A. Lau, 2014 The relative importance of rapid evolution for plant-microbe interactions depends on ecological context. Proc. Biol. Sci. 281(1785): 20140028.
    • (2014) Proc. Biol. Sci , vol.281 , Issue.1785 , pp. 1785
    • Terhorst, C.P.1    Lennon, J.T.2    Lau, J.A.3
  • 114
    • 34250380386 scopus 로고    scopus 로고
    • Confounding factors in HGT detection: statistical error, coalescent effects, and multiple solutions
    • Than, C., D. Ruths, H. Innan, and L. Nakhleh, 2007 Confounding factors in HGT detection: statistical error, coalescent effects, and multiple solutions. J. Comput. Biol. 14(4): 517-535.
    • (2007) J. Comput. Biol , vol.14 , Issue.4 , pp. 4
    • Than, C.1    Ruths, D.2    Innan, H.3    Nakhleh, L.4
  • 115
    • 84896547853 scopus 로고    scopus 로고
    • Genome sequencing provides insight into the reproductive biology, nutritional mode and ploidy of the fern pathogen Mixia osmundae
    • Toome, M., R. A. Ohm, R. W. Riley, T. Y. James, K. L. Lazarus et al., 2014 Genome sequencing provides insight into the reproductive biology, nutritional mode and ploidy of the fern pathogen Mixia osmundae. New Phytol. 202(2): 554-564.
    • (2014) New Phytol , vol.202 , Issue.2 , pp. 2
    • Toome, M.1    Ohm, R.A.2    Riley, R.W.3    James, T.Y.4    Lazarus, K.L.5
  • 116
    • 33748329373 scopus 로고    scopus 로고
    • Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis
    • Tyler, B.M., S. Tripathy, X. Zhang, P. Dehal, R. H. Jiang et al., 2006 Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science 313(5791): 1261-1266.
    • (2006) Science , vol.313 , Issue.5791 , pp. 5791
    • Tyler, B.M.1    Tripathy, S.2    Zhang, X.3    Dehal, P.4    Jiang, R.H.5
  • 117
    • 35448965597 scopus 로고    scopus 로고
    • Visualizing differences in phylogenetic information content of alignments and distinction of three classes of long-branch effects
    • Wägele, J. W., and C. Mayer, 2007 Visualizing differences in phylogenetic information content of alignments and distinction of three classes of long-branch effects. BMC Evol. Biol. 7: 147.
    • (2007) BMC Evol. Biol , vol.7 , pp. 147
    • Wägele, J.W.1    Mayer, C.2
  • 118
    • 69949152972 scopus 로고    scopus 로고
    • A fungal phylogeny based on 82 complete genomes using the composition vector method
    • Wang, H., Z. Xu, L. Gao, and B. Hao, 2009 A fungal phylogeny based on 82 complete genomes using the composition vector method. BMC Evol. Biol. 9: 195.
    • (2009) BMC Evol. Biol , vol.9 , pp. 195
    • Wang, H.1    Xu, Z.2    Gao, L.3    Hao, B.4
  • 119
    • 84906264612 scopus 로고    scopus 로고
    • kdetrees: non-parametric estimation of phylogenetic tree distributions
    • Weyenberg, G., P. M. Huggins, C. L. Schardl, D. K. Howe, and R. Yoshida, 2014 kdetrees: non-parametric estimation of phylogenetic tree distributions. Bioinformatics 30(16): 2280-2287.
    • (2014) Bioinformatics , vol.30 , Issue.16 , pp. 16
    • Weyenberg, G.1    Huggins, P.M.2    Schardl, C.L.3    Howe, D.K.4    Yoshida, R.5
  • 120
    • 84902492013 scopus 로고    scopus 로고
    • Supertrees based on the subtree prune-and-regraft distance
    • Whidden, C., N. Zeh, and R. G. Beiko, 2014 Supertrees based on the subtree prune-and-regraft distance. Syst. Biol. 63(4): 566-581.
    • (2014) Syst. Biol , vol.63 , Issue.4 , pp. 4
    • Whidden, C.1    Zeh, N.2    Beiko, R.G.3
  • 121
    • 84919683973 scopus 로고    scopus 로고
    • The evolution of fungal metabolic pathways
    • Wisecaver, J. H., J. C. Slot, and A. Rokas, 2014 The evolution of fungal metabolic pathways. PLoS Genet. 10(12): e1004816.
    • (2014) PLoS Genet , vol.10 , Issue.12 , pp. 12
    • Wisecaver, J.H.1    Slot, J.C.2    Rokas, A.3
  • 122
    • 0025318864 scopus 로고
    • The 'effective number of codons' used in a gene
    • Wright, F., 1990 The 'effective number of codons' used in a gene. Gene 87(1): 23-29.
    • (1990) Gene , vol.87 , Issue.1 , pp. 1
    • Wright, F.1
  • 123
    • 65549102123 scopus 로고    scopus 로고
    • Detection and quantitative assessment of horizontal gene transfer
    • Zhaxybayeva, O., 2009 Detection and quantitative assessment of horizontal gene transfer. Methods Mol. Biol. 532: 195-213.
    • (2009) Methods Mol. Biol , vol.532 , pp. 195-213
    • Zhaxybayeva, O.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.