메뉴 건너뛰기




Volumn 15, Issue 1, 2017, Pages

Time-resolved dual transcriptomics reveal early induced Nicotiana benthamiana root genes and conserved infection-promoting Phytophthora palmivora effectors

Author keywords

De novo transcriptome assembly; Dual transcriptomics; Effectors; N. benthamiana; Non model species; P. palmivora; RXLR effectors; Secretome

Indexed keywords

PLANT PROTEIN; TRANSCRIPTOME;

EID: 85019130041     PISSN: None     EISSN: 17417007     Source Type: Journal    
DOI: 10.1186/s12915-017-0379-1     Document Type: Article
Times cited : (63)

References (128)
  • 1
    • 0004282131 scopus 로고    scopus 로고
    • Phytophthora diseases worldwide
    • St. Paul: American Phytopathological Society (APS Press);
    • Erwin DD, Ribeiro OK. Phytophthora diseases worldwide. St. Paul: American Phytopathological Society (APS Press); 1996.
    • (1996)
    • Erwin, D.D.1    Ribeiro, O.K.2
  • 2
    • 84879907835 scopus 로고    scopus 로고
    • The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine
    • Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, et al. The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine. Elife. 2013;2013:1-25.
    • (2013) Elife. , vol.2013 , pp. 1-25
    • Yoshida, K.1    Schuenemann, V.J.2    Cano, L.M.3    Pais, M.4    Mishra, B.5    Sharma, R.6
  • 3
    • 0028055562 scopus 로고
    • Isozyme diversity in Phytophthora palmivora: evidence for a southeast Asian centre of origin
    • McHau GRA, Coffey MD. Isozyme diversity in Phytophthora palmivora: evidence for a southeast Asian centre of origin. Mycol Res. 1994;98:1035-43.
    • (1994) Mycol Res. , vol.98 , pp. 1035-1043
    • McHau, G.R.A.1    Coffey, M.D.2
  • 5
    • 34347364335 scopus 로고    scopus 로고
    • Economic impact of Phytophthora diseases in Southeast Asia
    • In: Drenth A, Guest DI, editors. Canberra: Australian Centre for International Agricultural Research (ACIAR);
    • Drenth A, Sendall B. Economic impact of Phytophthora diseases in Southeast Asia. In: Drenth A, Guest DI, editors. Diversity and management of Phytophthora in Southeast Asia. Canberra: Australian Centre for International Agricultural Research (ACIAR); 2004. p. 10-28.
    • (2004) Diversity and management of Phytophthora in Southeast Asia , pp. 10-28
    • Drenth, A.1    Sendall, B.2
  • 7
    • 85019052907 scopus 로고    scopus 로고
    • Phytophthora palmivora
    • Brooks F. Phytophthora palmivora. Most. 2005;4:2.
    • (2005) Most. , vol.4 , pp. 2
    • Brooks, F.1
  • 8
    • 84963585167 scopus 로고    scopus 로고
    • Bud rot caused by Phytophthora palmivora: a destructive emerging disease of oil palm
    • Torres GA, Sarria GA, Martinez G, Varon F, Drenth A, Guest DI. Bud rot caused by Phytophthora palmivora: a destructive emerging disease of oil palm. Phytopathology. 2016;106:320-9. doi: 10.1094/PHYTO-09-15-0243-RVW.
    • (2016) Phytopathology. , vol.106 , pp. 320-329
    • Torres, G.A.1    Sarria, G.A.2    Martinez, G.3    Varon, F.4    Drenth, A.5    Guest, D.I.6
  • 9
    • 84925236395 scopus 로고    scopus 로고
    • Medicago truncatula symbiosis mutants affected in the interaction with a biotrophic root pathogen
    • Rey T, Chatterjee A, Buttay M, Toulotte J, Schornack S. Medicago truncatula symbiosis mutants affected in the interaction with a biotrophic root pathogen. New Phytol. 2015;206:497-500.
    • (2015) New Phytol. , vol.206 , pp. 497-500
    • Rey, T.1    Chatterjee, A.2    Buttay, M.3    Toulotte, J.4    Schornack, S.5
  • 10
    • 84968616020 scopus 로고    scopus 로고
    • Colonization of barley by the broad-host hemibiotrophic pathogen Phytophthora palmivora uncovers a leaf development dependent involvement of MLO
    • Le Fevre R, O'Boyle B, Moscou MJ, Schornack S. Colonization of barley by the broad-host hemibiotrophic pathogen Phytophthora palmivora uncovers a leaf development dependent involvement of MLO. Mol Plant-Microbe Interact. 2016;29:385-95.
    • (2016) Mol Plant-Microbe Interact. , vol.29 , pp. 385-395
    • Fevre, R.1    O'Boyle, B.2    Moscou, M.J.3    Schornack, S.4
  • 11
    • 33646938366 scopus 로고    scopus 로고
    • Defence responses induced by potassium phosphonate in Phytophthora palmivora-challenged Arabidopsis thaliana
    • Daniel R, Guest D. Defence responses induced by potassium phosphonate in Phytophthora palmivora-challenged Arabidopsis thaliana. Physiol Mol Plant Pathol. 2006;67:194-201.
    • (2006) Physiol Mol Plant Pathol. , vol.67 , pp. 194-201
    • Daniel, R.1    Guest, D.2
  • 12
    • 11144348955 scopus 로고    scopus 로고
    • The spores of Phytophthora: weapons of the plant destroyer
    • Judelson HS, Blanco FA. The spores of Phytophthora: weapons of the plant destroyer. Nat Rev Microbiol. 2005;3:47-58.
    • (2005) Nat Rev Microbiol. , vol.3 , pp. 47-58
    • Judelson, H.S.1    Blanco, F.A.2
  • 13
    • 84895476812 scopus 로고    scopus 로고
    • How do filamentous pathogens deliver effector proteins into plant cells?
    • Petre B, Kamoun S. How do filamentous pathogens deliver effector proteins into plant cells? PLoS Biol. 2014;12, e1001801.
    • (2014) PLoS Biol. , vol.12
    • Petre, B.1    Kamoun, S.2
  • 14
    • 33845478792 scopus 로고    scopus 로고
    • Cell biology of plant-oomycete interactions
    • Hardham AR. Cell biology of plant-oomycete interactions. Cell Microbiol. 2007;9:31-9.
    • (2007) Cell Microbiol. , vol.9 , pp. 31-39
    • Hardham, A.R.1
  • 15
    • 13944270713 scopus 로고    scopus 로고
    • Large-scale gene discovery in the oomycete Phytophthora infestans reveals likely components of phytopathogenicity shared with true fungi
    • Randall TA, Dwyer RA, Huitema E, Beyer K, Cvitanich C, Kelkar H, et al. Large-scale gene discovery in the oomycete Phytophthora infestans reveals likely components of phytopathogenicity shared with true fungi. Mol Plant-Microbe Interact. 2005;18:229-43.
    • (2005) Mol Plant-Microbe Interact. , vol.18 , pp. 229-243
    • Randall, T.A.1    Dwyer, R.A.2    Huitema, E.3    Beyer, K.4    Cvitanich, C.5    Kelkar, H.6
  • 16
    • 78650149135 scopus 로고    scopus 로고
    • Genome evolution following host jumps in the Irish potato famine pathogen lineage
    • Raffaele S, Farrer RA, Cano LM, Studholme DJ, MacLean D, Thines M, et al. Genome evolution following host jumps in the Irish potato famine pathogen lineage. Science. 2010;330:1540-3.
    • (2010) Science. , vol.330 , pp. 1540-1543
    • Raffaele, S.1    Farrer, R.A.2    Cano, L.M.3    Studholme, D.J.4    MacLean, D.5    Thines, M.6
  • 17
  • 19
    • 0037963480 scopus 로고    scopus 로고
    • EST mining and functional expression assays identify extracellular effector proteins from the plant pathogen Phytophthora
    • Torto TA, Li S, Styer A, Huitema E, Testa A, Gow NAR, et al. EST mining and functional expression assays identify extracellular effector proteins from the plant pathogen Phytophthora. Genome Res. 2003;13:1675-85.
    • (2003) Genome Res. , vol.13 , pp. 1675-1685
    • Torto, T.A.1    Li, S.2    Styer, A.3    Huitema, E.4    Testa, A.5    Gow, N.A.R.6
  • 21
    • 84881413993 scopus 로고    scopus 로고
    • Pivoting the plant immune system from dissection to deployment
    • Dangl JL, Horvath DM, Staskawicz BJ. Pivoting the plant immune system from dissection to deployment. Science. 2013;341:746-51.
    • (2013) Science. , vol.341 , pp. 746-751
    • Dangl, J.L.1    Horvath, D.M.2    Staskawicz, B.J.3
  • 23
    • 84865706478 scopus 로고    scopus 로고
    • Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L
    • Yang H, Tao Y, Zheng Z, Li C, Sweetingham MW, Howieson JG. Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L. BMC Genomics. 2012;13:318.
    • (2012) BMC Genomics. , vol.13 , pp. 318
    • Yang, H.1    Tao, Y.2    Zheng, Z.3    Li, C.4    Sweetingham, M.W.5    Howieson, J.G.6
  • 24
    • 84871941915 scopus 로고    scopus 로고
    • Homologous RXLR effectors from Hyaloperonospora arabidopsidis and Phytophthora sojae suppress immunity in distantly related plants
    • Anderson RG, Casady MS, Fee RA, Vaughan MM, Deb D, Fedkenheuer K, et al. Homologous RXLR effectors from Hyaloperonospora arabidopsidis and Phytophthora sojae suppress immunity in distantly related plants. Plant J. 2012;72:1-12.
    • (2012) Plant J , vol.72 , pp. 1-12
    • Anderson, R.G.1    Casady, M.S.2    Fee, R.A.3    Vaughan, M.M.4    Deb, D.5    Fedkenheuer, K.6
  • 26
    • 33751100626 scopus 로고    scopus 로고
    • The plant immune system
    • Jones JDG, Dangl JL. The plant immune system. Nature. 2006;444:323-9.
    • (2006) Nature. , vol.444 , pp. 323-329
    • Jones, J.D.G.1    Dangl, J.L.2
  • 27
    • 0027967403 scopus 로고
    • High affinity binding of a fungal oligopeptide elicitor to parsley plasma membranes triggers multiple defense responses
    • Nürnberger T, Nennstiel D, Jabs T, Sacks WR, Hahlbrock K, Scheel D. High affinity binding of a fungal oligopeptide elicitor to parsley plasma membranes triggers multiple defense responses. Cell. 1994;V78:449-60.
    • (1994) Cell. , vol.V78 , pp. 449-460
    • Nürnberger, T.1    Nennstiel, D.2    Jabs, T.3    Sacks, W.R.4    Hahlbrock, K.5    Scheel, D.6
  • 28
    • 0037121933 scopus 로고    scopus 로고
    • Pep-13, a plant defense-inducing pathogen-associated pattern from Phytophthora transglutaminases
    • Brunner F, Rosahl S, Lee J, Rudd JJ, Geiler C, Kauppinen S, et al. Pep-13, a plant defense-inducing pathogen-associated pattern from Phytophthora transglutaminases. EMBO J. 2002;21:6681-8.
    • (2002) EMBO J. , vol.21 , pp. 6681-6688
    • Brunner, F.1    Rosahl, S.2    Lee, J.3    Rudd, J.J.4    Geiler, C.5    Kauppinen, S.6
  • 29
    • 0344630197 scopus 로고    scopus 로고
    • Systemins: a functionally defined family of peptide signals that regulate defensive genes in Solanaceae species
    • Ryan CA, Pearce G. Systemins: a functionally defined family of peptide signals that regulate defensive genes in Solanaceae species. Proc Natl Acad Sci U S A. 2003;100:14577-80.
    • (2003) Proc Natl Acad Sci U S A. , vol.100 , pp. 14577-14580
    • Ryan, C.A.1    Pearce, G.2
  • 30
    • 79251496133 scopus 로고    scopus 로고
    • Post-translational modifications in secreted peptide hormones in plants
    • Matsubayashi Y. Post-translational modifications in secreted peptide hormones in plants. Plant Cell Physiol. 2011;52:5-13.
    • (2011) Plant Cell Physiol. , vol.52 , pp. 5-13
    • Matsubayashi, Y.1
  • 31
    • 84877617233 scopus 로고    scopus 로고
    • Peptides as danger signals: MAMPs and DAMPs
    • In: Irving H, Gehring C, editors. Heidelberg: Springer;
    • Boller T, Flury P. Peptides as danger signals: MAMPs and DAMPs. In: Irving H, Gehring C, editors. Plant signaling peptides. Heidelberg: Springer; 2012. p. 163-81.
    • (2012) Plant signaling peptides , pp. 163-181
    • Boller, T.1    Flury, P.2
  • 32
    • 84907573419 scopus 로고    scopus 로고
    • The secreted peptide PIP1 amplifies immunity through receptor-like kinase 7
    • Hou S, Wang X, Chen D, Yang X, Wang M, Turrà D, et al. The secreted peptide PIP1 amplifies immunity through receptor-like kinase 7. PLoS Pathog. 2014;10, e1004331.
    • (2014) PLoS Pathog. , vol.10
    • Hou, S.1    Wang, X.2    Chen, D.3    Yang, X.4    Wang, M.5    Turrà, D.6
  • 34
    • 33646525169 scopus 로고    scopus 로고
    • Perception of the bacterial PAMP EF-Tu by the receptor EFR restricts Agrobacterium-mediated transformation
    • Zipfel C, Kunze G, Chinchilla D, Caniard A, Jones JDG, Boller T, et al. Perception of the bacterial PAMP EF-Tu by the receptor EFR restricts Agrobacterium-mediated transformation. Cell. 2006;125:749-60.
    • (2006) Cell. , vol.125 , pp. 749-760
    • Zipfel, C.1    Kunze, G.2    Chinchilla, D.3    Caniard, A.4    Jones, J.D.G.5    Boller, T.6
  • 35
    • 0037297262 scopus 로고    scopus 로고
    • GFP-tagging of cell components reveals the dynamics of subcellular re-organization in response to infection of Arabidopsis by oomycete pathogens
    • Takemoto D, Jones DA, Hardham AR. GFP-tagging of cell components reveals the dynamics of subcellular re-organization in response to infection of Arabidopsis by oomycete pathogens. Plant J. 2003;33:775-92.
    • (2003) Plant J. , vol.33 , pp. 775-792
    • Takemoto, D.1    Jones, D.A.2    Hardham, A.R.3
  • 36
    • 15744395163 scopus 로고    scopus 로고
    • The cytoskeleton as a regulator and target of biotic interactions in plants
    • Takemoto D. The cytoskeleton as a regulator and target of biotic interactions in plants. Plant Physiol. 2004;136:3864-76.
    • (2004) Plant Physiol. , vol.136 , pp. 3864-3876
    • Takemoto, D.1
  • 37
    • 27944454718 scopus 로고    scopus 로고
    • Pre- and postinvasion defenses both contribute to nonhost resistance in Arabidopsis
    • Lipka V, Dittgen J, Bednarek P, Bhat R, Wiermer M, Stein M, et al. Pre- and postinvasion defenses both contribute to nonhost resistance in Arabidopsis. Science. 2005;310:1180-3.
    • (2005) Science. , vol.310 , pp. 1180-1183
    • Lipka, V.1    Dittgen, J.2    Bednarek, P.3    Bhat, R.4    Wiermer, M.5    Stein, M.6
  • 39
    • 33646428369 scopus 로고    scopus 로고
    • Multivesicular bodies participate in a cell wall-associated defence response in barley leaves attacked by the pathogenic powdery mildew fungus
    • An Q, Hückelhoven R, Kogel KH, van Bel AJE. Multivesicular bodies participate in a cell wall-associated defence response in barley leaves attacked by the pathogenic powdery mildew fungus. Cell Microbiol. 2006;8:1009-19.
    • (2006) Cell Microbiol. , vol.8 , pp. 1009-1019
    • An, Q.1    Hückelhoven, R.2    Kogel, K.H.3    Bel, A.J.E.4
  • 40
    • 33749989815 scopus 로고    scopus 로고
    • Multivesicular compartments proliferate in susceptible and resistant MLA12-barley leaves in response to infection by the biotrophic powdery mildew fungus
    • An Q, Ehlers K, Kogel KH, Van Bel AJE, Hückelhoven R. Multivesicular compartments proliferate in susceptible and resistant MLA12-barley leaves in response to infection by the biotrophic powdery mildew fungus. New Phytol. 2006;172:563-76.
    • (2006) New Phytol. , vol.172 , pp. 563-576
    • An, Q.1    Ehlers, K.2    Kogel, K.H.3    Bel, A.J.E.4    Hückelhoven, R.5
  • 41
    • 84862811544 scopus 로고    scopus 로고
    • Patterns of plant subcellular responses to successful oomycete infections reveal differences in host cell reprogramming and endocytic trafficking
    • Lu YJ, Schornack S, Spallek T, Geldner N, Chory J, Schellmann S, et al. Patterns of plant subcellular responses to successful oomycete infections reveal differences in host cell reprogramming and endocytic trafficking. Cell Microbiol. 2012;14:682-97.
    • (2012) Cell Microbiol. , vol.14 , pp. 682-697
    • Lu, Y.J.1    Schornack, S.2    Spallek, T.3    Geldner, N.4    Chory, J.5    Schellmann, S.6
  • 42
    • 84988407826 scopus 로고    scopus 로고
    • Modulation of plant RAB GTPase-mediated membrane trafficking pathway at the interface between plants and obligate biotrophic pathogens
    • Inada N, Betsuyaku S, Shimada TL, Ebine K, Ito E, Kutsuna N, et al. Modulation of plant RAB GTPase-mediated membrane trafficking pathway at the interface between plants and obligate biotrophic pathogens. Plant Cell Physiol. 2016;57:1854-64.
    • (2016) Plant Cell Physiol. , vol.57 , pp. 1854-1864
    • Inada, N.1    Betsuyaku, S.2    Shimada, T.L.3    Ebine, K.4    Ito, E.5    Kutsuna, N.6
  • 43
    • 0035983846 scopus 로고    scopus 로고
    • Molecular cloning and characterization of glucanase inhibitor proteins: coevolution of a counterdefense mechanism by plant pathogens
    • Rose JK, Ham KS, Darvill AG, Albersheim P. Molecular cloning and characterization of glucanase inhibitor proteins: coevolution of a counterdefense mechanism by plant pathogens. Plant Cell. 2002;14:1329-45.
    • (2002) Plant Cell. , vol.14 , pp. 1329-1345
    • Rose, J.K.1    Ham, K.S.2    Darvill, A.G.3    Albersheim, P.4
  • 44
    • 2942748298 scopus 로고    scopus 로고
    • A Kazal-like extracellular serine protease inhibitor from Phytophthora infestans targets the tomato pathogenesis-related protease P69B
    • Tian M, Huitema E, Da Cunha L, Torto-Alalibo T, Kamoun S. A Kazal-like extracellular serine protease inhibitor from Phytophthora infestans targets the tomato pathogenesis-related protease P69B. J Biol Chem. 2004;279:26370-7.
    • (2004) J Biol Chem. , vol.279 , pp. 26370-26377
    • Tian, M.1    Huitema, E.2    Cunha, L.3    Torto-Alalibo, T.4    Kamoun, S.5
  • 45
    • 25644432194 scopus 로고    scopus 로고
    • A second Kazal-like protease inhibitor from Phytophthora infestans inhibits and interacts with the apoplastic pathogenesis-related protease P69B of tomato
    • Tian M, Benedetti B, Kamoun S. A second Kazal-like protease inhibitor from Phytophthora infestans inhibits and interacts with the apoplastic pathogenesis-related protease P69B of tomato. Plant Physiol. 2005;138:1785-93.
    • (2005) Plant Physiol. , vol.138 , pp. 1785-1793
    • Tian, M.1    Benedetti, B.2    Kamoun, S.3
  • 46
    • 33846379634 scopus 로고    scopus 로고
    • A Phytophthora infestans cystatin-like protein targets a novel tomato papain-like apoplastic protease
    • Tian M, Win J, Song J, van der Hoorn RAL, van der Knaap E, Kamoun S. A Phytophthora infestans cystatin-like protein targets a novel tomato papain-like apoplastic protease. Plant Physiol. 2007;143:364-77.
    • (2007) Plant Physiol. , vol.143 , pp. 364-377
    • Tian, M.1    Win, J.2    Song, J.3    Hoorn, R.A.L.4    Knaap, E.5    Kamoun, S.6
  • 47
    • 60849124275 scopus 로고    scopus 로고
    • Apoplastic effectors secreted by two unrelated eukaryotic plant pathogens target the tomato defense protease Rcr3
    • Song J, Win J, Tian M, Schornack S, Kaschani F, Ilyas M, et al. Apoplastic effectors secreted by two unrelated eukaryotic plant pathogens target the tomato defense protease Rcr3. Proc Natl Acad Sci U S A. 2009;106:1654-9.
    • (2009) Proc Natl Acad Sci U S A. , vol.106 , pp. 1654-1659
    • Song, J.1    Win, J.2    Tian, M.3    Schornack, S.4    Kaschani, F.5    Ilyas, M.6
  • 48
    • 78649768763 scopus 로고    scopus 로고
    • An effector-targeted protease contributes to defense against Phytophthora infestans and is under diversifying selection in natural hosts
    • Kaschani F, Shabab M, Bozkurt TO, Shindo T, Schornack S, Gu C, et al. An effector-targeted protease contributes to defense against Phytophthora infestans and is under diversifying selection in natural hosts. Plant Physiol. 2010;154:1794-804.
    • (2010) Plant Physiol. , vol.154 , pp. 1794-1804
    • Kaschani, F.1    Shabab, M.2    Bozkurt, T.O.3    Shindo, T.4    Schornack, S.5    Gu, C.6
  • 49
    • 84855489042 scopus 로고    scopus 로고
    • Phytophthora infestans effector AVRblb2 prevents secretion of a plant immune protease at the haustorial interface
    • Bozkurt TO, Schornack S, Win J, Shindo T, Ilyas M, Oliva R, et al. Phytophthora infestans effector AVRblb2 prevents secretion of a plant immune protease at the haustorial interface. Proc Natl Acad Sci. 2011;108:20832-7.
    • (2011) Proc Natl Acad Sci. , vol.108 , pp. 20832-20837
    • Bozkurt, T.O.1    Schornack, S.2    Win, J.3    Shindo, T.4    Ilyas, M.5    Oliva, R.6
  • 50
    • 49449105359 scopus 로고    scopus 로고
    • Nicotiana benthamiana: its history and future as a model for plant-pathogen interactions
    • Goodin MM, Zaitlin D, Naidu RA, Lommel SA. Nicotiana benthamiana: its history and future as a model for plant-pathogen interactions. Mol Plant Microbe Interact. 2008;21:1015-26.
    • (2008) Mol. Plant. Microbe. Interact. , vol.21 , pp. 1015-1026
    • Goodin, M.M.1    Zaitlin, D.2    Naidu, R.A.3    Lommel, S.A.4
  • 51
    • 54049133297 scopus 로고    scopus 로고
    • A novel Phytophthora infestans haustorium-specific membrane protein is required for infection of potato
    • Avrova AO, Boevink PC, Young V, Grenville-Briggs LJ, Van West P, Birch PRJ, et al. A novel Phytophthora infestans haustorium-specific membrane protein is required for infection of potato. Cell Microbiol. 2008;10:2271-84.
    • (2008) Cell Microbiol. , vol.10 , pp. 2271-2284
    • Avrova, A.O.1    Boevink, P.C.2    Young, V.3    Grenville-Briggs, L.J.4    West, P.5    Birch, P.R.J.6
  • 52
    • 0142062036 scopus 로고    scopus 로고
    • Cell cycle regulator Cdc14 is expressed during sporulation but not hyphal growth in the fungus-like oomycete Phytophthora infestans
    • Ah Fong AMV, Judelson HS. Cell cycle regulator Cdc14 is expressed during sporulation but not hyphal growth in the fungus-like oomycete Phytophthora infestans. Mol Microbiol. 2003;50:487-94.
    • (2003) Mol Microbiol. , vol.50 , pp. 487-494
    • Ah Fong, A.M.V.1    Judelson, H.S.2
  • 54
    • 85019163248 scopus 로고    scopus 로고
    • Assessing the read content of the transcriptome assembly
    • Haas BJ. Assessing the read content of the transcriptome assembly. 2016. https://github.com/trinityrnaseq/trinityrnaseq/wiki/RNA-Seq-Read-Representation-by-Trinity-Assembly.
    • (2016)
    • Haas, B.J.1
  • 56
    • 84905266073 scopus 로고    scopus 로고
    • Profiling the secretome and extracellular proteome of the potato late blight pathogen Phytophthora infestans
    • Meijer HJG, Mancuso FM, Espadas G, Seidl MF, Chiva C, Govers F, et al. Profiling the secretome and extracellular proteome of the potato late blight pathogen Phytophthora infestans. Mol Cell Proteomics. 2014. doi: 10.1074/mcp.M113.035873.
    • (2014) Mol Cell Proteomics
    • Meijer, H.J.G.1    Mancuso, F.M.2    Espadas, G.3    Seidl, M.F.4    Chiva, C.5    Govers, F.6
  • 57
    • 84880266648 scopus 로고    scopus 로고
    • De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
    • Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013;8:1494-512.
    • (2013) Nat Protoc. , vol.8 , pp. 1494-1512
    • Haas, B.J.1    Papanicolaou, A.2    Yassour, M.3    Grabherr, M.4    Blood, P.D.5    Bowden, J.6
  • 58
    • 0031603460 scopus 로고    scopus 로고
    • Prediction of signal peptides and signal anchors by a hidden Markov model
    • Nielsen H, Krogh A. Prediction of signal peptides and signal anchors by a hidden Markov model. Intell Syst Mol Biol. 1998;6:122-30.
    • (1998) Intell Syst Mol Biol. , vol.6 , pp. 122-130
    • Nielsen, H.1    Krogh, A.2
  • 59
    • 3042521098 scopus 로고    scopus 로고
    • Improved prediction of signal peptides: SignalP 3.0
    • Bendtsen JD, Nielsen H, Von Heijne G, Brunak S. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol. 2004;340:783-95.
    • (2004) J Mol Biol , vol.340 , pp. 783-795
    • Bendtsen, J.D.1    Nielsen, H.2    Heijne, G.3    Brunak, S.4
  • 60
    • 34248531753 scopus 로고    scopus 로고
    • Locating proteins in the cell using TargetP, SignalP and related tools
    • Emanuelsson O, Brunak S, von Heijne G, Nielsen H. Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc. 2007;2:953-71.
    • (2007) Nat Protoc. , vol.2 , pp. 953-971
    • Emanuelsson, O.1    Brunak, S.2    Heijne, G.3    Nielsen, H.4
  • 61
    • 78149494002 scopus 로고    scopus 로고
    • Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora infestans
    • Raffaele S, Win J, Cano LM, Kamoun S. Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora infestans. BMC Genomics. 2010;11:637.
    • (2010) BMC Genomics. , vol.11 , pp. 637
    • Raffaele, S.1    Win, J.2    Cano, L.M.3    Kamoun, S.4
  • 62
    • 84954047945 scopus 로고    scopus 로고
    • Evaluation of secretion prediction highlights differing approaches needed for oomycete and fungal effectors
    • Sperschneider J, Williams AH, Hane JK, Singh KB, Taylor JM. Evaluation of secretion prediction highlights differing approaches needed for oomycete and fungal effectors. Front Plant Sci. 2015;6:1-14.
    • (2015) Front Plant Sci. , vol.6 , pp. 1-14
    • Sperschneider, J.1    Williams, A.H.2    Hane, J.K.3    Singh, K.B.4    Taylor, J.M.5
  • 63
    • 61349097249 scopus 로고    scopus 로고
    • Distinct amino acids of the Phytophthora infestans effector AVR3a condition activation of R3a hypersensitivity and suppression of cell death
    • Bos JIB, Chaparro-Garcia A, Quesada-Ocampo LM, McSpadden Gardener BB, Kamoun S. Distinct amino acids of the Phytophthora infestans effector AVR3a condition activation of R3a hypersensitivity and suppression of cell death. Mol Plant-Microbe Interact. 2009;22:269-81.
    • (2009) Mol Plant-Microbe Interact. , vol.22 , pp. 269-281
    • Bos, J.I.B.1    Chaparro-Garcia, A.2    Quesada-Ocampo, L.M.3    McSpadden Gardener, B.B.4    Kamoun, S.5
  • 64
    • 84966340234 scopus 로고    scopus 로고
    • Transposons to toxins: the provenance, architecture and diversification of a widespread class of eukaryotic effectors
    • Zhang D, Burroughs AM, Vidal ND, Iyer LM, Aravind L. Transposons to toxins: the provenance, architecture and diversification of a widespread class of eukaryotic effectors. Nucleic Acids Res. 2016;44:3513-33.
    • (2016) Nucleic Acids Res. , vol.44 , pp. 3513-3533
    • Zhang, D.1    Burroughs, A.M.2    Vidal, N.D.3    Iyer, L.M.4    Aravind, L.5
  • 65
    • 84866181996 scopus 로고    scopus 로고
    • The Irish potato famine pathogen Phytophthora infestans translocates the CRN8 kinase into host plant cells
    • van Damme M, Bozkurt TO, Cakir C, Schornack S, Sklenar J, Jones AME, et al. The Irish potato famine pathogen Phytophthora infestans translocates the CRN8 kinase into host plant cells. PLoS Pathog. 2012;8, e1002875.
    • (2012) PLoS Pathog. , vol.8
    • Damme, M.1    Bozkurt, T.O.2    Cakir, C.3    Schornack, S.4    Sklenar, J.5    Jones, A.M.E.6
  • 66
    • 84868523263 scopus 로고    scopus 로고
    • The unique architecture and function of cellulose-interacting proteins in oomycetes revealed by genomic and structural analyses
    • Larroque M, Barriot R, Bottin A, Barre A, Rougé P, Dumas B, et al. The unique architecture and function of cellulose-interacting proteins in oomycetes revealed by genomic and structural analyses. BMC Genomics. 2012;13:605.
    • (2012) BMC Genomics. , vol.13 , pp. 605
    • Larroque, M.1    Barriot, R.2    Bottin, A.3    Barre, A.4    Rougé, P.5    Dumas, B.6
  • 67
    • 84912117998 scopus 로고    scopus 로고
    • A conserved peptide pattern from a widespread microbial virulence factor triggers pattern-induced immunity in Arabidopsis
    • Böhm H, Albert I, Oome S, Raaymakers TM, Van den Ackerveken G, Nürnberger T. A conserved peptide pattern from a widespread microbial virulence factor triggers pattern-induced immunity in Arabidopsis. PLoS Pathog. 2014;10.
    • (2014) PLoS Pathog , pp. 10
    • Böhm, H.1    Albert, I.2    Oome, S.3    Raaymakers, T.M.4    Van den Ackerveken, G.5    Nürnberger, T.6
  • 68
    • 84897113991 scopus 로고    scopus 로고
    • Discovery and characterization of a new family of lytic polysaccharide monooxygenases
    • Hemsworth GR, Henrissat B, Davies GJ, Walton PH. Discovery and characterization of a new family of lytic polysaccharide monooxygenases. Nat Chem Biol. 2013;10:122-6.
    • (2013) Nat Chem Biol. , vol.10 , pp. 122-126
    • Hemsworth, G.R.1    Henrissat, B.2    Davies, G.J.3    Walton, P.H.4
  • 69
    • 61349177268 scopus 로고    scopus 로고
    • Mfuzz: a software package for soft clustering of microarray data
    • Kumar L, Futschik ME. Mfuzz: a software package for soft clustering of microarray data. Bioinformation. 2007;2:5-7.
    • (2007) Bioinformation. , vol.2 , pp. 5-7
    • Kumar, L.1    Futschik, M.E.2
  • 70
    • 68149091291 scopus 로고    scopus 로고
    • The Xanthomonas campestris pv. vesicatoria type III effector protein XopJ inhibits protein secretion: evidence for interference with cell wall-associated defense responses
    • Bartetzko V, Sonnewald S, Vogel F, Hartner K, Stadler R, Hammes UZ, et al. The Xanthomonas campestris pv. vesicatoria type III effector protein XopJ inhibits protein secretion: evidence for interference with cell wall-associated defense responses. Mol Plant Microbe Interact. 2009;22:655-64.
    • (2009) Mol Plant Microbe Interact , vol.22 , pp. 655-664
    • Bartetzko, V.1    Sonnewald, S.2    Vogel, F.3    Hartner, K.4    Stadler, R.5    Hammes, U.Z.6
  • 71
    • 79551573467 scopus 로고    scopus 로고
    • The receptor-like kinase SERK3/BAK1 is required for basal resistance against the late blight pathogen Phytophthora infestans in Nicotiana benthamiana
    • Chaparro-Garcia A, Wilkinson RC, Gimenez-Ibanez S, Findlay K, Coffey MD, Zipfel C, et al. The receptor-like kinase SERK3/BAK1 is required for basal resistance against the late blight pathogen Phytophthora infestans in Nicotiana benthamiana. PLoS One. 2011;6:1-10.
    • (2011) PLoS One. , vol.6 , pp. 1-10
    • Chaparro-Garcia, A.1    Wilkinson, R.C.2    Gimenez-Ibanez, S.3    Findlay, K.4    Coffey, M.D.5    Zipfel, C.6
  • 72
    • 84976899061 scopus 로고    scopus 로고
    • PlantPAN 2.0: an update of Plant Promoter Analysis Navigator for reconstructing transcriptional regulatory networks in plants
    • Chow CN, Zheng HQ, Wu NY, Chien CH, Da Huang H, Lee TY, et al. PlantPAN 2.0: an update of Plant Promoter Analysis Navigator for reconstructing transcriptional regulatory networks in plants. Nucleic Acids Res. 2016;44:D1154-64.
    • (2016) Nucleic Acids Res , vol.44 , pp. D1154-D1164
    • Chow, C.N.1    Zheng, H.Q.2    Wu, N.Y.3    Chien, C.H.4    Huang, H.5    Lee, T.Y.6
  • 74
    • 84994028277 scopus 로고    scopus 로고
    • Transcriptomic crosstalk between fungal invasive pathogens and their host cells: opportunities and challenges for next-generation sequencing methods
    • Enguita F, Costa M, Fusco-Almeida A, Mendes-Giannini M, Leitão A. Transcriptomic crosstalk between fungal invasive pathogens and their host cells: opportunities and challenges for next-generation sequencing methods. J Fungi. 2016;2:7.
    • (2016) J Fungi. , vol.2 , pp. 7
    • Enguita, F.1    Costa, M.2    Fusco-Almeida, A.3    Mendes-Giannini, M.4    Leitão, A.5
  • 75
    • 34249848751 scopus 로고    scopus 로고
    • CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes
    • Parra G, Bradnam K, Korf I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics. 2007;23:1061-7.
    • (2007) Bioinformatics. , vol.23 , pp. 1061-1067
    • Parra, G.1    Bradnam, K.2    Korf, I.3
  • 76
    • 84978175047 scopus 로고    scopus 로고
    • Sequencing of the litchi downy blight pathogen reveals it is a Phytophthora species with downy mildew-like characteristics
    • Ye W. Sequencing of the litchi downy blight pathogen reveals it is a Phytophthora species with downy mildew-like characteristics. Mol Plant-Microbe Interact. 2015;29:573-83.
    • (2015) Mol Plant-Microbe Interact. , vol.29 , pp. 573-583
    • Ye, W.1
  • 78
    • 84960116072 scopus 로고    scopus 로고
    • Dual RNA-sequencing of Eucalyptus nitens during Phytophthora cinnamomi challenge reveals pathogen and host factors influencing compatibility
    • Meyer FE, Shuey LS, Naidoo S, Mamni T, Berger DK, Myburg AA, et al. Dual RNA-sequencing of Eucalyptus nitens during Phytophthora cinnamomi challenge reveals pathogen and host factors influencing compatibility. Front Plant Sci. 2016;7:191.
    • (2016) Front Plant Sci. , vol.7 , pp. 191
    • Meyer, F.E.1    Shuey, L.S.2    Naidoo, S.3    Mamni, T.4    Berger, D.K.5    Myburg, A.A.6
  • 79
    • 84865693932 scopus 로고    scopus 로고
    • Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses
    • O'Connell RJ, Thon MR, Hacquard S, Amyotte SG, Kleemann J, Torres MF, et al. Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses. Nat Genet. 2012;44:1060-5.
    • (2012) Nat Genet. , vol.44 , pp. 1060-1065
    • O'Connell, R.J.1    Thon, M.R.2    Hacquard, S.3    Amyotte, S.G.4    Kleemann, J.5    Torres, M.F.6
  • 80
    • 84903244141 scopus 로고    scopus 로고
    • Transcriptome dynamics of Arabidopsis thaliana root penetration by the oomycete pathogen Phytophthora parasitica
    • Attard A, Evangelisti E, Kebdani-Minet N, Panabières F, Deleury E, Maggio C, et al. Transcriptome dynamics of Arabidopsis thaliana root penetration by the oomycete pathogen Phytophthora parasitica. BMC Genomics. 2014;15:538.
    • (2014) BMC Genomics. , vol.15 , pp. 538
    • Attard, A.1    Evangelisti, E.2    Kebdani-Minet, N.3    Panabières, F.4    Deleury, E.5    Maggio, C.6
  • 81
    • 81255211684 scopus 로고    scopus 로고
    • Digital gene expression profiling of the Phytophthora sojae transcriptome
    • Ye W, Wang X, Tao K, Lu Y, Dai T, Dong S, et al. Digital gene expression profiling of the Phytophthora sojae transcriptome. Mol Plant-Microbe Interact. 2011;24:1530-9.
    • (2011) Mol Plant-Microbe Interact. , vol.24 , pp. 1530-1539
    • Ye, W.1    Wang, X.2    Tao, K.3    Lu, Y.4    Dai, T.5    Dong, S.6
  • 82
    • 84868288164 scopus 로고    scopus 로고
    • Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis
    • Windram O, Madhou P, McHattie S, Hill C, Hickman R, Cooke E, et al. Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis. Plant Cell. 2012;24:3530-57.
    • (2012) Plant Cell. , vol.24 , pp. 3530-3557
    • Windram, O.1    Madhou, P.2    McHattie, S.3    Hill, C.4    Hickman, R.5    Cooke, E.6
  • 83
    • 77955534958 scopus 로고    scopus 로고
    • Age-related resistance of Nicotiana benthamiana against hemibiotrophic pathogen Phytophthora infestans requires both ethylene- and salicylic acid-mediated signaling pathways
    • Shibata Y, Kawakita K, Takemoto D. Age-related resistance of Nicotiana benthamiana against hemibiotrophic pathogen Phytophthora infestans requires both ethylene- and salicylic acid-mediated signaling pathways. Mol Plant-Microbe Interact. 2010;23:1130-42.
    • (2010) Mol Plant-Microbe Interact. , vol.23 , pp. 1130-1142
    • Shibata, Y.1    Kawakita, K.2    Takemoto, D.3
  • 84
    • 84897537533 scopus 로고    scopus 로고
    • Suppression of the auxin response pathway enhances susceptibility to Phytophthora cinnamomi while phosphite-mediated resistance stimulates the auxin signalling pathway
    • Eshraghi L, Anderson JP, Aryamanesh N, McComb JA, Shearer B, Hardy GSJE. Suppression of the auxin response pathway enhances susceptibility to Phytophthora cinnamomi while phosphite-mediated resistance stimulates the auxin signalling pathway. BMC Plant Biol. 2014;14:68.
    • (2014) BMC Plant Biol. , vol.14 , pp. 68
    • Eshraghi, L.1    Anderson, J.P.2    Aryamanesh, N.3    McComb, J.A.4    Shearer, B.5    Hardy, G.S.J.E.6
  • 85
    • 77956643905 scopus 로고    scopus 로고
    • NtKTI1, a Kunitz trypsin inhibitor with antifungal activity from Nicotiana tabacum, plays an important role in tobacco's defense response
    • Huang H, Qi SD, Qi F, Wu CA, Yang GD, Zheng CC. NtKTI1, a Kunitz trypsin inhibitor with antifungal activity from Nicotiana tabacum, plays an important role in tobacco's defense response. FEBS J. 2010;277:4076-88.
    • (2010) FEBS J. , vol.277 , pp. 4076-4088
    • Huang, H.1    Qi, S.D.2    Qi, F.3    Wu, C.A.4    Yang, G.D.5    Zheng, C.C.6
  • 86
    • 84855683101 scopus 로고    scopus 로고
    • Chitin, chitinase responses, and invasive fungal infections
    • Vega K, Kalkum M. Chitin, chitinase responses, and invasive fungal infections. Int J Microbiol. 2012;2012:920459.
    • (2012) Int J Microbiol. , vol.2012 , pp. 920459
    • Vega, K.1    Kalkum, M.2
  • 87
    • 70349983777 scopus 로고    scopus 로고
    • Kunitz trypsin inhibitor: an antagonist of cell death triggered by phytopathogens and fumonisin B1 in Arabidopsis
    • Li J, Brader G, Palva ET. Kunitz trypsin inhibitor: an antagonist of cell death triggered by phytopathogens and fumonisin B1 in Arabidopsis. Mol Plant. 2008;1:482-95.
    • (2008) Mol Plant. , vol.1 , pp. 482-495
    • Li, J.1    Brader, G.2    Palva, E.T.3
  • 88
    • 0041320812 scopus 로고    scopus 로고
    • Phenylpropanoid compounds and disease resistance in transgenic tobacco with altered expression of l-phenylalanine ammonia-lyase
    • Shadle GL, Wesley SV, Korth KL, Chen F, Lamb C, Dixon RA. Phenylpropanoid compounds and disease resistance in transgenic tobacco with altered expression of l-phenylalanine ammonia-lyase. Phytochemistry. 2003;64:153-61.
    • (2003) Phytochemistry. , vol.64 , pp. 153-161
    • Shadle, G.L.1    Wesley, S.V.2    Korth, K.L.3    Chen, F.4    Lamb, C.5    Dixon, R.A.6
  • 89
    • 84907371422 scopus 로고    scopus 로고
    • The role of the secondary cell wall in plant resistance to pathogens
    • Miedes E, Vanholme R, Boerjan W, Molina A. The role of the secondary cell wall in plant resistance to pathogens. Front Plant Sci. 2014;5:358.
    • (2014) Front Plant Sci. , vol.5 , pp. 358
    • Miedes, E.1    Vanholme, R.2    Boerjan, W.3    Molina, A.4
  • 90
    • 84894263733 scopus 로고    scopus 로고
    • Exogenous trehalose induces defenses in wheat before and during a biotic stress caused by powdery mildew
    • Tayeh C, Randoux B, Vincent D, Bourdon N, Reignault P. Exogenous trehalose induces defenses in wheat before and during a biotic stress caused by powdery mildew. Phytopathology. 2014;104:293-305.
    • (2014) Phytopathology. , vol.104 , pp. 293-305
    • Tayeh, C.1    Randoux, B.2    Vincent, D.3    Bourdon, N.4    Reignault, P.5
  • 91
    • 39749103413 scopus 로고    scopus 로고
    • Trehalose: protector of antioxidant enzymes or reactive oxygen species scavenger under heat stress?
    • Luo Y, Li WM, Wang W. Trehalose: protector of antioxidant enzymes or reactive oxygen species scavenger under heat stress? Environ Exp Bot. 2008;63:378-84.
    • (2008) Environ Exp Bot. , vol.63 , pp. 378-384
    • Luo, Y.1    Li, W.M.2    Wang, W.3
  • 92
    • 0030060164 scopus 로고    scopus 로고
    • Biosynthesis of the sesquiterpenic phytoalexin capsidiol in elicited root cultures of chili pepper (Capsicum annuum)
    • Chávez-Moctezuma MP, Lozoya-Gloria E. Biosynthesis of the sesquiterpenic phytoalexin capsidiol in elicited root cultures of chili pepper (Capsicum annuum). Plant Cell Rep. 1996;15:360-6.
    • (1996) Plant Cell Rep. , vol.15 , pp. 360-366
    • Chávez-Moctezuma, M.P.1    Lozoya-Gloria, E.2
  • 93
    • 0030433553 scopus 로고    scopus 로고
    • Capsidiol: its role in the resistance of Capsicum annuum to Phytophthora capsici
    • Egea C, Alcázar MD, Candela ME. Capsidiol: its role in the resistance of Capsicum annuum to Phytophthora capsici. Physiol Plant. 1996;98:737-42.
    • (1996) Physiol Plant. , vol.98 , pp. 737-742
    • Egea, C.1    Alcázar, M.D.2    Candela, M.E.3
  • 95
    • 84907329113 scopus 로고    scopus 로고
    • The ubiquitous distribution of late embryogenesis abundant proteins across cell compartments in Arabidopsis offers tailored protection against abiotic stress
    • Candat A, Paszkiewicz G, Neveu M, Gautier R, Logan DC, Avelange-Macherel M-H, et al. The ubiquitous distribution of late embryogenesis abundant proteins across cell compartments in Arabidopsis offers tailored protection against abiotic stress. Plant Cell. 2014;26:3148-66.
    • (2014) Plant Cell. , vol.26 , pp. 3148-3166
    • Candat, A.1    Paszkiewicz, G.2    Neveu, M.3    Gautier, R.4    Logan, D.C.5    Avelange-Macherel, M.-H.6
  • 97
    • 84960120750 scopus 로고    scopus 로고
    • Comparative RNA-Seq analysis of Nicotiana benthamiana in response to Phytophthora parasitica infection
    • Shen D, Chai C, Ma L, Zhang M, Dou D. Comparative RNA-Seq analysis of Nicotiana benthamiana in response to Phytophthora parasitica infection. Plant Growth Regul. 2016;80:59-67.
    • (2016) Plant Growth Regul. , vol.80 , pp. 59-67
    • Shen, D.1    Chai, C.2    Ma, L.3    Zhang, M.4    Dou, D.5
  • 99
    • 84908430805 scopus 로고    scopus 로고
    • Detection of the virulent form of AVR3a from Phytophthora infestans following artificial evolution of potato resistance gene R3a
    • Chapman S, Stevens LJ, Boevink PC, Engelhardt S, Alexander CJ, Harrower B, et al. Detection of the virulent form of AVR3a from Phytophthora infestans following artificial evolution of potato resistance gene R3a. PLoS One. 2014;9, e110158.
    • (2014) PLoS One. , vol.9
    • Chapman, S.1    Stevens, L.J.2    Boevink, P.C.3    Engelhardt, S.4    Alexander, C.J.5    Harrower, B.6
  • 102
    • 84995572472 scopus 로고    scopus 로고
    • Transcriptome responses of an ungrafted Phytophthora root rot tolerant avocado (Persea americana) rootstock to flooding and Phytophthora cinnamomi
    • Reeksting BJ, Olivier NA, van den Berg N. Transcriptome responses of an ungrafted Phytophthora root rot tolerant avocado (Persea americana) rootstock to flooding and Phytophthora cinnamomi. BMC Plant Biol. 2016;16:205.
    • (2016) BMC Plant Biol. , vol.16 , pp. 205
    • Reeksting, B.J.1    Olivier, N.A.2    Berg, N.3
  • 103
    • 84939605702 scopus 로고    scopus 로고
    • Peptides take centre stage in plant signalling
    • Simon R, Dresselhaus T. Peptides take centre stage in plant signalling. J Exp Bot. 2015;66:5135-8.
    • (2015) J Exp Bot. , vol.66 , pp. 5135-5138
    • Simon, R.1    Dresselhaus, T.2
  • 104
    • 84939638981 scopus 로고    scopus 로고
    • The IDA/IDA-LIKE and PIP/PIP-LIKE gene families in Arabidopsis: phylogenetic relationship, expression patterns, and transcriptional effect of the PIPL3 peptide
    • Vie AK, Najafi J, Liu B, Winge P, Butenko MA, Hornslien KS, et al. The IDA/IDA-LIKE and PIP/PIP-LIKE gene families in Arabidopsis: phylogenetic relationship, expression patterns, and transcriptional effect of the PIPL3 peptide. J Exp Bot. 2015;66:5351-65.
    • (2015) J Exp Bot. , vol.66 , pp. 5351-5365
    • Vie, A.K.1    Najafi, J.2    Liu, B.3    Winge, P.4    Butenko, M.A.5    Hornslien, K.S.6
  • 105
    • 77954148870 scopus 로고    scopus 로고
    • The immediate activation of defense responses in Arabidopsis roots is not sufficient to prevent Phytophthora parasitica infection
    • Attard A, Gourgues M, Callemeyn-Torre N, Keller H. The immediate activation of defense responses in Arabidopsis roots is not sufficient to prevent Phytophthora parasitica infection. New Phytol. 2010;187:449-60.
    • (2010) New Phytol. , vol.187 , pp. 449-460
    • Attard, A.1    Gourgues, M.2    Callemeyn-Torre, N.3    Keller, H.4
  • 106
    • 0004026274 scopus 로고
    • Biometry: the principles and practices of statistics in biological research
    • New York: W. H. Freeman;
    • Sokal RR, Rohlf FJ. Biometry: the principles and practices of statistics in biological research. New York: W. H. Freeman; 1995.
    • (1995)
  • 107
    • 46049108350 scopus 로고    scopus 로고
    • BatchPrimer3: a high throughput web application for PCR and sequencing primer design
    • You FM, Huo N, Gu YQ, Luo M-C, Ma Y, Hane D, et al. BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinformatics. 2008;9:253.
    • (2008) BMC Bioinformatics. , vol.9 , pp. 253
    • You, F.M.1    Huo, N.2    Gu, Y.Q.3    Luo, M.-C.4    Ma, Y.5    Hane, D.6
  • 108
    • 33646365324 scopus 로고    scopus 로고
    • Selection of internal control genes for real-time quantitative RT-PCR assays in the oomycete plant pathogen Phytophthora parasitica
    • Yan HZ, Liou RF. Selection of internal control genes for real-time quantitative RT-PCR assays in the oomycete plant pathogen Phytophthora parasitica. Fungal Genet Biol. 2006;43:430-8.
    • (2006) Fungal Genet Biol. , vol.43 , pp. 430-438
    • Yan, H.Z.1    Liou, R.F.2
  • 109
    • 84867005296 scopus 로고    scopus 로고
    • Validation of reference genes for gene expression studies in virus-infected Nicotiana benthamiana using quantitative real-time PCR
    • Liu D, Shi L, Han C, Yu J, Li D, Zhang Y. Validation of reference genes for gene expression studies in virus-infected Nicotiana benthamiana using quantitative real-time PCR. PLoS One. 2012;7, e46451.
    • (2012) PLoS One. , vol.7
    • Liu, D.1    Shi, L.2    Han, C.3    Yu, J.4    Li, D.5    Zhang, Y.6
  • 110
    • 34248653184 scopus 로고    scopus 로고
    • Rapid, transient expression of fluorescent fusion proteins in tobacco plants and generation of stably transformed plants
    • Sparkes IA, Runions J, Kearns A, Hawes C. Rapid, transient expression of fluorescent fusion proteins in tobacco plants and generation of stably transformed plants. Nat Protoc. 2006;1:2019-25.
    • (2006) Nat Protoc. , vol.1 , pp. 2019-2025
    • Sparkes, I.A.1    Runions, J.2    Kearns, A.3    Hawes, C.4
  • 111
    • 80255127234 scopus 로고    scopus 로고
    • Cutadapt removes adapter sequences from high-throughput sequencing reads
    • Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17:10-2.
    • (2011) EMBnet J. , vol.17 , pp. 10-12
    • Martin, M.1
  • 112
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14:R36.
    • (2013) Genome Biol. , vol.14 , pp. R36
    • Kim, D.1    Pertea, G.2    Trapnell, C.3    Pimentel, H.4    Kelley, R.5    Salzberg, S.L.6
  • 113
    • 0034697980 scopus 로고    scopus 로고
    • Predicting subcellular localization of proteins based on their N-terminal amino acid sequence
    • Emanuelsson O, Nielsen H, Brunak S, von Heijne G. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol. 2000;300:1005-16.
    • (2000) J Mol Biol. , vol.300 , pp. 1005-1016
    • Emanuelsson, O.1    Nielsen, H.2    Brunak, S.3    Heijne, G.4
  • 114
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes
    • Krogh A, Larsson B, von Heijne G, Sonnhammer ELL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001;305:567-80.
    • (2001) J Mol Biol. , vol.305 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    Heijne, G.3    Sonnhammer, E.L.L.4
  • 115
    • 0037339919 scopus 로고    scopus 로고
    • KDEL and KKXX retrieval signals appended to the same reporter protein determine different trafficking between endoplasmic reticulum, intermediate compartment, and Golgi complex
    • Stornaiuolo M. KDEL and KKXX retrieval signals appended to the same reporter protein determine different trafficking between endoplasmic reticulum, intermediate compartment, and Golgi complex. Mol Biol Cell. 2003;14:2372-84.
    • (2003) Mol Biol Cell. , vol.14 , pp. 2372-2384
    • Stornaiuolo, M.1
  • 116
    • 0034800374 scopus 로고    scopus 로고
    • InterProScan - an integration platform for the signature-recognition methods in InterPro
    • Zdobnov EM, Apweiler R. InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinformatics. 2001;17:847-8.
    • (2001) Bioinformatics. , vol.17 , pp. 847-848
    • Zdobnov, E.M.1    Apweiler, R.2
  • 117
    • 67650718130 scopus 로고    scopus 로고
    • NLStradamus: a simple hidden Markov model for nuclear localization signal prediction
    • Nguyen Ba AN, Pogoutse A, Provart N, Moses AM. NLStradamus: a simple hidden Markov model for nuclear localization signal prediction. BMC Bioinformatics. 2009;10:202.
    • (2009) BMC Bioinformatics. , vol.10 , pp. 202
    • Nguyen Ba, A.N.1    Pogoutse, A.2    Provart, N.3    Moses, A.M.4
  • 118
    • 0034331073 scopus 로고    scopus 로고
    • Finding nuclear localization signals
    • Cokol M, Nair R, Rost B. Finding nuclear localization signals. EMBO Rep. 2000;1:411-5.
    • (2000) EMBO Rep. , vol.1 , pp. 411-415
    • Cokol, M.1    Nair, R.2    Rost, B.3
  • 119
    • 84904815625 scopus 로고    scopus 로고
    • SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information
    • Biasini M, Bienert S, Waterhouse A, Arnold K, Studer G, Schmidt T, et al. SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res. 2014;42:252-8.
    • (2014) Nucleic Acids Res. , vol.42 , pp. 252-258
    • Biasini, M.1    Bienert, S.2    Waterhouse, A.3    Arnold, K.4    Studer, G.5    Schmidt, T.6
  • 120
    • 79961123152 scopus 로고    scopus 로고
    • RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
    • Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011;12:323.
    • (2011) BMC Bioinformatics. , vol.12 , pp. 323
    • Li, B.1    Dewey, C.N.2
  • 121
    • 77953176036 scopus 로고    scopus 로고
    • A scaling normalization method for differential expression analysis of RNA-seq data
    • Robinson MD, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 2010;11:R25.
    • (2010) Genome Biol. , vol.11 , pp. R25
    • Robinson, M.D.1    Oshlack, A.2
  • 122
    • 77749296886 scopus 로고    scopus 로고
    • ggplot2: elegant graphics for data analysis
    • New York: Springer;
    • Wickham H. ggplot2: elegant graphics for data analysis. New York: Springer; 2009.
    • (2009)
    • Wickham, H.1
  • 123
    • 84889095368 scopus 로고    scopus 로고
    • pheatmap: Pretty Heatmaps
    • Raivo K. pheatmap: Pretty Heatmaps. 2013. https://cran.r-project.org/web/packages/pheatmap/index.html.
    • (2013)
    • Raivo, K.1
  • 124
    • 84942863877 scopus 로고    scopus 로고
    • Venn diagrams in R with the Vennerable package
    • Swinton J. Venn diagrams in R with the Vennerable package. 2013. https://github.com/js229/Vennerable.
    • (2013)
    • Swinton, J.1
  • 125
    • 84974694271 scopus 로고    scopus 로고
    • cluster: cluster analysis basics and extensions
    • R package version 2.0.5.
    • Maechler M, Rousseeuw P, Struyf A, Hubert M, Hornik K. cluster: cluster analysis basics and extensions. R package version 2.0.5. 2016.
    • (2016)
    • Maechler, M.1    Rousseeuw, P.2    Struyf, A.3    Hubert, M.4    Hornik, K.5
  • 127
    • 84155170296 scopus 로고    scopus 로고
    • topGO: enrichment analysis for Gene Ontology
    • Alexa A, Rahnenfuhrer J. topGO: enrichment analysis for Gene Ontology. 2010. http://www.bioconductor.org/packages/release/bioc/html/topGO.html.
    • (2010)
    • Alexa, A.1    Rahnenfuhrer, J.2
  • 128
    • 79960610118 scopus 로고    scopus 로고
    • Revigo summarizes and visualizes long lists of gene ontology terms
    • Supek F, Bošnjak M, Škunca N, Šmuc T. Revigo summarizes and visualizes long lists of gene ontology terms. PLoS One. 2011;6. https://doi.org/ 10.1371/journal.pone.0021800.
    • (2011) PLoS One. , vol.6
    • Supek, F.1    Bošnjak, M.2    Škunca, N.3    Šmuc, T.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.