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Volumn 1, Issue 3, 2017, Pages

Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory

(33)  Fukushima, Kenji a,b,c   Fang, Xiaodong d,e   Alvarez Ponce, David f   Cai, Huimin d,e   Carretero Paulet, Lorenzo g,h   Chen, Cui d   Chang, Tien Hao h   Farr, Kimberly M h   Fujita, Tomomichi i   Hiwatashi, Yuji j   Hoshi, Yoshikazu k   Imai, Takamasa l   Kasahara, Masahiro l   Librado, Pablo m,n   Mao, Likai d   Mori, Hitoshi o   Nishiyama, Tomoaki p   Nozawa, Masafumi a,q   Pálfalvi, Gergo a,b   Pollard, Stephen T c   more..


Author keywords

[No Author keywords available]

Indexed keywords


EID: 85022052445     PISSN: None     EISSN: 2397334X     Source Type: Journal    
DOI: 10.1038/s41559-016-0059     Document Type: Article
Times cited : (99)

References (103)
  • 3
    • 0027117868 scopus 로고
    • Carnivorous plants: Phylogeny and structural evolution
    • Albert, V. A., Williams, S. E. & Chase, M. W. Carnivorous plants: phylogeny and structural evolution. Science 257, 1491-1495 (1992).
    • (1992) Science , vol.257 , pp. 1491-1495
    • Albert, V.A.1    Williams, S.E.2    Chase, M.W.3
  • 4
    • 84907200661 scopus 로고    scopus 로고
    • The coffee genome provides insight into the convergent evolution of caffeine biosynthesis
    • Denoeud, F. et al. The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science 345, 1181-1184 (2014).
    • (2014) Science , vol.345 , pp. 1181-1184
    • Denoeud, F.1
  • 5
    • 34848886909 scopus 로고    scopus 로고
    • The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
    • Jaillon, O. et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449, 463-467 (2007).
    • (2007) Nature , vol.449 , pp. 463-467
    • Jaillon, O.1
  • 6
    • 0141519279 scopus 로고    scopus 로고
    • OrthoMCL: Identification of ortholog groups for eukaryotic genomes
    • Li, L., Stoeckert, C. J. & Roos, D. S. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178-2189 (2003).
    • (2003) Genome Res , vol.13 , pp. 2178-2189
    • Li, L.1    Stoeckert, C.J.2    Roos, D.S.3
  • 7
    • 0031397607 scopus 로고    scopus 로고
    • Signal transduction in the carnivorous plant Sarracenia purpurea. Regulation of secretory hydrolase expression during development and in response to resources
    • Gallie, D. R. & Chang, S. C. Signal transduction in the carnivorous plant Sarracenia purpurea. Regulation of secretory hydrolase expression during development and in response to resources. Plant Physiol. 115, 1461-1471 (1997).
    • (1997) Plant Physiol , vol.115 , pp. 1461-1471
    • Gallie, D.R.1    Chang, S.C.2
  • 8
    • 26844455766 scopus 로고    scopus 로고
    • An S-like ribonuclease gene is used to generate a trap-leaf enzyme in the carnivorous plant Drosera adelae
    • Okabe, T., Yoshimoto, I., Hitoshi, M., Ogawa, T. & Ohyama, T. An S-like ribonuclease gene is used to generate a trap-leaf enzyme in the carnivorous plant Drosera adelae. FEBS Lett. 579, 5729-5733 (2005).
    • (2005) FEBS Lett , vol.579 , pp. 5729-5733
    • Okabe, T.1    Yoshimoto, I.2    Hitoshi, M.3    Ogawa, T.4    Ohyama, T.5
  • 9
    • 84886431409 scopus 로고    scopus 로고
    • S-like ribonuclease gene expression in carnivorous plants
    • Nishimura, E. et al. S-like ribonuclease gene expression in carnivorous plants. Planta 238, 955-967 (2013).
    • (2013) Planta , vol.238 , pp. 955-967
    • Nishimura, E.1
  • 10
    • 33751203804 scopus 로고    scopus 로고
    • Nutrient limitation and stoichiometry of carnivorous plants
    • Ellison, A. M. Nutrient limitation and stoichiometry of carnivorous plants. Plant Biol. 8, 740-747 (2006).
    • (2006) Plant Biol , vol.8 , pp. 740-747
    • Ellison, A.M.1
  • 11
    • 84555188912 scopus 로고    scopus 로고
    • Quite a few reasons for calling carnivores 'the most wonderful plants in the world
    • Król, E. et al. Quite a few reasons for calling carnivores 'the most wonderful plants in the world'. Ann. Bot. 109, 47-64 (2012).
    • (2012) Ann. Bot , vol.109 , pp. 47-64
    • Król, E.1
  • 12
    • 79551542415 scopus 로고    scopus 로고
    • Traps of carnivorous pitcher plants as a habitat: Composition of the fluid, biodiversity and mutualistic activities
    • Adlassnig, W., Peroutka, M. & Lendl, T. Traps of carnivorous pitcher plants as a habitat: composition of the fluid, biodiversity and mutualistic activities. Ann. Bot. 107, 181-194 (2011).
    • (2011) Ann. Bot , vol.107 , pp. 181-194
    • Adlassnig, W.1    Peroutka, M.2    Lendl, T.3
  • 13
    • 84873732124 scopus 로고    scopus 로고
    • Biomechanics of plant-insect interactions
    • Whitney, H. M. & Federle, W. Biomechanics of plant-insect interactions. Curr. Opin. Plant Biol. 16, 105-111 (2013).
    • (2013) Curr. Opin. Plant Biol , vol.16 , pp. 105-111
    • Whitney, H.M.1    Federle, W.2
  • 14
    • 84861705204 scopus 로고    scopus 로고
    • Cytochromes P450
    • Bak, S. et al. Cytochromes P450. Arab. B. 9, e0144 (2011).
    • (2011) Arab. B , vol.9 , pp. e0144
    • Bak, S.1
  • 15
    • 55549115700 scopus 로고    scopus 로고
    • Identification of the wax ester synthase/acyl-coenzyme A: Diacylglycerol acyltransferase WSD1 required for stem wax ester biosynthesis in Arabidopsis
    • Li, F. et al. Identification of the wax ester synthase/acyl-coenzyme A: diacylglycerol acyltransferase WSD1 required for stem wax ester biosynthesis in Arabidopsis. Plant Physiol. 148, 97-107 (2008).
    • (2008) Plant Physiol , vol.148 , pp. 97-107
    • Li, F.1
  • 16
    • 84874463966 scopus 로고    scopus 로고
    • Secreted pitfall-trap fluid of carnivorous Nepenthes plants is unsuitable for microbial growth
    • Buch, F. et al. Secreted pitfall-trap fluid of carnivorous Nepenthes plants is unsuitable for microbial growth. Ann. Bot. 111, 375-383 (2013).
    • (2013) Ann. Bot , vol.111 , pp. 375-383
    • Buch, F.1
  • 17
    • 84869208955 scopus 로고    scopus 로고
    • The protein composition of the digestive fluid from the Venus flytrap sheds light on prey digestion mechanisms
    • Schulze, W. X. et al. The protein composition of the digestive fluid from the Venus flytrap sheds light on prey digestion mechanisms. Mol. Cell. Proteomics 11, 1306-1319 (2012).
    • (2012) Mol. Cell. Proteomics , vol.11 , pp. 1306-1319
    • Schulze, W.X.1
  • 18
    • 84884674273 scopus 로고    scopus 로고
    • Glucan-rich diet is digested and taken up by the carnivorous sundew (Drosera rotundifolia L.): Implication for a novel role of plant β -1, 3-glucanases
    • Michalko, J. et al. Glucan-rich diet is digested and taken up by the carnivorous sundew (Drosera rotundifolia L.): implication for a novel role of plant β -1, 3-glucanases. Planta 238, 715-725 (2013).
    • (2013) Planta , vol.238 , pp. 715-725
    • Michalko, J.1
  • 19
    • 84973395027 scopus 로고    scopus 로고
    • Venus flytrap carnivorous lifestyle builds on herbivore defense strategies
    • Bemm, F. et al. Venus flytrap carnivorous lifestyle builds on herbivore defense strategies. Genome Res. 26, 1-14 (2016).
    • (2016) Genome Res , vol.26 , pp. 1-14
    • Bemm, F.1
  • 20
    • 33846200867 scopus 로고    scopus 로고
    • Molecular phylogeny and character evolution of carnivorous plant families in Caryophyllales - Revisited
    • Heubl, G., Bringmann, G. & Meimberg, H. Molecular phylogeny and character evolution of carnivorous plant families in Caryophyllales - revisited. Plant Biol. 8, 821-830 (2006).
    • (2006) Plant Biol , vol.8 , pp. 821-830
    • Heubl, G.1    Bringmann, G.2    Meimberg, H.3
  • 21
    • 67049119180 scopus 로고    scopus 로고
    • Evidence for an ancient adaptive episode of convergent molecular evolution
    • Castoe, T. A. et al. Evidence for an ancient adaptive episode of convergent molecular evolution. Proc. Natl Acad. Sci. USA 106, 8986-8991 (2009).
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , pp. 8986-8991
    • Castoe, T.A.1
  • 22
    • 39149119250 scopus 로고    scopus 로고
    • Coexpression coregulation, and cofunctionality of neighboring genes in eukaryotic genomes
    • Michalak, P. Coexpression, coregulation, and cofunctionality of neighboring genes in eukaryotic genomes. Genomics 91, 243-248 (2008).
    • (2008) Genomics , vol.91 , pp. 243-248
    • Michalak, P.1
  • 23
    • 0023666025 scopus 로고
    • Adaptive evolution in the stomach lysozymes of foregut fermenters
    • Stewart, C. B., Schilling, J. W. & Wilson, A. C. Adaptive evolution in the stomach lysozymes of foregut fermenters. Nature 330, 401-404 (1987).
    • (1987) Nature , vol.330 , pp. 401-404
    • Stewart, C.B.1    Schilling, J.W.2    Wilson, A.C.3
  • 24
    • 33745543629 scopus 로고    scopus 로고
    • Parallel adaptive origins of digestive RNases in Asian and African leaf monkeys
    • Zhang, J. Parallel adaptive origins of digestive RNases in Asian and African leaf monkeys. Nat. Genet. 38, 819-823 (2006).
    • (2006) Nat. Genet , vol.38 , pp. 819-823
    • Zhang, J.1
  • 25
    • 33749559644 scopus 로고    scopus 로고
    • Systematically assessing the influence of 3-dimensional structural context on the molecular evolution of mammalian proteomes
    • Choi, S. S., Vallender, E. J. & Lahn, B. T. Systematically assessing the influence of 3-dimensional structural context on the molecular evolution of mammalian proteomes. Mol. Biol. Evol. 23, 2131-2133 (2006).
    • (2006) Mol. Biol. Evol , vol.23 , pp. 2131-2133
    • Choi, S.S.1    Vallender, E.J.2    Lahn, B.T.3
  • 26
    • 0033969946 scopus 로고    scopus 로고
    • Solvent accessibility and purifying selection within proteins of Escherichia coli and Salmonella enterica
    • Bustamante, C. D., Townsend, J. P. & Hartl, D. L. Solvent accessibility and purifying selection within proteins of Escherichia coli and Salmonella enterica. Mol. Biol. Evol. 17, 301-308 (2000).
    • (2000) Mol. Biol. Evol , vol.17 , pp. 301-308
    • Bustamante, C.D.1    Townsend, J.P.2    Hartl, D.L.3
  • 27
    • 0031805465 scopus 로고    scopus 로고
    • Assessing the impact of secondary structure and solvent accessibility on protein evolution
    • Goldman, N., Thorne, J. L. & Jones, D. T. Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics 149, 445-458 (1998).
    • (1998) Genetics , vol.149 , pp. 445-458
    • Goldman, N.1    Thorne, J.L.2    Jones, D.T.3
  • 28
    • 84930721455 scopus 로고    scopus 로고
    • Nonadaptive amino acid convergence rates decrease over time
    • Goldstein, R. A., Pollard, S. T., Shah, S. D. & Pollock, D. D. Nonadaptive amino acid convergence rates decrease over time. Mol. Biol. Evol. 32, 1373-1381 (2015).
    • (2015) Mol. Biol. Evol , vol.32 , pp. 1373-1381
    • Goldstein, R.A.1    Pollard, S.T.2    Shah, S.D.3    Pollock, D.D.4
  • 29
    • 60149102143 scopus 로고    scopus 로고
    • Energetics and the evolution of carnivorous plants-Darwin's 'most wonderful plants in the world
    • Ellison, A. M. & Gotelli, N. J. Energetics and the evolution of carnivorous plants-Darwin's 'most wonderful plants in the world'. J. Exp. Bot. 60, 19-42 (2009).
    • (2009) J. Exp. Bot , vol.60 , pp. 19-42
    • Ellison, A.M.1    Gotelli, N.J.2
  • 30
    • 84883810272 scopus 로고    scopus 로고
    • The Dionaea muscipula ammonium channel DmAMT1 provides NH4+ uptake associated with Venus flytrap's prey digestion
    • Scherzer, S. et al. The Dionaea muscipula ammonium channel DmAMT1 provides NH4+ uptake associated with Venus flytrap's prey digestion. Curr. Biol. 23, 1649-1657 (2013).
    • (2013) Curr. Biol , vol.23 , pp. 1649-1657
    • Scherzer, S.1
  • 31
    • 84982358134 scopus 로고
    • A revised medium for rapid growth and bio assays with tobacco tissue cultures
    • Murashige, T. & Skoog, F. A revised medium for rapid growth and bio assays with tobacco tissue cultures. Physiol. Plant. 15, 473-497 (1962).
    • (1962) Physiol. Plant , vol.15 , pp. 473-497
    • Murashige, T.1    Skoog, F.2
  • 32
    • 79952592810 scopus 로고    scopus 로고
    • A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
    • Marcais, G. & Kingsford, C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27, 764-770 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 764-770
    • Marcais, G.1    Kingsford, C.2
  • 33
    • 79952178131 scopus 로고    scopus 로고
    • High-quality draft assemblies of mammalian genomes from massively parallel sequence data
    • Gnerre, S. et al. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc. Natl Acad. Sci. USA 108, 1513-1518 (2011).
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , pp. 1513-1518
    • Gnerre, S.1
  • 35
    • 84942887758 scopus 로고    scopus 로고
    • SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler
    • Luo, R. et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 1, 18 (2012).
    • (2012) GigaScience , vol.1 , pp. 18
    • Luo, R.1
  • 36
    • 84869814079 scopus 로고    scopus 로고
    • Mind the gap: Upgrading genomes with Pacific Biosciences RS long-read sequencing technology
    • English, A. C. et al. Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PLoS ONE 7, e47768 (2012).
    • (2012) PLoS ONE , vol.7 , pp. e47768
    • English, A.C.1
  • 37
    • 0033555906 scopus 로고    scopus 로고
    • Tandem repeats finder: A program to analyze DNA sequences
    • Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27, 573-580 (1999).
    • (1999) Nucleic Acids Res , vol.27 , pp. 573-580
    • Benson, G.1
  • 38
    • 77956340995 scopus 로고    scopus 로고
    • Comprehensive comparative analysis of strand-specific RNA sequencing methods
    • Levin, J. Z. et al. Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat. Methods 7, 709-715 (2010).
    • (2010) Nat. Methods , vol.7 , pp. 709-715
    • Levin, J.Z.1
  • 39
    • 0034098730 scopus 로고    scopus 로고
    • Using GeneWise in the Drosophila annotation experiment
    • Birney, E. & Durbin, R. Using GeneWise in the Drosophila annotation experiment. Genome Res. 10, 547-548 (2000).
    • (2000) Genome Res , vol.10 , pp. 547-548
    • Birney, E.1    Durbin, R.2
  • 40
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation
    • Trapnell, C. et al. Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511-515 (2010).
    • (2010) Nat. Biotechnol , vol.28 , pp. 511-515
    • Trapnell, C.1
  • 41
    • 84946074739 scopus 로고    scopus 로고
    • The InterPro protein families database: The classification resource after 15 years
    • Mitchell, A. et al. The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res. 43, D213-D221 (2014).
    • (2014) Nucleic Acids Res , vol.43 , pp. D213-D221
    • Mitchell, A.1
  • 42
    • 23144458473 scopus 로고    scopus 로고
    • InterProScan: Protein domains identifier
    • Quevillon, E. et al. InterProScan: protein domains identifier. Nucleic Acids Res. 33, W116-W120 (2005).
    • (2005) Nucleic Acids Res , vol.33 , pp. W116-W120
    • Quevillon, E.1
  • 43
    • 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 23, 1061-1067 (2007).
    • (2007) Bioinformatics , vol.23 , pp. 1061-1067
    • Parra, G.1    Bradnam, K.2    Korf, I.3
  • 44
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: The European molecular biology open software suite
    • Rice, P., Longden, I. & Bleasby, A. EMBOSS: the European molecular biology open software suite. Trends Genet. 16, 276-277 (2000).
    • (2000) Trends Genet , vol.16 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 45
    • 84878022987 scopus 로고    scopus 로고
    • ShortStack: Comprehensive annotation and quantification of small RNA genes
    • Axtell, M. J. ShortStack: comprehensive annotation and quantification of small RNA genes. RNA 19, 740-751 (2013).
    • (2013) RNA , vol.19 , pp. 740-751
    • Axtell, M.J.1
  • 46
    • 84891818318 scopus 로고    scopus 로고
    • MiRBase: Annotating high confidence microRNAs using deep sequencing data
    • Kozomara, A. & Griffiths-Jones, S. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 42, D68-D73 (2014).
    • (2014) Nucleic Acids Res , vol.42 , pp. D68-D73
    • Kozomara, A.1    Griffiths-Jones, S.2
  • 47
    • 0031438685 scopus 로고    scopus 로고
    • Searching for patterns in genomic data
    • Dsouza, M., Larsen, N. & Overbeek, R. Searching for patterns in genomic data. Trends Genet. 13, 497-498 (1997).
    • (1997) Trends Genet , vol.13 , pp. 497-498
    • Dsouza, M.1    Larsen, N.2    Overbeek, R.3
  • 48
    • 82055164092 scopus 로고    scopus 로고
    • ViennaRNA package 2.0
    • Lorenz, R. et al. ViennaRNA package 2.0. Algorithms Mol. Biol. 6, 26 (2011).
    • (2011) Algorithms Mol. Biol , vol.6 , pp. 26
    • Lorenz, R.1
  • 49
    • 2942672580 scopus 로고    scopus 로고
    • Computational identification of plant microRNAs and their targets, including a stress-induced miRNA
    • Jones-Rhoades, M. W. & Bartel, D. P. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell 14, 787-799 (2004).
    • (2004) Mol. Cell , vol.14 , pp. 787-799
    • Jones-Rhoades, M.W.1    Bartel, D.P.2
  • 50
    • 79959967431 scopus 로고    scopus 로고
    • PsRNATarget: A plant small RNA target analysis server
    • Dai, X. & Zhao, P. X. psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res. 39, W155-W159 (2011).
    • (2011) Nucleic Acids Res , vol.39 , pp. W155-W159
    • Dai, X.1    Zhao, P.X.2
  • 51
    • 84899553363 scopus 로고    scopus 로고
    • RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies
    • Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312-1313 (2014).
    • (2014) Bioinformatics , vol.30 , pp. 1312-1313
    • Stamatakis, A.1
  • 52
    • 84919900743 scopus 로고    scopus 로고
    • Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times
    • Zeng, L. et al. Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times. Nat. Commun. 5, 4956 (2014).
    • (2014) Nat. Commun , vol.5 , pp. 4956
    • Zeng, L.1
  • 53
    • 84909619344 scopus 로고    scopus 로고
    • Phylotranscriptomic analysis of the origin and early diversification of land plants
    • Wickett, N. J. et al. Phylotranscriptomic analysis of the origin and early diversification of land plants. Proc. Natl Acad. Sci. USA 111, E4859-E4868 (2014).
    • (2014) Proc. Natl Acad. Sci. USA , vol.111 , pp. E4859-E4868
    • Wickett, N.J.1
  • 54
    • 77955991477 scopus 로고    scopus 로고
    • The age and diversification of the angiosperms re-revisited
    • Bell, C. D., Soltis, D. E. & Soltis, P. S. The age and diversification of the angiosperms re-revisited. Am. J. Bot. 97, 1296-1303 (2010).
    • (2010) Am. J. Bot , vol.97 , pp. 1296-1303
    • Bell, C.D.1    Soltis, D.E.2    Soltis, P.S.3
  • 55
    • 0346494835 scopus 로고    scopus 로고
    • The TIGR Plant Repeat Databases: A collective resource for the identification of repetitive sequences in plants
    • Ouyang, S. & Buell, C. R. The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants. Nucleic Acids Res. 32, D360-D363 (2004).
    • (2004) Nucleic Acids Res , vol.32 , pp. D360-D363
    • Ouyang, S.1    Buell, C.R.2
  • 57
    • 67650757433 scopus 로고    scopus 로고
    • TrimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses
    • Capella-Gutierrez, S., Silla-Martinez, J. M. & Gabaldon, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972-1973 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1972-1973
    • Capella-Gutierrez, S.1    Silla-Martinez, J.M.2    Gabaldon, T.3
  • 58
    • 79954529507 scopus 로고    scopus 로고
    • ProtTest 3: Fast selection of best-fit models of protein evolution
    • Darriba, D., Taboada, G. L., Doallo, R. & Posada, D. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27, 1164-1165 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 1164-1165
    • Darriba, D.1    Taboada, G.L.2    Doallo, R.3    Posada, D.4
  • 59
    • 0037314098 scopus 로고    scopus 로고
    • R8s: Inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock
    • Sanderson, M. J. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19, 301-302 (2003).
    • (2003) Bioinformatics , vol.19 , pp. 301-302
    • Sanderson, M.J.1
  • 60
    • 84856121183 scopus 로고    scopus 로고
    • BadiRate: Estimating family turnover rates by likelihood-based methods
    • Librado, P., Vieira, F. G. & Rozas, J. BadiRate: estimating family turnover rates by likelihood-based methods. Bioinformatics 28, 279-281 (2012).
    • (2012) Bioinformatics , vol.28 , pp. 279-281
    • Librado, P.1    Vieira, F.G.2    Rozas, J.3
  • 61
    • 84929645881 scopus 로고    scopus 로고
    • High gene family turnover rates and gene space adaptation in the compact genome of the carnivorous plant Utricularia gibba
    • Carretero-Paulet, L. et al. High gene family turnover rates and gene space adaptation in the compact genome of the carnivorous plant Utricularia gibba. Mol. Biol. Evol. 32, 1284-1295 (2015).
    • (2015) Mol. Biol. Evol , vol.32 , pp. 1284-1295
    • Carretero-Paulet, L.1
  • 62
    • 23844525077 scopus 로고    scopus 로고
    • Repbase Update, a database of eukaryotic repetitive elements
    • Jurka, J. et al. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110, 462-467 (2005).
    • (2005) Cytogenet. Genome Res , vol.110 , pp. 462-467
    • Jurka, J.1
  • 63
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B 57, 289-300 (1995).
    • (1995) J. R. Stat. Soc. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 64
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).
    • (2013) Genome Biol , vol.14 , pp. R36
    • Kim, D.1
  • 65
    • 84897397058 scopus 로고    scopus 로고
    • FeatureCounts: An efficient general purpose program for assigning sequence reads to genomic features
    • Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923-930 (2014).
    • (2014) Bioinformatics , vol.30 , pp. 923-930
    • Liao, Y.1    Smyth, G.K.2    Shi, W.3
  • 66
    • 84880002392 scopus 로고    scopus 로고
    • TCC: An R package for comparing tag count data with robust normalization strategies
    • Sun, J., Nishiyama, T., Shimizu, K. & Kadota, K. TCC: an R package for comparing tag count data with robust normalization strategies. BMC Bioinformatics 14, 219 (2013).
    • (2013) BMC Bioinformatics , vol.14 , pp. 219
    • Sun, J.1    Nishiyama, T.2    Shimizu, K.3    Kadota, K.4
  • 67
    • 77953176036 scopus 로고    scopus 로고
    • A scaling normalization method for differential expression analysis of RNA-seq data
    • Robinson, M. D. & Oshlack, A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 11, 2010-2011 (2010).
    • (2010) Genome Biol , vol.11 , pp. 2010-2011
    • Robinson, M.D.1    Oshlack, A.2
  • 68
    • 75249087100 scopus 로고    scopus 로고
    • EdgeR: A bioconductor package for differential expression analysis of digital gene expression data
    • Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 69
    • 41149085992 scopus 로고    scopus 로고
    • Small-sample estimation of negative binomial dispersion with applications to SAGE data
    • Robinson, M. D. & Smyth, G. K. Small-sample estimation of negative binomial dispersion, with applications to SAGE data. Biostatistics 9, 321-332 (2008).
    • (2008) Biostatistics , vol.9 , pp. 321-332
    • Robinson, M.D.1    Smyth, G.K.2
  • 70
    • 79960264362 scopus 로고    scopus 로고
    • Full-length transcriptome assembly from RNA-seq data without a reference genome
    • Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat. Biotechnol. 29, 644-652 (2011).
    • (2011) Nat. Biotechnol , vol.29 , pp. 644-652
    • Grabherr, M.G.1
  • 72
    • 84890282706 scopus 로고    scopus 로고
    • Secreted major Venus flytrap chitinase enables digestion of Arthropod prey
    • Paszota, P. et al. Secreted major Venus flytrap chitinase enables digestion of Arthropod prey. Biochim. Biophys. Acta 2, 374-383 (2014).
    • (2014) Biochim. Biophys. Acta , vol.2 , pp. 374-383
    • Paszota, P.1
  • 73
    • 79952120555 scopus 로고    scopus 로고
    • A cysteine endopeptidase ('dionain') is involved in the digestive fluid of Dionaea muscipula (Venus's fly-trap)
    • Takahashi, K. et al. A cysteine endopeptidase ('dionain') is involved in the digestive fluid of Dionaea muscipula (Venus's fly-trap). Biosci. Biotechnol. Biochem. 75, 346-348 (2011).
    • (2011) Biosci. Biotechnol. Biochem , vol.75 , pp. 346-348
    • Takahashi, K.1
  • 74
    • 3142679311 scopus 로고    scopus 로고
    • Enzymic and structural characterization of nepenthesin, a unique member of a novel subfamily of aspartic proteinases
    • Athauda, S. B. et al. Enzymic and structural characterization of nepenthesin, a unique member of a novel subfamily of aspartic proteinases. Biochem. J. 381, 295-306 (2004).
    • (2004) Biochem. J , vol.381 , pp. 295-306
    • Athauda, S.B.1
  • 75
    • 84897639416 scopus 로고    scopus 로고
    • Characterization and heterologous expression of a PR-1 protein from traps of the carnivorous plant Nepenthes mirabilis
    • Buch, F., Pauchet, Y., Rott, M. & Mithofer, A. Characterization and heterologous expression of a PR-1 protein from traps of the carnivorous plant Nepenthes mirabilis. Phytochemistry 100, 43-50 (2014).
    • (2014) Phytochemistry , vol.100 , pp. 43-50
    • Buch, F.1    Pauchet, Y.2    Rott, M.3    Mithofer, A.4
  • 76
    • 80052911154 scopus 로고    scopus 로고
    • Functional characterization of a class III acid endochitinase from the traps of the carnivorous pitcher plant genus
    • Rottloff, S. et al. Functional characterization of a class III acid endochitinase from the traps of the carnivorous pitcher plant genus, Nepenthes. J. Exp. Bot. 62, 4639-4647 (2011).
    • (2011) Nepenthes. J. Exp. Bot , vol.62 , pp. 4639-4647
    • Rottloff, S.1
  • 77
    • 39749087658 scopus 로고    scopus 로고
    • Proteome analysis of pitcher fluid of the carnivorous plant Nepenthes alata
    • Hatano, N. & Hamada, T. Proteome analysis of pitcher fluid of the carnivorous plant Nepenthes alata. J. Proteome Res. 7, 809-816 (2008).
    • (2008) J. Proteome Res , vol.7 , pp. 809-816
    • Hatano, N.1    Hamada, T.2
  • 78
    • 84864103899 scopus 로고    scopus 로고
    • Proteomic analysis of secreted protein induced by a component of prey in pitcher fluid of the carnivorous plant Nepenthes alata
    • Hatano, N. & Hamada, T. Proteomic analysis of secreted protein induced by a component of prey in pitcher fluid of the carnivorous plant Nepenthes alata. J. Proteomics 75, 4844-4852 (2012).
    • (2012) J. Proteomics , vol.75 , pp. 4844-4852
    • Hatano, N.1    Hamada, T.2
  • 79
    • 84866887347 scopus 로고    scopus 로고
    • Molecular and functional evolution of class i chitinases for plant carnivory in the Caryophyllales
    • Renner, T. & Specht, C. D. Molecular and functional evolution of class I chitinases for plant carnivory in the Caryophyllales. Mol. Biol. Evol. 29, 2971-2985 (2012).
    • (2012) Mol. Biol. Evol , vol.29 , pp. 2971-2985
    • Renner, T.1    Specht, C.D.2
  • 80
    • 33747871549 scopus 로고    scopus 로고
    • Isolation and characterization of chitinase genes from pitchers of the carnivorous plant Nepenthes khasiana
    • Eilenberg, H., Pnini-Cohen, S., Schuster, S., Movtchan, A. & Zilberstein, A. Isolation and characterization of chitinase genes from pitchers of the carnivorous plant Nepenthes khasiana. J. Exp. Bot. 57, 2775-2784 (2006).
    • (2006) J. Exp. Bot , vol.57 , pp. 2775-2784
    • Eilenberg, H.1    Pnini-Cohen, S.2    Schuster, S.3    Movtchan, A.4    Zilberstein, A.5
  • 81
    • 28244492028 scopus 로고    scopus 로고
    • Tentacles of in vitro-grown round-leaf sundew (Drosera rotundifolia L.) show induction of chitinase activity upon mimicking the presence of prey
    • Matusíková, I. et al. Tentacles of in vitro-grown round-leaf sundew (Drosera rotundifolia L.) show induction of chitinase activity upon mimicking the presence of prey. Planta 222, 1020-1027 (2005).
    • (2005) Planta , vol.222 , pp. 1020-1027
    • Matusíková, I.1
  • 82
    • 0036934796 scopus 로고    scopus 로고
    • Aspartic proteinases are expressed in pitchers of the carnivorous plant Nepenthes alata Blanco
    • An, C.-I., Fukusaki, E. & Kobayashi, A. Aspartic proteinases are expressed in pitchers of the carnivorous plant Nepenthes alata Blanco. Planta 214, 661-667 (2002).
    • (2002) Planta , vol.214 , pp. 661-667
    • An, C.-I.1    Fukusaki, E.2    Kobayashi, A.3
  • 83
    • 80052020960 scopus 로고    scopus 로고
    • Transcriptome analysis of Sarracenia, an insectivorous plant
    • Srivastava, A., Rogers, W. L., Breton, C. M., Cai, L. & Malmberg, R. L. Transcriptome analysis of Sarracenia, an insectivorous plant. DNA Res. 18, 253-261 (2011).
    • (2011) DNA Res , vol.18 , pp. 253-261
    • Srivastava, A.1    Rogers, W.L.2    Breton, C.M.3    Cai, L.4    Malmberg, R.L.5
  • 84
    • 84929498011 scopus 로고    scopus 로고
    • Transcriptome and genome size analysis of the Venus flytrap
    • Jensen, M. K. et al. Transcriptome and genome size analysis of the Venus flytrap. PLoS ONE 10, e0123887 (2015).
    • (2015) PLoS ONE , vol.10 , pp. e0123887
    • Jensen, M.K.1
  • 85
    • 84875619226 scopus 로고    scopus 로고
    • MAFFT multiple sequence alignment software version 7: Improvements in performance and usability
    • Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772-780 (2013).
    • (2013) Mol. Biol. Evol , vol.30 , pp. 772-780
    • Katoh, K.1    Standley, D.M.2
  • 87
    • 36448938389 scopus 로고    scopus 로고
    • The human phylome
    • Huerta-Cepas, J. et al. The human phylome. Genome Biol. 8, 934-941 (2007).
    • (2007) Genome Biol , vol.8 , pp. 934-941
    • Huerta-Cepas, J.1
  • 88
    • 84962897215 scopus 로고    scopus 로고
    • ETE 3: Reconstruction, analysis, and visualization of phylogenomic data
    • Huerta-Cepas, J., Serra, F. & Bork, P. ETE 3: reconstruction, analysis, and visualization of phylogenomic data. Mol. Biol. Evol. 33, 1635-1638 (2016).
    • (2016) Mol. Biol. Evol , vol.33 , pp. 1635-1638
    • Huerta-Cepas, J.1    Serra, F.2    Bork, P.3
  • 89
    • 79960004119 scopus 로고    scopus 로고
    • Interactive Tree of Life v2: Online annotation and display of phylogenetic trees made easy
    • Letunic, I. & Bork, P. Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res. 39, W475-W478 (2011).
    • (2011) Nucleic Acids Res , vol.39 , pp. W475-W478
    • Letunic, I.1    Bork, P.2
  • 90
    • 84941103248 scopus 로고    scopus 로고
    • ArrayExpress update-simplifying data submissions
    • Kolesnikov, N. et al. ArrayExpress update-simplifying data submissions. Nucleic Acids Res. 43, D1113-D1116 (2015).
    • (2015) Nucleic Acids Res , vol.43 , pp. D1113-D1116
    • Kolesnikov, N.1
  • 91
    • 0142121516 scopus 로고    scopus 로고
    • Exploration, normalization, and summaries of high density oligonucleotide array probe level data
    • Irizarry, R. A. et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4, 249-264 (2003).
    • (2003) Biostatistics , vol.4 , pp. 249-264
    • Irizarry, R.A.1
  • 92
    • 79955109754 scopus 로고    scopus 로고
    • PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment
    • Sipos, B., Massingham, T., Jordan, G. E. & Goldman, N. PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment. BMC Bioinformatics 12, 104 (2011).
    • (2011) BMC Bioinformatics , vol.12 , pp. 104
    • Sipos, B.1    Massingham, T.2    Jordan, G.E.3    Goldman, N.4
  • 93
    • 78650481676 scopus 로고    scopus 로고
    • A Bayesian approach for fast and accurate gene tree reconstruction
    • Rasmussen, M. D. & Kellis, M. A Bayesian approach for fast and accurate gene tree reconstruction. Mol. Biol. Evol. 28, 273-290 (2011).
    • (2011) Mol. Biol. Evol , vol.28 , pp. 273-290
    • Rasmussen, M.D.1    Kellis, M.2
  • 94
    • 84871822882 scopus 로고    scopus 로고
    • TreeFix: Statistically informed gene tree error correction using species trees
    • Wu, Y. C., Rasmussen, M. D., Bansal, M. S. & Kellis, M. TreeFix: statistically informed gene tree error correction using species trees. Syst. Biol. 62, 110-120 (2013).
    • (2013) Syst. Biol , vol.62 , pp. 110-120
    • Wu, Y.C.1    Rasmussen, M.D.2    Bansal, M.S.3    Kellis, M.4
  • 95
    • 0342614926 scopus 로고    scopus 로고
    • Codon usage tabulated from international DNA sequence databases: Status for the year 2000
    • Nakamura, Y., Gojobori, T. & Ikemura, T. Codon usage tabulated from international DNA sequence databases: status for the year 2000. Nucleic Acids Res. 28, 292 (2000).
    • (2000) Nucleic Acids Res , vol.28 , pp. 292
    • Nakamura, Y.1    Gojobori, T.2    Ikemura, T.3
  • 96
    • 0032766857 scopus 로고    scopus 로고
    • Multiple comparisons of log-likelihoods with applications to phylogenetic inference
    • Shimodaira, H. & Hasegawa, M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16, 1114-1116 (1999).
    • (1999) Mol. Biol. Evol , vol.16 , pp. 1114-1116
    • Shimodaira, H.1    Hasegawa, M.2
  • 97
    • 69949126557 scopus 로고    scopus 로고
    • PhyloBayes 3: A Bayesian software package for phylogenetic reconstruction and molecular dating
    • Lartillot, N., Lepage, T. & Blanquart, S. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25, 2286-2288 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 2286-2288
    • Lartillot, N.1    Lepage, T.2    Blanquart, S.3
  • 98
    • 84946650481 scopus 로고
    • Probable inference, the law of succession, and statistical inference
    • Wilson, E. B. Probable inference, the law of succession, and statistical inference. J. Am. Stat. Assoc. 22, 209-212 (1927).
    • (1927) J. Am. Stat. Assoc , vol.22 , pp. 209-212
    • Wilson, E.B.1
  • 99
    • 0000993098 scopus 로고
    • Contingency tables involving small numbers and the χ 2 test
    • Yates, F. Contingency tables involving small numbers and the χ 2 test. J. R. Stat. Soc. 1(suppl.) 217-235 (1934).
    • (1934) J. R. Stat. Soc , vol.1 , pp. 217-235
    • Yates, F.1
  • 100
    • 0000992663 scopus 로고
    • On the use and interpretation of certain test criteria for purposes of statistical inference: Part i
    • Neyman, J. & Pearson, E. S. On the use and interpretation of certain test criteria for purposes of statistical inference: part I. Biometrika 20A, 175-240 (1928).
    • (1928) Biometrika , vol.20 A , pp. 175-240
    • Neyman, J.1    Pearson, E.S.2
  • 101
    • 84904815625 scopus 로고    scopus 로고
    • SWISS-MODEL: Modelling protein tertiary and quaternary structure using evolutionary information
    • Biasini, M. et al. SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res. 42, W252-W258 (2014).
    • (2014) Nucleic Acids Res , vol.42 , pp. W252-W258
    • Biasini, M.1
  • 102
    • 4444221565 scopus 로고    scopus 로고
    • UCSF Chimera -a visualization system for exploratory research and analysis
    • Pettersen, E. F. et al. UCSF Chimera -a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605-1612 (2004).
    • (2004) J. Comput. Chem , vol.25 , pp. 1605-1612
    • Pettersen, E.F.1
  • 103
    • 84888331478 scopus 로고    scopus 로고
    • Maximum allowed solvent accessibilites of residues in proteins
    • Tien, M. Z., Meyer, A. G., Sydykova, D. K., Spielman, S. J. & Wilke, C. O. Maximum allowed solvent accessibilites of residues in proteins. PLoS ONE 8, e80635 (2013).
    • (2013) PLoS ONE , vol.8 , pp. e80635
    • Tien, M.Z.1    Meyer, A.G.2    Sydykova, D.K.3    Spielman, S.J.4    Wilke, C.O.5


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