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Volumn 6, Issue SEP, 2015, Pages

Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1

Author keywords

Endophyte genomics; Endophytes; Endophytic yeast; Microbiome; Phytobiome; Plant microbe interactions; Populus; Symbiosis

Indexed keywords

ARTICLE; DNA PURIFICATION; ENDOPHYTIC FUNGUS; FUNGAL GENETICS; GENE ONTOLOGY; GENOME ANALYSIS; NONHUMAN; PLANT GROWTH; RHODOTORULA GRAMINIS; RNA EXTRACTION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; TRANSCRIPTOMICS; YEAST;

EID: 84949644520     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2015.00978     Document Type: Article
Times cited : (76)

References (69)
  • 1
    • 84855264889 scopus 로고    scopus 로고
    • Horizontal gene exchange in environmental microbiota
    • Aminov, R.I. (2011). Horizontal gene exchange in environmental microbiota. Front. Microbiol. 2:158. doi: 10.3389/fmicb.2011.00158.
    • (2011) Front. Microbiol. , vol.2 , pp. 158
    • Aminov, R.I.1
  • 3
    • 70349427105 scopus 로고    scopus 로고
    • Acetolactate synthase from Bacillus subtilis serves as a 2-ketoisovalerate decarboxylase for isobutanol biosynthesis in Escherichia coli
    • Atsumi, S., Li, Z., and Liao, J.C. (2009). Acetolactate synthase from Bacillus subtilis serves as a 2-ketoisovalerate decarboxylase for isobutanol biosynthesis in Escherichia coli. Appl. Environ. Microbiol. 75, 6306-6311. doi: 10.1128/AEM. 01160-09.
    • (2009) Appl. Environ. Microbiol. , vol.75 , pp. 6306-6311
    • Atsumi, S.1    Li, Z.2    Liao, J.C.3
  • 4
    • 85008548682 scopus 로고
    • Studies on the sexuality of Rhodotorula
    • Banno, I. (1967). Studies on the sexuality of Rhodotorula. J. Gen. Appl. Microbiol. 13, 167-196.
    • (1967) J. Gen. Appl. Microbiol. , vol.13 , pp. 167-196
    • Banno, I.1
  • 5
    • 70449482476 scopus 로고    scopus 로고
    • Complete genome sequence of the sugarcane nitrogen-fixing endophyte Gluconacetobacter diazotrophicus Pal5
    • Bertalan, M., Albano, R., de, P.V., Rouws, L., Rojas, C., Hemerly, A., et al. (2009). Complete genome sequence of the sugarcane nitrogen-fixing endophyte Gluconacetobacter diazotrophicus Pal5. BMC Genomics 10:450. doi: 10.1186/1471-2164-10-450.
    • (2009) BMC Genomics , vol.10 , pp. 450
    • Bertalan, M.1    Albano, R.2    de, P.V.3    Rouws, L.4    Rojas, C.5    Hemerly, A.6
  • 6
    • 34547869583 scopus 로고    scopus 로고
    • EuSplice: a unified resource for the analysis of splice signals and alternative splicing in eukaryotic genes
    • Bhasi, A., Pandey, R.V., Utharasamy, S.P., and Senapathy, P. (2007). EuSplice: a unified resource for the analysis of splice signals and alternative splicing in eukaryotic genes. Bioinformatics 23, 1815-1823. doi: 10.1093/bioinformatics/btm084.
    • (2007) Bioinformatics , vol.23 , pp. 1815-1823
    • Bhasi, A.1    Pandey, R.V.2    Utharasamy, S.P.3    Senapathy, P.4
  • 7
    • 0034098730 scopus 로고    scopus 로고
    • Using GeneWise in the Drosophila annotation experiment
    • Birney, E., and Durbin, R. (2000). Using GeneWise in the Drosophila annotation experiment. Genome. Res. 10, 547-548. doi: 10.1101/gr.10.4.547.
    • (2000) Genome. Res. , vol.10 , pp. 547-548
    • Birney, E.1    Durbin, R.2
  • 10
    • 84896736910 scopus 로고    scopus 로고
    • Volatiles produced by soil-borne endophytic bacteria increase plant pathogen resistance and affect tritrophic interactions
    • D'Alessandro, M., Erb, M., Ton, J., Brandenburg, A., Karlen, D., Zopfi, J., et al. (2014). Volatiles produced by soil-borne endophytic bacteria increase plant pathogen resistance and affect tritrophic interactions. Plant Cell Environ. 37, 813-826. doi: 10.1111/pce.12220.
    • (2014) Plant Cell Environ , vol.37 , pp. 813-826
    • D'Alessandro, M.1    Erb, M.2    Ton, J.3    Brandenburg, A.4    Karlen, D.5    Zopfi, J.6
  • 11
    • 84876449249 scopus 로고    scopus 로고
    • Growth-promoting endophytic fungi of forest trees
    • eds A. M. Pirttilä and A. C. Carolin (Dordrecht; Heidelberg; London, UK; New York, NY: Springer)
    • Doty, S.L. (2011). "Growth-promoting endophytic fungi of forest trees," in Endophytes of Forest Trees: Biology and Applications, eds A. M. Pirttilä and A. C. Carolin (Dordrecht; Heidelberg; London, UK; New York, NY: Springer), 151-156.
    • (2011) Endophytes of Forest Trees: Biology and Applications , pp. 151-156
    • Doty, S.L.1
  • 12
    • 84949664717 scopus 로고    scopus 로고
    • Endophytic Yeast Strains, Methods for Ethanol and Xylitol Production
    • Methods for Biological Nitrogen Fixation, and a Genetic Source for Improvement of Industrial Strains. Patent No. 8,728
    • Doty, S.L. (2014). Endophytic Yeast Strains, Methods for Ethanol and Xylitol Production, Methods for Biological Nitrogen Fixation, and a Genetic Source for Improvement of Industrial Strains. Patent No. 8,728,781.
    • (2014) , pp. 781
    • Doty, S.L.1
  • 13
    • 84903950527 scopus 로고    scopus 로고
    • Indole-3-acetic acid in plant-microbe interactions
    • Duca, D., Lorv, J., Patten, C.L., Rose, D., and Glick, B.R. (2014). Indole-3-acetic acid in plant-microbe interactions. Anton. Leeuwen. 106, 85-125. doi: 10.1007/s10482-013-0095-y.
    • (2014) Anton. Leeuwen. , vol.106 , pp. 85-125
    • Duca, D.1    Lorv, J.2    Patten, C.L.3    Rose, D.4    Glick, B.R.5
  • 14
    • 0034697980 scopus 로고    scopus 로고
    • Predicting subcellular localization of proteins based on their N-terminal amino acid sequence
    • Emanuelsson, O., Nielsen, H., Brunak, S., and von, H.G. (2000). Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J. Mol. Biol. 300, 1005-1016. doi: 10.1006/jmbi.2000.3903.
    • (2000) J. Mol. Biol. , vol.300 , pp. 1005-1016
    • Emanuelsson, O.1    Nielsen, H.2    Brunak, S.3    von, H.G.4
  • 15
    • 84907781344 scopus 로고    scopus 로고
    • Functional diversity of 2-oxoglutarate/Fe(II)-dependent dioxygenases in plant metabolism
    • Farrow, S.C., and Facchini, P.J. (2014). Functional diversity of 2-oxoglutarate/Fe(II)-dependent dioxygenases in plant metabolism. Front. Plant Sci. 5:524. doi: 10.3389/fpls.2014.00524.
    • (2014) Front. Plant Sci. , vol.5 , pp. 524
    • Farrow, S.C.1    Facchini, P.J.2
  • 16
    • 48249088509 scopus 로고    scopus 로고
    • Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice
    • Fouts, D.E., Tyler, H.L., DeBoy, R.T., Daugherty, S., Ren, Q., Badger, J., et al. (2008). Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice. PLoS. Genet. 4:e1000141. doi: 10.1371/journal.pgen.1000141.
    • (2008) PLoS. Genet. , vol.4
    • Fouts, D.E.1    Tyler, H.L.2    DeBoy, R.T.3    Daugherty, S.4    Ren, Q.5    Badger, J.6
  • 17
    • 84885834835 scopus 로고    scopus 로고
    • Insights into auxin signaling in plant-pathogen interactions
    • Fu, J., and Wang, S. (2011). Insights into auxin signaling in plant-pathogen interactions. Front. Plant Sci. 2:74. doi: 10.3389/fpls.2011.00074.
    • (2011) Front. Plant Sci. , vol.2 , pp. 74
    • Fu, J.1    Wang, S.2
  • 18
    • 11144291814 scopus 로고    scopus 로고
    • Cryptococcus neoformans CAP59 (or Cap59p) is involved in the extracellular trafficking of capsular glucuronoxylomannan
    • García-Rivera, J., Chang, Y.C., Kwon-Chung, K.J., and Casadevall, A. (2004). Cryptococcus neoformans CAP59 (or Cap59p) is involved in the extracellular trafficking of capsular glucuronoxylomannan. Eukaryot. Cell 3, 385-392. doi: 10.1128/EC.3.2.385-392.2004.
    • (2004) Eukaryot. Cell. , vol.3 , pp. 385-392
    • García-Rivera, J.1    Chang, Y.C.2    Kwon-Chung, K.J.3    Casadevall, A.4
  • 21
    • 84922771365 scopus 로고    scopus 로고
    • Towards a holistic understanding of the beneficial interactions across the Populus microbiome
    • Hacquard, S., and Schadt, C.W. (2015). Towards a holistic understanding of the beneficial interactions across the Populus microbiome. New Phytol. 205, 1424-1430. doi: 10.1111/nph.13133.
    • (2015) New Phytol , vol.205 , pp. 1424-1430
    • Hacquard, S.1    Schadt, C.W.2
  • 22
    • 53049086655 scopus 로고    scopus 로고
    • Properties of bacterial endophytes and their proposed role in plant growth
    • Hardoim, P.R., van Overbeek, L.S., and Elsas, J.D. (2008). Properties of bacterial endophytes and their proposed role in plant growth. Trends Microbiol. 16, 463-471. doi: 10.1016/j.tim.2008.07.008.
    • (2008) Trends Microbiol , vol.16 , pp. 463-471
    • Hardoim, P.R.1    van Overbeek, L.S.2    Elsas, J.D.3
  • 23
    • 58349084876 scopus 로고    scopus 로고
    • A conserved mechanism for nitrile metabolism in bacteria and plants
    • Howden, A.J., Harrison, C.J., and Preston, G.M. (2009). A conserved mechanism for nitrile metabolism in bacteria and plants. Plant J. 57, 243-253. doi: 10.1111/j.1365-313X. 2008.03682.x.
    • (2009) Plant J , vol.57 , pp. 243-253
    • Howden, A.J.1    Harrison, C.J.2    Preston, G.M.3
  • 24
    • 70350245908 scopus 로고    scopus 로고
    • Nitrilase enzymes and their role in plant-microbe interactions
    • Howden, A.J., and Preston, G.M. (2009). Nitrilase enzymes and their role in plant-microbe interactions. Microb. Biotechnol. 2, 441-451. doi: 10.1111/j.1751-7915.2009.00111.x.
    • (2009) Microb. Biotechnol. , vol.2 , pp. 441-451
    • Howden, A.J.1    Preston, G.M.2
  • 26
    • 79958030351 scopus 로고    scopus 로고
    • Conservation and diversity of seed associated endophytes in Zea across boundaries of evolution, ethnography and ecology
    • Johnston-Monje, D., and Raizada, M.N. (2011). Conservation and diversity of seed associated endophytes in Zea across boundaries of evolution, ethnography and ecology. PLoS ONE 6:e20396. doi: 10.1371/journal.pone.0020396.
    • (2011) PLoS ONE , vol.6
    • Johnston-Monje, D.1    Raizada, M.N.2
  • 29
    • 84910028926 scopus 로고    scopus 로고
    • Bacterial and yeast endophytes from poplar and willow promote growth in crop plants and grasses
    • Khan, Z., Guelich, G., Phan, H., Redman, R.S., and Doty, S.L. (2012). Bacterial and yeast endophytes from poplar and willow promote growth in crop plants and grasses. ISRN Agron. 2012:890280. doi: 10.5402/2012/890280.
    • (2012) ISRN Agron , vol.2012
    • Khan, Z.1    Guelich, G.2    Phan, H.3    Redman, R.S.4    Doty, S.L.5
  • 30
    • 84878722837 scopus 로고    scopus 로고
    • Effects of cross host species inoculation of nitrogen-fixing endophytes on growth and leaf physiology of maize
    • Knoth, J., Kim, S.-H., Ettl, G., and Doty, S.L. (2013). Effects of cross host species inoculation of nitrogen-fixing endophytes on growth and leaf physiology of maize. GCB Bioenery 5, 408-418. doi: 10.1111/gcbb.12006.
    • (2013) GCB Bioenery , vol.5 , pp. 408-418
    • Knoth, J.1    Kim, S.-H.2    Ettl, G.3    Doty, S.L.4
  • 31
    • 84890795522 scopus 로고    scopus 로고
    • Biological nitrogen fixation and biomass accumulation within poplar clones as a result of inoculations with diazotrophic endophyte consortia
    • Knoth, J.L., Kim, S.H., Ettl, G.J., and Doty, S.L. (2014). Biological nitrogen fixation and biomass accumulation within poplar clones as a result of inoculations with diazotrophic endophyte consortia. New Phytol. 201, 599-609. doi: 10.1111/nph.12536.
    • (2014) New Phytol , vol.201 , pp. 599-609
    • Knoth, J.L.1    Kim, S.H.2    Ettl, G.J.3    Doty, S.L.4
  • 32
    • 16444381885 scopus 로고    scopus 로고
    • A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes
    • Koonin, E.V., Fedorova, N.D., Jackson, J.D., Jacobs, A.R., Krylov, D.M., Makarova, K.S., et al. (2004). A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome. Biol. 5:R7. doi: 10.1186/gb-2004-5-2-r7.
    • (2004) Genome. Biol. , vol.5 , pp. R7
    • Koonin, E.V.1    Fedorova, N.D.2    Jackson, J.D.3    Jacobs, A.R.4    Krylov, D.M.5    Makarova, K.S.6
  • 33
    • 79955866499 scopus 로고    scopus 로고
    • Using next generation transcriptome sequencing to predict an ectomycorrhizal metabolome
    • Larsen, P.E., Sreedasyam, A., Trivedi, G., Podila, G.K., Cseke, L.J., and Collart, F.R. (2011). Using next generation transcriptome sequencing to predict an ectomycorrhizal metabolome. BMC Syst. Biol. 5:70. doi: 10.1186/1752-0509-5-70.
    • (2011) BMC Syst. Biol. , vol.5 , pp. 70
    • Larsen, P.E.1    Sreedasyam, A.2    Trivedi, G.3    Podila, G.K.4    Cseke, L.J.5    Collart, F.R.6
  • 35
    • 0030854739 scopus 로고    scopus 로고
    • tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
    • Lowe, T.M., and Eddy, S.R. (1997). tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955-964. doi: 10.1093/nar/25.5.0955.
    • (1997) Nucleic Acids Res , vol.25 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 36
    • 72449164089 scopus 로고    scopus 로고
    • Acquisition of prokaryotic genes by fungal genomes
    • Marcet-Houben, M., and Gabaldon, T. (2010). Acquisition of prokaryotic genes by fungal genomes. Trends Genet. 26, 5-8. doi: 10.1016/j.tig.2009.11.007.
    • (2010) Trends Genet , vol.26 , pp. 5-8
    • Marcet-Houben, M.1    Gabaldon, T.2
  • 37
    • 40449120632 scopus 로고    scopus 로고
    • The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis
    • Martin, F., Aerts, A., Ahren, D., Brun, A., Danchin, E.G., Duchaussoy, F., et al. (2008). The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 452, 88-92. doi: 10.1038/nature06556.
    • (2008) Nature , vol.452 , pp. 88-92
    • Martin, F.1    Aerts, A.2    Ahren, D.3    Brun, A.4    Danchin, E.G.5    Duchaussoy, F.6
  • 38
    • 25444492854 scopus 로고    scopus 로고
    • Specific antibody can prevent fungal biofilm formation and this effect correlates with protective efficacy
    • Martinez, L.R., and Casadevall, A. (2005). Specific antibody can prevent fungal biofilm formation and this effect correlates with protective efficacy. Infect. Immun. 73, 6350-6362. doi: 10.1128/IAI.73.10.6350-6362.2005.
    • (2005) Infect. Immun. , vol.73 , pp. 6350-6362
    • Martinez, L.R.1    Casadevall, A.2
  • 39
    • 0344406716 scopus 로고    scopus 로고
    • Reliability measures for membrane protein topology prediction algorithms
    • Melén, K., Krogh, A., and von, H.G. (2003). Reliability measures for membrane protein topology prediction algorithms. J. Mol. Biol. 327, 735-744. doi: 10.1016/S0022-2836(03)00182-7.
    • (2003) J. Mol. Biol. , vol.327 , pp. 735-744
    • Melén, K.1    Krogh, A.2    von, H.G.3
  • 40
    • 0028786641 scopus 로고
    • Cryptococcosis in the era of AIDS-100 years after the discovery of Cryptococcus neoformans
    • Mitchell, T.G., and Perfect, J.R. (1995). Cryptococcosis in the era of AIDS-100 years after the discovery of Cryptococcus neoformans. Clin. Microbiol. Rev. 8, 515-548.
    • (1995) Clin. Microbiol. Rev. , vol.8 , pp. 515-548
    • Mitchell, T.G.1    Perfect, J.R.2
  • 41
    • 84982358134 scopus 로고
    • A revised medium for rapid growth and bioassays with tobacco tissue culture
    • Murashige, T., and Skoog, F. (1962). A revised medium for rapid growth and bioassays with tobacco tissue culture. Physiol. Plant 15, 473-497. doi: 10.1111/j.1399-3054.1962.tb08052.x.
    • (1962) Physiol. Plant. , vol.15 , pp. 473-497
    • Murashige, T.1    Skoog, F.2
  • 42
    • 84904613129 scopus 로고    scopus 로고
    • Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts
    • Nagy, L.G., Ohm, R.A., Kovács, G.M., Floudas, D., Riley, R., Gácser, A., et al. (2014). Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts. Nat. Commun. 5, 4471. doi: 10.1038/ncomms5471.
    • (2014) Nat. Commun. , vol.5 , pp. 4471
    • Nagy, L.G.1    Ohm, R.A.2    Kovács, G.M.3    Floudas, D.4    Riley, R.5    Gácser, A.6
  • 43
    • 27444446428 scopus 로고    scopus 로고
    • Promotion of plant growth by an auxin-producing isolate of the yeast Williopsis saturnus endophytic in maize (Zea mays L.) roots
    • Nassar, A.H., El-Tarabily, K.A., and Sivasithamparam, K. (2005). Promotion of plant growth by an auxin-producing isolate of the yeast Williopsis saturnus endophytic in maize (Zea mays L.) roots. Biol. Fertil. Soils 42, 97-108. doi: 10.1007/s00374-005-0008-y.
    • (2005) Biol. Fertil. Soils. , vol.42 , pp. 97-108
    • Nassar, A.H.1    El-Tarabily, K.A.2    Sivasithamparam, K.3
  • 44
    • 0030614959 scopus 로고    scopus 로고
    • Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
    • Nielsen, H., Engelbrecht, J., Brunak, S., and von, H.G. (1997). Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 10, 1-6. doi: 10.1093/protein/10.1.1.
    • (1997) Protein Eng , vol.10 , pp. 1-6
    • Nielsen, H.1    Engelbrecht, J.2    Brunak, S.3    von, H.G.4
  • 45
    • 0036322479 scopus 로고    scopus 로고
    • Role of Pseudomonas putida indoleacetic acid in development of the host plant root system
    • Patten, C.L., and Glick, B.R. (2002). Role of Pseudomonas putida indoleacetic acid in development of the host plant root system. Appl. Environ. Microbiol. 68, 3795-3801. doi: 10.1128/AEM.68.8.3795-3801.2002.
    • (2002) Appl. Environ. Microbiol. , vol.68 , pp. 3795-3801
    • Patten, C.L.1    Glick, B.R.2
  • 46
    • 84903713328 scopus 로고    scopus 로고
    • Duplications and losses in gene families of rust pathogens highlight putative effectors
    • Pendleton, A.L., Smith, K.E., Feau, N., Martin, F.M., Grigoriev, I.V., Hamelin, R., et al. (2014). Duplications and losses in gene families of rust pathogens highlight putative effectors. Front. Plant Sci. 5:299. doi: 10.3389/fpls.2014.00299.
    • (2014) Front. Plant Sci. , vol.5 , pp. 299
    • Pendleton, A.L.1    Smith, K.E.2    Feau, N.3    Martin, F.M.4    Grigoriev, I.V.5    Hamelin, R.6
  • 47
    • 0029931717 scopus 로고    scopus 로고
    • A putative cyclic peptide efflux pump encoded by the TOXA gene of the plant-pathogenic fungus Cochliobolus carbonum
    • Pitkin, J.W., Panaccione, D.G., and Walton, J.D. (1996). A putative cyclic peptide efflux pump encoded by the TOXA gene of the plant-pathogenic fungus Cochliobolus carbonum. Microbiology 142(Pt 6), 1557-1565. doi: 10.1099/13500872-142-6-1557.
    • (1996) Microbiology , vol.142 , pp. 1557-1565
    • Pitkin, J.W.1    Panaccione, D.G.2    Walton, J.D.3
  • 48
    • 84923148253 scopus 로고    scopus 로고
    • The mutualist laccaria bicolor expresses a core gene regulon during the colonization of diverse host plants and a variable regulon to counteract host-specific defenses
    • Plett, J.M., Tisserant, E., Brun, A., Morin, E., Grigoriev, I.V., Kuo, A., et al. (2015). The mutualist laccaria bicolor expresses a core gene regulon during the colonization of diverse host plants and a variable regulon to counteract host-specific defenses. Mol. Plant Microbe Interact. 28, 261-273. doi: 10.1094/MPMI-05-14-0129-FI.
    • (2015) Mol. Plant Microbe Interact. , vol.28 , pp. 261-273
    • Plett, J.M.1    Tisserant, E.2    Brun, A.3    Morin, E.4    Grigoriev, I.V.5    Kuo, A.6
  • 49
    • 77449084911 scopus 로고    scopus 로고
    • Populus rhizosphere and the ectomycorrhizal interactome
    • Podila, G.K., Sreedasyam, A., and Muratet, M. (2009). Populus rhizosphere and the ectomycorrhizal interactome. Crit. Rev. Plant Sci. 28, 359-367. doi: 10.1080/07352680903241220.
    • (2009) Crit. Rev. Plant Sci. , vol.28 , pp. 359-367
    • Podila, G.K.1    Sreedasyam, A.2    Muratet, M.3
  • 50
    • 0033854668 scopus 로고    scopus 로고
    • The iron(II) and 2-oxoacid-dependent dioxygenases and their role in metabolism
    • Prescott, A.G., and Lloyd, M.D. (2000). The iron(II) and 2-oxoacid-dependent dioxygenases and their role in metabolism. Nat. Prod. Rep. 17, 367-383. doi: 10.1039/a902197c.
    • (2000) Nat. Prod. Rep. , vol.17 , pp. 367-383
    • Prescott, A.G.1    Lloyd, M.D.2
  • 51
    • 29144455282 scopus 로고    scopus 로고
    • De novo identification of repeat families in large genomes
    • Price, A.L., Jones, N.C., and Pevzner, P.A. (2005). De novo identification of repeat families in large genomes. Bioinformatics 21(Suppl. 1), i351-i358. doi: 10.1093/bioinformatics/bti1018.
    • (2005) Bioinformatics , vol.21 , pp. i351-i358
    • Price, A.L.1    Jones, N.C.2    Pevzner, P.A.3
  • 53
    • 84887534107 scopus 로고    scopus 로고
    • Effector candidates in the secretome of Piriformospora indica, a ubiquitous plant-associated fungus
    • Rafiqi, M., Jelonek, L., Akum, N.F., Zhang, F., and Kogel, K.H. (2013). Effector candidates in the secretome of Piriformospora indica, a ubiquitous plant-associated fungus. Front. Plant Sci. 4:228. doi: 10.3389/fpls.2013.00228.
    • (2013) Front. Plant Sci. , vol.4 , pp. 228
    • Rafiqi, M.1    Jelonek, L.2    Akum, N.F.3    Zhang, F.4    Kogel, K.H.5
  • 55
    • 0030787856 scopus 로고    scopus 로고
    • Analysis of donor splice sites in different eukaryotic organisms
    • Rogozin, I.B., and Milanesi, L. (1997). Analysis of donor splice sites in different eukaryotic organisms. J. Mol. Evol. 45, 50-59. doi: 10.1007/PL00006200.
    • (1997) J. Mol. Evol. , vol.45 , pp. 50-59
    • Rogozin, I.B.1    Milanesi, L.2
  • 56
    • 0034065724 scopus 로고    scopus 로고
    • Ab initio gene finding in Drosophila genomic DNA
    • Salamov, A.A., and Solovyev, V.V. (2000). Ab initio gene finding in Drosophila genomic DNA. Genome. Res. 10, 516-522. doi: 10.1101/gr.10.4.516.
    • (2000) Genome. Res. , vol.10 , pp. 516-522
    • Salamov, A.A.1    Solovyev, V.V.2
  • 57
    • 84055193613 scopus 로고    scopus 로고
    • Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis
    • Sessitsch, A., Hardoim, P., Döring, J., Weilharter, A., Krause, A., Woyke, T., et al. (2012). Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis. Mol. Plant Microbe Interact. 25, 28-36. doi: 10.1094/MPMI-08-11-0204.
    • (2012) Mol. Plant Microbe Interact. , vol.25 , pp. 28-36
    • Sessitsch, A.1    Hardoim, P.2    Döring, J.3    Weilharter, A.4    Krause, A.5    Woyke, T.6
  • 58
    • 84949663342 scopus 로고    scopus 로고
    • Repeat Masker Open-3.0. Available online at
    • Smit, A.F. A., Hubley, R., and Green, P. (2010). Repeat Masker Open-3.0. Available online at: http://www.repeatmasker.org.
    • (2010)
    • Smit, A.F.A.1    Hubley, R.2    Green, P.3
  • 59
    • 84919499222 scopus 로고    scopus 로고
    • 1000 fungal genomes project
    • Available online at
    • Spatafora, J.W., Stajich, J.E., and Grigoriev, I. (2013). 1000 fungal genomes project. Phytopathology 103, 137. Available online at: http://1000.fungalgenomes.org/home/webcite.
    • (2013) Phytopathology , vol.103 , pp. 137
    • Spatafora, J.W.1    Stajich, J.E.2    Grigoriev, I.3
  • 60
    • 84876144592 scopus 로고    scopus 로고
    • Involvement of auxin pathways in modulating root architecture during beneficial plant-microorganism interactions
    • Sukumar, P., Legué, V., Vayssierès, A., Martin, F., Tuskan, G.A., and Kalluri, U.C. (2013). Involvement of auxin pathways in modulating root architecture during beneficial plant-microorganism interactions. Plant Cell Environ. 36, 909-919. doi: 10.1111/pce.12036.
    • (2013) Plant Cell Environ , vol.36 , pp. 909-919
    • Sukumar, P.1    Legué, V.2    Vayssierès, A.3    Martin, F.4    Tuskan, G.A.5    Kalluri, U.C.6
  • 61
    • 29144469077 scopus 로고    scopus 로고
    • Horizontal gene transfer to endogenous endophytic bacteria from poplar improves phytoremediation of toluene
    • Taghavi, S., Barac, T., Greenberg, B., Borremans, B., Vangronsveld, J., and van der Lelie, D. (2005). Horizontal gene transfer to endogenous endophytic bacteria from poplar improves phytoremediation of toluene. Appl. Environ. Microbiol. 71, 8500-8505. doi: 10.1128/AEM.71.12.8500-8505.2005.
    • (2005) Appl. Environ. Microbiol. , vol.71 , pp. 8500-8505
    • Taghavi, S.1    Barac, T.2    Greenberg, B.3    Borremans, B.4    Vangronsveld, J.5    van der Lelie, D.6
  • 62
    • 77953227536 scopus 로고    scopus 로고
    • Genome sequence of the plant growth promoting endophytic bacterium Enterobacter sp 638
    • Taghavi, S., van der Lelie, D., Hoffman, A., Zhang, Y.B., Walla, M.D., Vangronsveld, J., et al. (2010). Genome sequence of the plant growth promoting endophytic bacterium Enterobacter sp. 638. PLoS. Genet. 6:e1000943. doi: 10.1371/journal.pgen.1000943.
    • (2010) PLoS. Genet. , vol.6
    • Taghavi, S.1    van der Lelie, D.2    Hoffman, A.3    Zhang, Y.B.4    Walla, M.D.5    Vangronsveld, J.6
  • 63
    • 84921922528 scopus 로고    scopus 로고
    • Transcriptional responses to sucrose mimic the plant-associated life style of the plant growth promoting endophyte Enterobacter sp 638
    • Taghavi, S., Wu, X., Ouyang, L., Zhang, Y.B., Stadler, A., McCorkle, S., et al. (2015). Transcriptional responses to sucrose mimic the plant-associated life style of the plant growth promoting endophyte Enterobacter sp. 638. PLoS ONE 10:e0115455. doi: 10.1371/journal.pone.0115455.
    • (2015) PLoS ONE , vol.10 , pp. e0115455
    • Taghavi, S.1    Wu, X.2    Ouyang, L.3    Zhang, Y.B.4    Stadler, A.5    McCorkle, S.6
  • 64
    • 57149099395 scopus 로고    scopus 로고
    • Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training
    • Ter-Hovhannisyan, V., Lomsadze, A., Chernoff, Y.O., and Borodovsky, M. (2008). Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. Genome. Res. 18, 1979-1990. doi: 10.1101/gr.081612.108.
    • (2008) Genome. Res. , vol.18 , pp. 1979-1990
    • Ter-Hovhannisyan, V.1    Lomsadze, A.2    Chernoff, Y.O.3    Borodovsky, M.4
  • 65
    • 33748760611 scopus 로고    scopus 로고
    • The genome of black cottonwood Populus trichocarpa (Torr. & Gray)
    • Tuskan, G.A., Difazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., Hellsten, U., et al. (2006). The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313, 1596-1604. doi: 10.1126/science.1128691.
    • (2006) Science , vol.313 , pp. 1596-1604
    • Tuskan, G.A.1    Difazio, S.2    Jansson, S.3    Bohlmann, J.4    Grigoriev, I.5    Hellsten, U.6
  • 66
    • 84868283696 scopus 로고    scopus 로고
    • Genome sequence of Enterobacter radicincitans DSM16656(T), a plant growth-promoting endophyte
    • Witzel, K., Gwinn-Giglio, M., Nadendla, S., Shefchek, K., and Ruppel, S. (2012). Genome sequence of Enterobacter radicincitans DSM16656(T), a plant growth-promoting endophyte. J. Bacteriol. 194, 5469. doi: 10.1128/JB. 01193-12.
    • (2012) J. Bacteriol. , vol.194 , pp. 5469
    • Witzel, K.1    Gwinn-Giglio, M.2    Nadendla, S.3    Shefchek, K.4    Ruppel, S.5
  • 67
    • 70349152182 scopus 로고    scopus 로고
    • Characterization of three endophytic, indole-3-acetic acid-producing yeasts occurring in Populus trees
    • Xin, G., Glawe, D., and Doty, S.L. (2009). Characterization of three endophytic, indole-3-acetic acid-producing yeasts occurring in Populus trees. Mycol. Res. 113, 973-980. doi: 10.1016/j.mycres.2009.06.001.
    • (2009) Mycol. Res. , vol.113 , pp. 973-980
    • Xin, G.1    Glawe, D.2    Doty, S.L.3
  • 68
    • 80051725871 scopus 로고    scopus 로고
    • Genetic analysis of D-xylose metabolism by endophytic yeast strains of Rhodotorula graminis and Rhodotorula mucilaginosa
    • Xu, P., Bura, R., and Doty, S.L. (2011). Genetic analysis of D-xylose metabolism by endophytic yeast strains of Rhodotorula graminis and Rhodotorula mucilaginosa. Genet. Mol. Biol. 34, 471-478. doi: 10.1590/S1415-47572011000300018.
    • (2011) Genet. Mol. Biol. , vol.34 , pp. 471-478
    • Xu, P.1    Bura, R.2    Doty, S.L.3
  • 69
    • 84885373147 scopus 로고    scopus 로고
    • A role for a dioxygenase in auxin metabolism and reproductive development in rice
    • Zhao, Z., Zhang, Y., Liu, X., Zhang, X., Liu, S., Yu, X., et al. (2013). A role for a dioxygenase in auxin metabolism and reproductive development in rice. Dev. Cell 27, 113-122. doi: 10.1016/j.devcel.2013.09.005.
    • (2013) Dev. Cell. , vol.27 , pp. 113-122
    • Zhao, Z.1    Zhang, Y.2    Liu, X.3    Zhang, X.4    Liu, S.5    Yu, X.6


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