Midgut transcriptome profiling of Anoplophora glabripennis, a lignocellulose degrading cerambycid beetle

详细信息    查看全文

• 作者：Erin D Scully (13)
  Kelli Hoover (14)
  John E Carlson (15) (16)
  Ming Tien (17)
  Scott M Geib (18)
  
• 关键词：Cellulase ; Carboxylesterase ; Cytochrome P450 ; Xylanase ; Comparative transcriptomics ; Hemicellulose ; Biofuels ; Beta ; glucosidase
• 刊名：BMC Genomics
• 出版年：2013
• 出版时间：December 2013
• 年：2013
• 卷：14
• 期：1
• 全文大小：1,415 KB
• 参考文献：1. Grimaldi DA: 400 million years on six legs: on the origin and early evolution of Hexapoda. / Arthropod Struct Dev 2010,39(2-):191-03.
  2. Schowalter TD: Insect responses to major landscape-level disturbance. / Annu Rev Entomol 2012, 57:1-0.
  3. Friend WG: Nutritional requirements of phytophagous insects. / Annu Rev Entomol 1958, 3:57-4.
  4. Schloss PD, Delalibera I, Handelsman J, Raffa KF: Bacteria associated with the guts of two wood-boring beetles: Anoplophora glabripennis and Saperda vestita (Cerambycidae). / Environ Entomol 2006,35(3):625-29.
  5. Xueyan Y, Jiaxi Z, Fugui W, Min C: A study on the feeding habits of the larvae of two species of longicorn (Anoplophora) to different tree species. / J Northwest Forest Coll 1995,2(10):1-.
  6. Hu JF, Angeli S, Schuetz S, Luo YQ, Hajek AE: Ecology and management of exotic and endemic Asian longhorned beetle Anoplophora glabripennis. / Agric For Entomol 2009,11(4):359-75.
  7. Haack RA, Law KR, Mastro VC, Ossenbruggen HS, Raimo BJ: New York’s battle with the Asian long-horned beetle. / J Forest 1997,95(12):11-5.
  8. Nowak DJ, Pasek JE, Sequeira RA, Crane DE, Mastro VC: Potential effect of Anoplophora glabripennis (Coleoptera : Cerambycidae) on urban trees in the United States. / J Econ Entomol 2001,94(1):116-22.
  9. Haack RA, Herard F, Sun JH, Turgeon JJ: Managing Invasive Populations of Asian Longhorned Beetle and Citrus Longhorned Beetle: A Worldwide Perspective. In / Annual Review of Entomology. / Volume 55. Palo Alto: Annual Reviews; 2010:521-46.
  10. Ugine TA, Gardescu S, Lewis PA, Hajek AE: Efficacy of imidacloprid, trunk-injected into Acer platanoides, for control of adult Asian longhorned beetles (Coleoptera: Cerambycidae). / J Econ Entomol 2012,105(6):2015-028.
  11. Ugine TA, Gardescu S, Hajek AE: The effect of exposure to imidacloprid on Asian longhorned beetle (Coleoptera: Cerambycidae) survival and reproduction. / J Econ Entomol 2011,104(6):1942-949.
  12. Lingafelter SW, Hoebke ER: / Revision of Anoplophora (Coleoptera: Cerambycidae). Washington, DC: Entomological Society of Washington; 2002:236.
  13. Petterson RC: The chemical composition of wood . In / The Chemistry of Solid Wood. Edited by: Roger R. Washington, D.C: American Chemical Society; 1984:57-26.
  14. Kirk TK, Farrell RL: Enzymatic combustion - the microbial-degradation of lignin. / Annu Rev Microbiol 1987, 41:465-05.
  15. Tien M, Kirk TK: Lignin-degrading enzyme from Phanerochaete chrysosporium - purification, characterization, and catalytic properties of a unique H2o2-requiring xxygenase. / Proc Natl Acad Sci USA Biol Sci 1984,81(8):2280-284.
  16. Mattson WJ: Herbivory in relation to plant nitrogen-content. / Annu Rev Ecol Syst 1980, 11:119-61.
  17. Keller B, Templeton MD, Lamb CJ: Specific localization of a plant-cell wall glycine-rich protein in protoxylem cells of the vascular system. / Proc Natl Acad Sci USA 1989,86(5):1529-533.
  18. Dillon RJ, Dillon VM: The gut bacteria of insects: nonpathogenic interactions. / Annu Rev Entomol 2004, 49:71-2.
  19. Werren JH: Symbionts provide pesticide detoxification. / Proc Natl Acad Sci USA 2012,109(22):8364-365.
  20. Beaver R, Wilding N, Collins N, Hammond P, Webber J: / Insect-Fungus Relationships in the Bark and Ambrosia Beetles. Academic Press; 1989:121-43. [ / Insect-Fungus Interactions 14th Symposium of the Royal Entomological Society of London in Collaboration with the British Mycological Society]
  21. Raffa KF: Genetic engineering of trees to enhance resistance to insects. / Bioscience 1989,39(8):524-34.
  22. Geib SM, Filley TR, Hatcher PG, Hoover K, Carlson JE, Jimenez-Gasco Mdel M, Nakagawa-Izumi A, Sleighter RL, Tien M: Lignin degradation in wood-feeding insects. / Proc Natl Acad Sci USA 2008,105(35):12932-2937.
  23. Geib SM, Jimenez-Gasco Mdel M, Carlson JE, Tien M, Hoover K: Effect of host tree species on cellulase activity and bacterial community composition in the gut of larval Asian longhorned beetle. / Environ Entomol 2009,38(3):686-99.
  24. Geib SM, Tien M, Hoover K: Identification of proteins involved in lignocellulose degradation using in gel zymogram analysis combined with mass spectroscopy-based peptide analysis of gut proteins from larval Asian longhorned beetles, Anoplophora glabripennis. / Insect Sci 2010,17(3):253-64.
  25. Scully ED, Geib SM, Hoover K, Tien M, Tringe SG, Barry KW, del Rio TG, Chovatia M, Herr JR, Carlson JE: Metagenomic profiling reveals lignocellulose degrading system in a microbial community associated with a wood-feeding beetle. / PloS One 2013,8(9):e73827.
  26. Sugimura M, Watanabe H, Lo N, Saito H: Purification, characterization, cDNA cloning and nucleotide sequencing of a cellulase from the yellow-spotted longicorn beetle, Psacothea hilaris. / Eur J Biochem 2003,270(16):3455-460.
  27. Calderon-Cortes N, Watanabe H, Cano-Camacho H, Zavala-Paramo G, Quesada M: cDNA cloning, homology modelling and evolutionary insights into novel endogenous cellulases of the borer beetle Oncideres albomarginata chamela (Cerambycidae). / Insect Mol Biol 2010,19(3):323-36.
  28. Pauchet Y, Wilkinson P, van Munster M, Augustin S, Pauron D, Ffrench-Constant RH: Pyrosequencing of the midgut transcriptome of the poplar leaf beetle Chrysomela tremulae reveals new gene families in Coleoptera. / Insect Biochem Mol Biol 2009,39(5-):403-13.
  29. Jongsma MA, Bolter C: The adaptation of insects to plant protease inhibitors. / J Insect Physiol 1997,43(10):885-95.
  30. Levin DA: The chemical defenses of plants to pathogens and herbivores. / Annu Rev Ecol Syst 1976, 7:121-59.
  31. Walling LL: Avoiding effective defenses: strategies employed by phloem-feeding insects. / Plant Physiol 2008,146(3):859-66.
  32. Scott JG, Liu N, Wen Z: Insect cytochromes P450: diversity, insecticide resistance and tolerance to plant toxins. / Comp Biochem Physiol C Pharmacol Toxicol Endocrinol 1998,121(1-):147-55.
  33. Li X, Berenbaum MR, Schuler MA: Plant allelochemicals differentially regulate Helicoverpa zea cytochrome P450 genes. / Insect Mol Biol 2002,11(4):343-51.
  34. Scrivener AM, Watanabe H, Noda H: Diet and carbohydrate digestion in the yellow-spotted longicorn beetle Psacothea hilaris. / J Insect Physiol 1997,43(11):1039-052.
  35. Brennan Y, Callen WN, Christoffersen L, Dupree P, Goubet F, Healey S, Hernandez M, Keller M, Li K, Palackal N, / et al.: Unusual microbial xylanases from insect guts. / Appl Environ Microbiol 2004,70(6):3609-617.
  36. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B: The carbohydrate-active EnZymes database (CAZy): an expert resource for glycogenomics. / Nucleic Acids Res 2009, 37:D233-D238.
  37. Suh SO, Marshall CJ, McHugh JV, Blackwell M: Wood ingestion by passalid beetles in the presence of xylose-fermenting gut yeasts. / Mol Ecol 2003,12(11):3137-145.
  38. Suh SO, Noda H, Blackwell M: Insect symbiosis: derivation of yeast-like endosymbionts within an entomopathogenic filamentous lineage. / Mol Biol Evol 2001,18(6):995-000.
  39. Scheller HV, Ulvskov P: Hemicelluloses. / Annu Rev Plant Biol 2010,61(1):263-89.
  40. Lee SJ, Kim SR, Yoon HJ, Kim I, Lee KS, Je YH, Lee SM, Seo SJ, Sohn HD, Jin BR: cDNA cloning, expression, and enzymatic activity of a cellulase from the mulberry longicorn beetle, Apriona germari. / Comp Biochem Phys B 2004,139(1):107-16.
  41. Keeling CI, Yuen MM, Liao NY, Docking TR, Chan SK, Taylor GA, Palmquist DL, Jackman SD, Nguyen A, Li M: Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest. / Genome Biol 2013,14(3):R27.
  42. Pauchet Y, Wilkinson P, Chauhan R, Ffrench-Constant RH: Diversity of beetle genes encoding novel plant cell wall degrading enzymes. / PLoS One 2010,5(12):e15635.
  43. Johnson KS, Rabosky D: Phylogenetic distribution of cysteine proteinases in beetles: evidence for an evolutionary shift to an alkaline digestive strategy in Cerambycidae. / Comp Biochem Physiol B Biochem Mol Biol 2000,126(4):609-19.
  44. Brás JL, Cartmell A, Carvalho ALM, Verzé G, Bayer EA, Vazana Y, Correia MA, Prates JA, Ratnaparkhe S, Boraston AB: Structural insights into a unique cellulase fold and mechanism of cellulose hydrolysis. / Proc Natl Acad Sci 2011,108(13):5237-242.
  45. Irwin DC, Spezio M, Walker LP, Wilson DB: Activity studies of eight purified cellulases: specificity, synergism, and binding domain effects. / Biotechnol Bioeng 1993,42(8):1002-013.
  46. Andri? P, Meyer AS, Jensen PA, Dam-Johansen K: Reactor design for minimizing product inhibition during enzymatic lignocellulose hydrolysis: I Significance and mechanism of cellobiose and glucose inhibition on cellulolytic enzymes. / Biotechnol Adv 2010,28(3):308-24.
  47. Spicer R: Senescence in secondary xylem: heartwood formation as an active developmental program. In / Vascular Transport in Plants. Edited by: Holbrook N, Zwieniecki M. Oxford: Elsevier; 2005:457-75.
  48. Eggert C, Temp U, Eriksson KEL: Laccase is essential for lignin degradation by the white-rot fungus Pycnoporus cinnabarinus. / FEBS Lett 1997,407(1):89-2.
  49. Coy MR, Salem TZ, Denton JS, Kovaleva ES, Liu Z, Barber DS, Campbell JH, Davis DC, Buchman GW, Boucias DG, / et al.: Phenol-oxidizing laccases from the termite gut. / Insect Biochem Mol Biol 2010,40(10):723-32.
  50. Eggert C, Temp U, Dean JF, Eriksson KE: A fungal metabolite mediates degradation of non-phenolic lignin structures and synthetic lignin by laccase. / FEBS Lett 1996,391(1-):144-48.
  51. Brunet P: The metabolism of the aromatic amino acids concerned in the cross-linking of insect cuticle. / Insect Biochem 1980,10(5):467-00.
  52. Sethi A, Slack JM, Kovaleva ES, Buchman GW, Scharf ME: Lignin-associated metagene expression in a lignocellulose-digesting termite. / Insect Biochem Mol Biol 2013,43(1):91-01.
  53. Kavanagh KL, Klimacek M, Nidetzky B, Wilson DK: The structure of apo and holo forms of xylose reductase, a dimeric aldo-keto reductase from Candida tenuis. / Biochemistry 2002,41(28):8785-795.
  54. Ford G, Ellis EM: Three aldo–keto reductases of the yeast Saccharomyces cerevisiae. / Chem Biol Interact 2001, 130-32:685-98.
  55. Muheima A, Walder R, Sanglard D, Reiser J, Schoemaker HE, Leisola MS: Purification and properties of an aryl?alcohol dehydrogenase from the white?rot fungus Phanerochaete chrysosporium. / Eur J Biochem 1991,195(2):369-75.
  56. Tam LT, Eymann C, Albrecht D, Sietmann R, Schauer F, Hecker M, Antelmann H: Differential gene expression in response to phenol and catechol reveals different metabolic activities for the degradation of aromatic compounds in Bacillus subtilis. / Environ Microbiol 2006,8(8):1408-427.
  57. Jeffries TW: Biodegradation of lignin-carbohydrate complexes. / Biodegradation 1990,1(2-):163-76.
  58. Butler J, Buckerfield J: Digestion of lignin by termites. / Soil Biol Biochem 1979,11(5):507-13.
  59. Dowd PF, Lagrimini LM: The role of peroxidase in insect defenses. In / Advances in Insect Control: the Role of Transgenic Plants. Edited by: Carozzi N, Koziel M. New York: ; 1997:195-23.
  60. Fretland AJ, Omiecinski CJ: Epoxide hydrolases: biochemistry and molecular biology. / Chem Biol Interact 2000,129(1-):41-9.
  61. Dunn JP, Potter DA, Kimmerer TW: Carbohydrate reserves, radial growth, and mechanisms of resistance of oak trees to phloem-boring insects. / Oecologia 1990,83(4):458-68.
  62. Taylor AM, Gartner BL, Morrell JJ: Heartwood formation and natural durability—a review. / Wood Fiber Sci 2002,34(4):587-11.
  63. Lee K, Berenbaum MR: Action of antioxidant enzymes and cytochrome P-50 monooxygenases in the cabbage looper in response to plant phototoxins. / Arch Insect Biochem 1989,10(2):151-62.
  64. Bernhardt R: Cytochromes P450 as versatile biocatalysts. / J Biotechnol 2006,124(1):128-45.
  65. Zhu F, Moural TW, Shah K, Palli SR: Integrated analysis of cytochrome P450 gene superfamily in the red flour beetle, Tribolium castaneum. / BMC Genomics 2013,14(1):174.
  66. Consortium TS: The genome of the model beetle and pest Tribolium castaneum. / Nature 2008,452(7190):949-55.
  67. Scott JG, Wen Z: Cytochromes P450 of insects: the tip of the iceberg. / Pest Manag Sci 2001,57(10):958-67.
  68. Ishida Y, Leal WS: Rapid inactivation of a moth pheromone. / Proc Natl Acad Sci USA 2005,102(39):14075-4079.
  69. Oakeshott J, Claudianos C, Newcomb R, Russell R: Biochemical genetics and genomics of insect esterases. In / Insect pharmacology: channels, receptors, toxins and enzymes. Edited by: Gilbert LI, Gill SS. London: Elsevier; 2010:229-01.
  70. Lindroth RL: Host plant alteration of detoxication activity in Papilio glaucus glaucus. / Entomologia experimentalis et applicata 1989,50(1):29-5.
  71. Teese MG, Campbell PM, Scott C, Gordon KH, Southon A, Hovan D, Robin C, Russell RJ, Oakeshott JG: Gene identification and proteomic analysis of the esterases of the cotton bollworm, Helicoverpa armigera. / Insect Biochem Mol Biol 2010,40(1):1-6.
  72. Boeckler GA, Gershenzon J, Unsicker SB: Phenolic glycosides of the Salicaceae and their role as anti-herbivore defenses. / Phytochemistry 2011,72(13):1497-509.
  73. Kostaropoulos I, Papadopoulos AI, Metaxakis A, Boukouvala E, Papadopoulou-Mourkidou E: Glutathione S–transferase in the defence against pyrethroids in insects. / Insect Biochem Mol Biol 2001,31(4):313-19.
  74. Enayati AA, Ranson H, Hemingway J: Insect glutathione transferases and insecticide resistance. / Insect Mol Biol 2005,14(1):3-.
  75. Wadleigh RW, Yu SJ: Metabolism of an organothiocyanate allelochemical by glutathione transferase in three lepidopterous insects. / J Econ Entomol 1988,81(3):776-80.
  76. Lee K: Glutathione S-transferase activities in phytophagous insects: Induction and inhibition by plant phototoxins and phenols. / Insect Biochemistry 1991,21(4):353-61.
  77. Cowling EB, Merrill W: Nitrogen in wood and its role in wood deterioration. / Can J Bot 1966,44(11):1539-554.
  78. Sasaki T, Ishikawa H: Production of essential amino acids from glutamate by mycetocyte symbionts of the pea aphid, Acyrthosiphon pisum. / J Insect Physiol 1995,41(1):41-6.
  79. Isoe J, Scaraffia PY: Urea synthesis and excretion in Aedes aegypti mosquitoes are regulated by a unique cross-talk mechanism. / PloS One 2013,8(6):e65393.
  80. Nagaoka S, Takata Y, Kato K: Identification of two arginases generated by alternative splicing in the silkworm, Bombyx mori. / Arch Insect Biochem 2011,76(2):97-13.
  81. Ryan CA: Protease inhibitors in plants: genes for improving defenses against insects and pathogens. / Annu Rev Phytopathol 1990,28(1):425-49.
  82. Bian X, Shaw BD, Han Y, Christeller JT: Midgut proteinase activities in larvae of Anoplophora glabripennis (Coleoptera: Cerambycidae) and their interaction with proteinase inhibitors. / Arch Insect Biochem 1996,31(1):23-7.
  83. Suh SO, McHugh JV, Pollock DD, Blackwell M: The beetle gut: a hyperdiverse source of novel yeasts. / Mycol Res 2005,109(Pt 3):261-65.
  84. Ha E-M, Oh C-T, Bae YS, Lee W-J: A direct role for dual oxidase in Drosophila gut immunity. / Sci Signal 2005,310(5749):847.
  85. Korayem AM, Fabbri M, Takahashi K, Scherfer C, Lindgren M, Schmidt O, Ueda R, Dushay MS, Theopold U: A Drosophila salivary gland mucin is also expressed in immune tissues: evidence for a function in coagulation and the entrapment of bacteria. / Insect Biochem Mol Biol 2004,34(12):1297-304.
  86. Johannessen BR, Skov LK, Kastrup JS, Kristensen O, Bolwig C, Larsen JN, Spangfort M, Lund K, Gajhede M: Structure of the house dust mite allergen Der f 2: implications for function and molecular basis of IgE cross-reactivity. / FEBS Lett 2005,579(5):1208-212.
  87. Pick C, Schneuer M, Burmester T: The occurrence of hemocyanin in Hexapoda. / FEBS J 2009,276(7):1930-941.
  88. Kawabata T, Yasuhara Y, Ochiai M, Matsuura S, Ashida M: Molecular cloning of insect pro-phenol oxidase: a copper-containing protein homologous to arthropod hemocyanin. / Proc Natl Acad Sci 1995,92(17):7774-778.
  89. King AJ, Cragg SM, Li Y, Dymond J, Guille MJ, Bowles DJ, Bruce NC, Graham IA, McQueen-Mason SJ: Molecular insight into lignocellulose digestion by a marine isopod in the absence of gut microbes. / Proc Natl Acad Sci USA 2010,107(12):5345-350.
  90. Dixit R, Arakane Y, Specht CA, Richard C, Kramer KJ, Beeman RW, Muthukrishnan S: Domain organization and phylogenetic analysis of proteins from the chitin deacetylase gene family of Tribolium castaneum and three other species of insects. / Insect Biochem Mol Biol 2008,38(4):440-51.
  91. Whelan S, Goldman N: A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. / Mol Biol Evol 2001,18(5):691-99.
  92. Le SQ, Gascuel O: An improved general amino acid replacement matrix. / Mol Biol Evol 2008,25(7):1307-320.
  93. Scully ED, Hoover K, Carlson J, Tien M, Geib SM: Proteomic analysis of Fusarium solani isolated from the Asian longhorned beetle, Anoplophora glabripennis. / PloS One 2012,7(4):e32990.
  94. Geib SM, Scully ED, Jimenez-Gasco MM, Carlson JE, Tien M, Hoover K: Phylogenetic analysis of Fusarium solani associated with the Asian longhorned beetle, Anoplophora glabripennis. / Insects 2012,3(1):141-60.
  95. Martin MMC: The evolution of insect-fungus associations: from contact to stable symbiosis. / Am Zool 1992,32(4):593-05.
  96. Lowe TM, Eddy SR: tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. / Nucleic Acids Res 1997,25(5):0955-964.
  97. Eddy SR: HMMER: profile hidden Markov models for biological sequence analysis. / Bioinformatics 1998, 14:755-63.
  98. Huang Y, Gilna P, Li W: Identification of ribosomal RNA genes in metagenomic fragments. / Bioinformatics 2009,25(10):1338-340.
  99. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. / Nucleic Acids Res 1997,25(17):3389-402.
  100. Huson DH, Auch AF, Qi J, Schuster SC: MEGAN analysis of metagenomic data. / Genome Res 2007,17(3):377-86.
  101. Conesa A, G?tz S, García-Gómez JM, Terol J, Talón M, Robles M: Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. / Bioinformatics 2005,21(18):3674-676.
  102. Sun Y, Buhler J: Designing patterns for profile HMM search. / Bioinformatics 2007,23(2):e36-e43.
  103. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths?Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer ELL, / et al.: The Pfam protein families database . / Nucleic Acids Res 2004,32(1):D138-D141.
  104. Mittapalli O, Bai X, Mamidala P, Rajarapu SP, Bonello P, Herms DA: Tissue-specific transcriptomics of the exotic invasive insect pest emerald ash borer (Agrilus planipennis). / PloS One 2010,5(10):e13708.
  105. Pauchet Y, Wilkinson P, Vogel H, Nelson DR, Reynolds SE, Heckel DG, Ffrench-Constant RH: Pyrosequencing the Manduca sexta larval midgut transcriptome: messages for digestion, detoxification and defence. / Insect Mol Biol 2010,19(1):61-5.
  106. Whitfield AE, Rotenberg D, Aritua V, Hogenhout SA: Analysis of expressed sequence tags from Maize mosaic rhabdovirus-infected gut tissues of Peregrinus maidis reveals the presence of key components of insect innate immunity. / Insect Mol Biol 2011,20(2):225-42.
  107. Khajuria C, Zhu Y, Chen M-S, Buschman L, Higgins R, Yao J, Crespo A, Siegfried B, Muthukrishnan S, Zhu K: Expressed sequence tags from larval gut of the European corn borer (Ostrinia nubilalis): Exploring candidate genes potentially involved in Bacillus thuringiensis toxicity and resistance. / BMC Genomics 2009,10(1):286.
  108. Aw T, Schlauch K, Keeling C, Young S, Bearfield J, Blomquist G, Tittiger C: Functional genomics of mountain pine beetle (Dendroctonus ponderosae) midguts and fat bodies. / BMC Genomics 2010,11(1):215.
  109. Tartar A, Wheeler MM, Zhou XG, Coy MR, Boucias DG, Scharf ME: Parallel metatranscriptome analyses of host and symbiont gene expression in the gut of the termite Reticulitermes flavipes. / Biotechnol Biofuels 2009.,2(25): doi:10.1186/1754-834--25. doi:10.1186/1754-6834-2-25.
  110. Xie L, Zhang L, Zhong Y, Liu N, Long Y, Wang S, Zhou X, Zhou Z, Huang Y, Wang Q: Profiling the metatranscriptome of the protistan community in Coptotermes formosanus with emphasis on the lignocellulolytic system. / Genomics 2012,99(4):246-55.
  111. Li W, Godzik A: Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. / Bioinformatics 2006,22(13):1658-659.
  112. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, / et al.: Clustal W and Clustal X version 2.0. / Bioinformatics 2007,23(21):2947-948.
  113. Kumar S, Nei M, Dudley J, Tamura K: MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. / Brief Bioinform 2008,9(4):299-06.
  114. Abascal F, Zardoya R, Posada D: ProtTest: selection of best-fit models of protein evolution. / Bioinformatics 2005,21(9):2104-105.
  115. Guindon S, Gascuel O: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. / Syst Biol 2003,52(5):696-04.
  116. Zwickl D: Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maxmum likelihood criterion. PhD dissertation available at http://www.nescent.org/wg_garli/Main_Page (Univ of Texas, Austin) 2006.
  117. Sukumaran J, Holder MT: DendroPy: a Python library for phylogenetic computing. / Bioinformatics 2010,26(12):1569-571.
  118. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R: The sequence alignment/map format and SAMtools. / Bioinformatics 2009,25(16):2078-079.
  119. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng QD, / et al.: Full-length transcriptome assembly from RNA-Seq data without a reference genome. / Nat Biotechnol 2011,29(7):644-U130.
  120. Marchler-Bauer A, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, / et al.: CDD: specific functional annotation with the Conserved Domain Database. / Nucleic Acids Res 2009,37(suppl 1):D205-D210.
  121. Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. / Genome Biol 2009,10(3):R25.
  122. Li B, Dewey C: RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. / BMC Bioinforma 2011,12(1):323.
  123. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B: Mapping and quantifying mammalian transcriptomes by RNA-Seq. / Nat Meth 2008,5(7):621-28.
  124. Petersen TN, Brunak S, Von Heijne G, Nielsen H: SignalP 4.0: discriminating signal peptides from transmembrane regions. / Nat Methods 2011,8(10):785-86.
  
• 作者单位：Erin D Scully (13)
  Kelli Hoover (14)
  John E Carlson (15) (16)
  Ming Tien (17)
  Scott M Geib (18)
  
  13. Intercollege Program in Genetics at the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
  14. Department of Entomology and Center for Chemical Ecology, The Pennsylvania State University, University Park, PA, 16802, USA
  15. The Schatz Center for Tree Molecular Genetics, Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, USA
  16. Department of Bioenergy Science and Technology (World Class University), Chonnam National University, Buk-Gu, Gwangju, 500-757, Korea
  17. Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
  18. Tropical Crop and Commodity Protection Research Unit, USDA-ARS Pacific Basin Agricultural Research Center, Hilo, HI, 96720, USA
  
• ISSN：1471-2164

文摘

Background Wood-feeding insects often work in collaboration with microbial symbionts to degrade lignin biopolymers and release glucose and other fermentable sugars from recalcitrant plant cell wall carbohydrates, including cellulose and hemicellulose. Here, we present the midgut transcriptome of larval Anoplophora glabripennis, a wood-boring beetle with documented lignin-, cellulose-, and hemicellulose- degrading capabilities, which provides valuable insights into how this insect overcomes challenges associated with feeding in woody tissue. Results Transcripts from putative protein coding regions of over 9,000 insect-derived genes were identified in the A. glabripennis midgut transcriptome using a combination of 454 shotgun and Illumina paired-end reads. The most highly-expressed genes predicted to encode digestive-related enzymes were trypsins, carboxylesterases, β-glucosidases, and cytochrome P450s. Furthermore, 180 unigenes predicted to encode glycoside hydrolases (GHs) were identified and included several GH 5, 45, and 48 cellulases, GH 1 xylanases, and GH 1 β-glucosidases. In addition, transcripts predicted to encode enzymes involved in detoxification were detected, including a substantial number of unigenes classified as cytochrome P450s (CYP6B) and carboxylesterases, which are hypothesized to play pivotal roles in detoxifying host tree defensive chemicals and could make important contributions to A. glabripennis-/em> expansive host range. While a large diversity of insect-derived transcripts predicted to encode digestive and detoxification enzymes were detected, few transcripts predicted to encode enzymes required for lignin degradation or synthesis of essential nutrients were identified, suggesting that collaboration with microbial enzymes may be required for survival in woody tissue. Conclusions A. glabripennis produces a number of enzymes with putative roles in cell wall digestion, detoxification, and nutrient extraction, which likely contribute to its ability to thrive in a broad range of host trees. This system is quite different from the previously characterized termite fermentation system and provides new opportunities to discover enzymes that could be exploited for cellulosic ethanol biofuel production or the development of novel methods to control wood-boring pests.