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Volumn 29, Issue 11, 2012, Pages 3371-3384

In silico characterization and molecular evolutionary analysis of a novel superfamily of fungal effector proteins

Author keywords

adaptive evolution; birth and death; diversification; effectors; fungi; GH18 chitinases

Indexed keywords

ECP2 PROTEIN; FUNGAL PROTEIN; GLYCOSIDASE; HCE2 PROTEIN; UNCLASSIFIED DRUG;

EID: 84867820378     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mss143     Document Type: Article
Times cited : (79)

References (58)
  • 1
    • 79951945582 scopus 로고    scopus 로고
    • Dissecting the effect of a heterogeneous environment on the interaction between host and parasite fitness traits
    • Allen D, Little T. 2011. Dissecting the effect of a heterogeneous environment on the interaction between host and parasite fitness traits. Evol Ecol. 25:499-508.
    • (2011) Evol Ecol , vol.25 , pp. 499-508
    • Allen, D.1    Little, T.2
  • 2
    • 33747823564 scopus 로고    scopus 로고
    • MEME: Discovering and analyzing DNA and protein sequence motifs
    • Bailey TL, Williams N, Misleh C, Li WW. 2006. MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res. 34: W369-W373.
    • (2006) Nucleic Acids Res , vol.34
    • Bailey, T.L.1    Williams, N.2    Misleh, C.3    Li, W.W.4
  • 3
    • 51549107755 scopus 로고    scopus 로고
    • A review of fungal phytotoxins: From basic studies to practical use
    • Berestetskiy A. 2008. A review of fungal phytotoxins: from basic studies to practical use. Appl Biochem Microbiol. 44:453-465.
    • (2008) Appl Biochem Microbiol , vol.44 , pp. 453-465
    • Berestetskiy, A.1
  • 5
    • 79960957443 scopus 로고    scopus 로고
    • Multiple translocation of the AVR-Pita effector gene among chromosomes of the rice blast fungus Magnaporthe oryzae and related species
    • (12 co-authors)
    • Chuma I, Isobe C, Hotta Y, et al. (12 co-authors). 2011. Multiple translocation of the AVR-Pita effector gene among chromosomes of the rice blast fungus Magnaporthe oryzae and related species. PLoS Pathog. 7:e1002147.
    • (2011) PLoS Pathog , vol.7
    • Chuma, I.1    Isobe, C.2    Hotta, Y.3
  • 6
    • 56549119570 scopus 로고    scopus 로고
    • Turning a hobby into a job: How duplicated genes find new functions
    • Conant GC,Wolfe KH. 2008. Turning a hobby into a job: how duplicated genes find new functions. Nat Rev Genet. 9:938-950.
    • (2008) Nat Rev Genet , vol.9 , pp. 938-950
    • Conant, G.C.1    Wolfe, K.H.2
  • 7
    • 3543051830 scopus 로고    scopus 로고
    • Mauve: Multiple alignment of conserved genomic sequence with rearrangements
    • Darling AC, Mau B, Blattner FR, Perna NT. 2004. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14:1394-1403.
    • (2004) Genome Res , vol.14 , pp. 1394-1403
    • Darling, A.C.1    Mau, B.2    Blattner, F.R.3    Perna, N.T.4
  • 8
    • 63349108180 scopus 로고    scopus 로고
    • Fungal LysM effectors: Extinguishers of host immunity?
    • de Jonge R, Thomma BP. 2009. Fungal LysM effectors: extinguishers of host immunity? Trends Microbiol. 17:151-157.
    • (2009) Trends Microbiol , vol.17 , pp. 151-157
    • De Jonge, R.1    Thomma, B.P.2
  • 9
    • 33645981936 scopus 로고    scopus 로고
    • A hybrid micromacroevolutionary approach to gene tree reconstruction
    • Durand D, Halldorsson BV, Vernot B. 2006. A hybrid micromacroevolutionary approach to gene tree reconstruction. J Comput Biol. 13:320-335.
    • (2006) J Comput Biol , vol.13 , pp. 320-335
    • Durand, D.1    Halldorsson, B.V.2    Vernot, B.3
  • 11
    • 33845452848 scopus 로고    scopus 로고
    • A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis
    • Fitzpatrick DA, Logue ME, Stajich JE, Butler G. 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
  • 12
    • 44949239504 scopus 로고    scopus 로고
    • Discovering sequence motifs with arbitrary insertions and deletions
    • Frith MC, Saunders NF, Kobe B, Bailey TL. 2008. Discovering sequence motifs with arbitrary insertions and deletions. PLoS Comput Biol. 4: e1000071.
    • (2008) PLoS Comput Biol , vol.4
    • Frith, M.C.1    Saunders, N.F.2    Kobe, B.3    Bailey, T.L.4
  • 13
    • 0037464589 scopus 로고    scopus 로고
    • The genome sequence of the filamentous fungus Neurospora crassa
    • Galagan JE, Calvo SE, Borkovich KA, et al. 2003. The genome sequence of the filamentous fungus Neurospora crassa. Nature 422: 859-868.
    • (2003) Nature , vol.422 , pp. 859-868
    • Galagan, J.E.1    Calvo, S.E.2    Borkovich, K.A.3
  • 14
    • 0032728408 scopus 로고    scopus 로고
    • Statistical methods for testing functional divergence after gene duplication
    • Gu X. 1999. Statistical methods for testing functional divergence after gene duplication. Mol Biol Evol. 16:1664-1674.
    • (1999) Mol Biol Evol , vol.16 , pp. 1664-1674
    • Gu, X.1
  • 15
    • 0035061686 scopus 로고    scopus 로고
    • Maximum-likelihood approach for gene family evolution under functional divergence
    • Gu X. 2001. Maximum-likelihood approach for gene family evolution under functional divergence. Mol Biol Evol. 18:453-464.
    • (2001) Mol Biol Evol , vol.18 , pp. 453-464
    • Gu, X.1
  • 16
    • 33748784344 scopus 로고    scopus 로고
    • A simple statistical method for estimating type-II (cluster-specific) functional divergence of protein sequences
    • Gu X. 2006. A simple statistical method for estimating type-II (cluster-specific) functional divergence of protein sequences. Mol Biol Evol. 23:1937-1945.
    • (2006) Mol Biol Evol , vol.23 , pp. 1937-1945
    • Gu, X.1
  • 17
    • 69949188053 scopus 로고    scopus 로고
    • A "repertoire for repertoire" hypothesis: Repertoires of type three effectors are candidate determinants of host specificity in Xanthomonas
    • Hajri A, Brin C, Hunault G, Lardeux F, Lemaire C, Manceau C, Boureau T, Poussier S. 2009. A "repertoire for repertoire" hypothesis: repertoires of type three effectors are candidate determinants of host specificity in Xanthomonas. PLoS One 4:e6632.
    • (2009) PLoS One , vol.4
    • Hajri, A.1    Brin, C.2    Hunault, G.3    Lardeux, F.4    Lemaire, C.5    Manceau, C.6    Boureau, T.7    Poussier, S.8
  • 19
    • 0035175582 scopus 로고    scopus 로고
    • Kluyveromyces lactis zymocin mode of action is linked to RNA polymerase II function via Elongator
    • Jablonowski D, Frohloff F, Fichtner L, Stark MJ, Schaffrath R. 2001. Kluyveromyces lactis zymocin mode of action is linked to RNA polymerase II function via Elongator. Mol Microbiol. 42:1095-1105.
    • (2001) Mol Microbiol , vol.42 , pp. 1095-1105
    • Jablonowski, D.1    Frohloff, F.2    Fichtner, L.3    Stark, M.J.4    Schaffrath, R.5
  • 20
    • 33750329972 scopus 로고    scopus 로고
    • Reconstructing the early evolution of fungi using a six-gene phylogeny
    • (70 co-authors)
    • James TY, Kauff F, Schoch CL, et al. (70 co-authors). 2006. Reconstructing the early evolution of fungi using a six-gene phylogeny. Nature 443:818-822.
    • (2006) Nature , vol.443 , pp. 818-822
    • James, T.Y.1    Kauff, F.2    Schoch, C.L.3
  • 21
    • 77958182267 scopus 로고    scopus 로고
    • Type VI secretion: Not just for pathogenesis anymore
    • Jani AJ, Cotter PA. 2010. Type VI secretion: not just for pathogenesis anymore. Cell Host Microbe 8:2-6.
    • (2010) Cell Host Microbe , vol.8 , pp. 2-6
    • Jani, A.J.1    Cotter, P.A.2
  • 22
    • 42449116668 scopus 로고    scopus 로고
    • RXLR effector reservoir in two Phytophthora species is dominated by a single rapidly evolving superfamily with more than 700 members
    • Jiang RH, Tripathy S, Govers F, Tyler BM. 2008. RXLR effector reservoir in two Phytophthora species is dominated by a single rapidly evolving superfamily with more than 700 members. Proc Natl Acad Sci USA. 105:4874-4879.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 4874-4879
    • Jiang, R.H.1    Tripathy, S.2    Govers, F.3    Tyler, B.M.4
  • 24
    • 44949159619 scopus 로고    scopus 로고
    • The current excitement about copy-number variation: How it relates to gene duplications and protein families
    • Korbel JO, Kim PM, Chen X, Urban AE,Weissman S, Snyder M, Gerstein MB. 2008. The current excitement about copy-number variation: how it relates to gene duplications and protein families. Curr Opin Struct Biol. 18:366-374.
    • (2008) Curr Opin Struct Biol , vol.18 , pp. 366-374
    • Korbel, J.O.1    Kim, P.M.2    Chen, X.3    Urban Aeweissman, S.4    Snyder, M.5    Gerstein, M.B.6
  • 26
    • 0034634395 scopus 로고    scopus 로고
    • The evolutionary fate and consequences of duplicate genes
    • Lynch M, Conery JS. 2000. The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155.
    • (2000) Science , vol.290 , pp. 1151-1155
    • Lynch, M.1    Conery, J.S.2
  • 27
    • 33845985994 scopus 로고    scopus 로고
    • Type III effector diversification via both pathoadaptation and horizontal transfer in response to a coevolutionary arms race
    • Ma W, Dong FF, Stavrinides J, Guttman DS. 2006. Type III effector diversification via both pathoadaptation and horizontal transfer in response to a coevolutionary arms race. PLoS Genet. 2:e209.
    • (2006) PLoS Genet , vol.2
    • Ma, W.1    Dong, F.F.2    Stavrinides, J.3    Guttman, D.S.4
  • 28
    • 0034614924 scopus 로고    scopus 로고
    • Testing character correlation using pairwise comparisons on a phylogeny
    • Maddison WP. 2000. Testing character correlation using pairwise comparisons on a phylogeny. J Theor Biol. 202:195-204.
    • (2000) J Theor Biol , vol.202 , pp. 195-204
    • Maddison, W.P.1
  • 30
    • 74549162702 scopus 로고    scopus 로고
    • Expanding the paradigms of plant pathogen life history and evolution of parasitic fitness beyond agricultural bundaries
    • Morris CE, Bardin M, Kinkel LL, Moury B, Nicot PC, Sands DC. 2009. Expanding the paradigms of plant pathogen life history and evolution of parasitic fitness beyond agricultural bundaries. PLoS Pathog. 5:e1000693.
    • (2009) PLoS Pathog , vol.5
    • Morris, C.E.1    Bardin, M.2    Kinkel, L.L.3    Moury, B.4    Nicot, P.C.5    Sands, D.C.6
  • 31
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman SB, Wunsch CD. 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol. 48:443-453.
    • (1970) J Mol Biol , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 32
    • 0030791307 scopus 로고    scopus 로고
    • Evolution by the birth-and-death process in multigene families of the vertebrate immune system
    • NeiM, Gu X, Sitnikova T. 1997. Evolution by the birth-and-death process in multigene families of the vertebrate immune system. Proc Natl Acad Sci USA. 94:7799-7806.
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 7799-7806
    • Neim Gu, X.1    Sitnikova, T.2
  • 33
    • 27944477670 scopus 로고    scopus 로고
    • Concerted and birth-and-death evolution of multigene families
    • Nei M, Rooney AP. 2005. Concerted and birth-and-death evolution of multigene families. Annu Rev Genet. 39:121-152.
    • (2005) Annu Rev Genet , vol.39 , pp. 121-152
    • Nei, M.1    Rooney, A.P.2
  • 34
    • 0031972161 scopus 로고    scopus 로고
    • Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
    • Nielsen R, Yang Z. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148:929-936.
    • (1998) Genetics , vol.148 , pp. 929-936
    • Nielsen, R.1    Yang, Z.2
  • 35
    • 0037396440 scopus 로고    scopus 로고
    • The contribution of melanin to microbial pathogenesis
    • Nosanchuk JD, Casadevall A. 2003. The contribution of melanin to microbial pathogenesis. Cell Microbiol. 5:203-223.
    • (2003) Cell Microbiol , vol.5 , pp. 203-223
    • Nosanchuk, J.D.1    Casadevall, A.2
  • 36
    • 0028280685 scopus 로고
    • Divergent evolution and evolution by the birth-and-death process in the immunoglobulin VH gene family
    • Ota T, Nei M. 1994. Divergent evolution and evolution by the birth-and-death process in the immunoglobulin VH gene family. Mol Biol Evol. 11:469-482.
    • (1994) Mol Biol Evol , vol.11 , pp. 469-482
    • Ota, T.1    Nei, M.2
  • 37
    • 35349003200 scopus 로고    scopus 로고
    • Bacterial pathogenomics
    • Pallen MJ, Wren BW. 2007. Bacterial pathogenomics. Nature 449: 835-842.
    • (2007) Nature , vol.449 , pp. 835-842
    • Pallen, M.J.1    Wren, B.W.2
  • 39
    • 0028932195 scopus 로고
    • Inference from binary comparative data
    • Read AF, Nee S. 1995. Inference from binary comparative data. J Theor Biol. 173:99-108.
    • (1995) J Theor Biol , vol.173 , pp. 99-108
    • Read, A.F.1    Nee, S.2
  • 40
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes 3: Bayesian phylogenetic inference under mixed models
    • Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
    • (2003) Bioinformatics , vol.19 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 41
    • 33750471586 scopus 로고    scopus 로고
    • Comparative genomics of host-specific virulence in Pseudomonas syringae
    • Sarkar SF, Gordon JS, Martin GB, Guttman DS. 2006. Comparative genomics of host-specific virulence in Pseudomonas syringae. Genetics 174:1041-1056.
    • (2006) Genetics , vol.174 , pp. 1041-1056
    • Sarkar, S.F.1    Gordon, J.S.2    Martin, G.B.3    Guttman, D.S.4
  • 42
    • 67749119915 scopus 로고    scopus 로고
    • The Ascomycota tree of life: A phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits
    • (64 co-authors)
    • Schoch CL, Sung GH, Lopez-Giraldez F, et al. (64 co-authors) 2009. The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits. Syst Biol. 58:224-239.
    • (2009) Syst Biol , vol.58 , pp. 224-239
    • Schoch, C.L.1    Sung, G.H.2    Lopez-Giraldez, F.3
  • 43
    • 4544311532 scopus 로고    scopus 로고
    • Molecular population genetic analysis differentiates two virulence mechanisms of the fungal avirulence gene NIP1
    • Schurch S, Linde CC, Knogge W, Jackson LF, McDonald BA. 2004. Molecular population genetic analysis differentiates two virulence mechanisms of the fungal avirulence gene NIP1. Mol Plant Microbe In. 17:1114-1125.
    • (2004) Mol Plant Microbe in , vol.17 , pp. 1114-1125
    • Schurch, S.1    Linde, C.C.2    Knogge, W.3    Jackson, L.F.4    McDonald, B.A.5
  • 44
    • 28044450149 scopus 로고    scopus 로고
    • A complete survey of Trichoderma chitinases reveals three distinct subgroups of family 18 chitinases
    • Seidl V, Huemer B, Seiboth B, Kubicek CP. 2005. A complete survey of Trichoderma chitinases reveals three distinct subgroups of family 18 chitinases. FEBS J. 272:5923-5939.
    • (2005) FEBS J , vol.272 , pp. 5923-5939
    • Seidl, V.1    Huemer, B.2    Seiboth, B.3    Kubicek, C.P.4
  • 45
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
    • (2006) Bioinformatics , vol.22 , pp. 2688-2690
    • Stamatakis, A.1
  • 46
    • 50249100595 scopus 로고    scopus 로고
    • A rapid bootstrap algorithm for the RAxML Web servers
    • Stamatakis A, Hoover P, Rougemont J. 2008. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol. 57:758-771.
    • (2008) Syst Biol , vol.57 , pp. 758-771
    • Stamatakis, A.1    Hoover, P.2    Rougemont, J.3
  • 47
    • 0024987238 scopus 로고
    • The plasmid-encoded killer system of Kluyveromyces lactis: A review
    • Stark MJ, Boyd A, Mileham AJ, Romanos MA. 1990. The plasmid-encoded killer system of Kluyveromyces lactis: a review. Yeast 6:1-29.
    • (1990) Yeast , vol.6 , pp. 1-29
    • Stark, M.J.1    Boyd, A.2    Mileham, A.J.3    Romanos, M.A.4
  • 48
    • 38049184489 scopus 로고    scopus 로고
    • Host-pathogen interplay and the evolution of bacterial effectors
    • Stavrinides J, McCann HC, Guttman DS. 2008. Host-pathogen interplay and the evolution of bacterial effectors. Cell Microbiol. 10: 285-292.
    • (2008) Cell Microbiol , vol.10 , pp. 285-292
    • Stavrinides, J.1    McCann, H.C.2    Guttman, D.S.3
  • 49
    • 34548694060 scopus 로고    scopus 로고
    • Allelic variation in the effector genes of the tomato pathogen Cladosporium fulvum reveals different modes of adaptive evolution
    • Stergiopoulos I, De Kock MJ, Lindhout P, De Wit PJGM. 2007. Allelic variation in the effector genes of the tomato pathogen Cladosporium fulvum reveals different modes of adaptive evolution. Mol Plant Microbe In. 20:1271-1283.
    • (2007) Mol Plant Microbe in , vol.20 , pp. 1271-1283
    • Stergiopoulos, I.1    De Kock, M.J.2    Lindhout, P.3    De Wit, P.J.G.M.4
  • 52
    • 64749114678 scopus 로고    scopus 로고
    • Population genetics of fungal and oomycete effectors involved in gene-for-gene interactions
    • Stukenbrock EH, McDonald BA. 2009. Population genetics of fungal and oomycete effectors involved in gene-for-gene interactions. Mol Plant Microbe In. 22:371-380.
    • (2009) Mol Plant Microbe in , vol.22 , pp. 371-380
    • Stukenbrock, E.H.1    McDonald, B.A.2
  • 54
    • 34548501747 scopus 로고    scopus 로고
    • Natural history and evolutionary principles of gene duplication in fungi
    • Wapinski I, Pfeffer A, Friedman N, Regev A. 2007. Natural history and evolutionary principles of gene duplication in fungi. Nature 449: 54-61.
    • (2007) Nature , vol.449 , pp. 54-61
    • Wapinski, I.1    Pfeffer, A.2    Friedman, N.3    Regev, A.4
  • 55
    • 65349092727 scopus 로고    scopus 로고
    • Environment can alter selection in host parasite interactions
    • Wolinska J, King KC. 2009. Environment can alter selection in host parasite interactions. Trends Parasitol. 25:236-244.
    • (2009) Trends Parasitol , vol.25 , pp. 236-244
    • Wolinska, J.1    King, K.C.2
  • 56
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • Yang Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 13:555-556.
    • (1997) Comput Appl Biosci , vol.13 , pp. 555-556
    • Yang, Z.1
  • 57
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: Phylogenetic analysis by maximum likelihood
    • Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586-1591.
    • (2007) Mol Biol Evol , vol.24 , pp. 1586-1591
    • Yang, Z.1
  • 58
    • 16344378246 scopus 로고    scopus 로고
    • Bayes empirical bayes inference of amino acid sites under positive selection
    • Yang Z, Wong WS, Nielsen R. 2005. Bayes empirical bayes inference of amino acid sites under positive selection. Mol Biol Evol. 22: 1107-1118.
    • (2005) Mol Biol Evol , vol.22 , pp. 1107-1118
    • Yang, Z.1    Wong, W.S.2    Nielsen, R.3


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