[1] | Wei H, Xu Q, Taylor LE 2nd, Baker JO, Tucker MP, et al. (2009) Natural paradigms of plant cell wall degradation. Curr Opin Biotechnol 20: 330–338. doi: 10.1016/j.copbio.2009.05.008
|
[2] | Tomme P, Warren RAJ, Gilkes NR (1995) Cellulose hydrolysis by bacteria and fungi. In: Poole RK, editor. Advances in Microbial Physiology: Academic Press. 1–81.
|
[3] | Kamm B, Kamm M (2004) Principles of biorefineries. Appl Microbiol Biotechnol 64: 137–145. doi: 10.1007/s00253-003-1537-7
|
[4] | Wyman CE (2003) Potential synergies and challenges in refining cellulosic biomass to fuels, chemicals, and power. Biotechnol Prog 19: 254–262. doi: 10.1021/bp025654l
|
[5] | Zhang Y-HP, Lynd LR (2005) Cellulose utilization by Clostridium thermocellum: bioenergetics and hydrolysis product assimilation. Proc Natl Acad Sci USA 102: 7321–7325. doi: 10.1073/pnas.0408734102
|
[6] | Cleveland LR (1924) The physiological and symbiotic relationships between the intestinal protozoa of termites and their host, with special reference to Reticulitermes flavipes Kollar. Biol Bull Mar Biol Lab 46: 117–227. doi: 10.2307/1536724
|
[7] | Martin M (1991) The evolution of cellulose digestion in insects. Philos Trans R Soc Lond Ser B 333: 281–288.
|
[8] | Breznak JA, Brune A (1994) Role of microorganisms in the digestion of lignocellulose by termites. Annu Rev Entomol 39: 453–487. doi: 10.1146/annurev.en.39.010194.002321
|
[9] | Watanabe H, Noda H, Tokuda G, Lo N (1998) A cellulase gene of termite origin. Nature 394: 330–331. doi: 10.1038/28527
|
[10] | Smant G, Stokkermans JP, Yan Y, de Boer JM, Baum TJ, et al. (1998) Endogenous cellulases in animals: isolation of beta-1,4-endoglucanase genes from two species of plant-parasitic cyst nematodes. Proc Natl Acad Sci USA 95: 4906–4911. doi: 10.1073/pnas.95.9.4906
|
[11] | Watanabe H, Tokuda G (2010) Cellulolytic systems in insects. Annu Rev Entomol 55: 609–632. doi: 10.1146/annurev-ento-112408-085319
|
[12] | Calderón-Cortés N, Quesada M, Watanabe H, Cano-Camacho H, Oyama K (2012) Endogenous plant cell wall digestion: a key mechanism in insect evolution. Annu Rev Ecol, Evol Syst 43: 45–71. doi: 10.1146/annurev-ecolsys-110411-160312
|
[13] | Nakashima K, Watanabe H, Saitoh H, Tokuda G, Azuma JI (2002) Dual cellulose-digesting system of the wood-feeding termite, Coptotermes formosanus Shiraki. Insect Biochem Mol Biol 32: 777–784. doi: 10.1016/s0965-1748(01)00160-6
|
[14] | Zhou X, Smith JA, Oi FM, Koehler PG, Bennett GW, et al. (2007) Correlation of cellulase gene expression and cellulolytic activity throughout the gut of the termite Reticulitermes flavipes. Gene 395: 29–39. doi: 10.1016/j.gene.2007.01.004
|
[15] | Warnecke F, Luginbuhl P, Ivanova N, Ghassemian M, Richardson TH, et al. (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450: 560–565. doi: 10.1038/nature06269
|
[16] | Tokuda G, Watanabe H (2007) Hidden cellulases in termites: revision of an old hypothesis. Biol Lett 3: 336–339. doi: 10.1098/rsbl.2007.0073
|
[17] | Tokuda G, Watanabe H, Lo N (2007) Does correlation of cellulase gene expression and cellulolytic activity in the gut of termite suggest synergistic collaboration of cellulases? Gene 401: 131–134. doi: 10.1016/j.gene.2007.06.028
|
[18] | Scharf ME, Karl ZJ, Sethi A, Boucias DG (2011) Multiple levels of synergistic collaboration in termite lignocellulose digestion. PloS one 6: e21709. doi: 10.1371/journal.pone.0021709
|
[19] | Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, et al. (2009) The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res 37: D233–D238. doi: 10.1093/nar/gkn663
|
[20] | Ketudat CairnsJR, Esen A (2010) β-Glucosidases. Cell Mol Life Sci 67: 3389–3405. doi: 10.1007/s00018-010-0399-2
|
[21] | Chang CJ, Wu CP, Lu SC, Chao AL, Ho TH, et al. (2012) A novel exo-cellulase from white spotted longhorn beetle (Anoplophora malasiaca). Insect Biochem Mol Biol 42: 629–636. doi: 10.1016/j.ibmb.2012.05.002
|
[22] | Pauchet Y, Wilkinson P, Chauhan R, ffrench-Constant RH (2010) Diversity of beetle genes encoding novel plant cell wall degrading enzymes. PloS one 5: e15635. doi: 10.1371/journal.pone.0015635
|
[23] | Calderón-Cortés N, Watanabe H, Cano-Camacho H, Zavala-Páramo G, Quesada M (2010) cDNA cloning, homology modelling and evolutionary insights into novel endogenous cellulases of the borer beetle Oncideres albomarginata chamela (Cerambycidae). Insect Mol Biol 19: 323–336. doi: 10.1111/j.1365-2583.2010.00991.x
|
[24] | Pauchet Y, Heckel DG (2013) The genome of the mustard leaf beetle encodes two active xylanases originally acquired from bacteria through horizontal gene transfer. Proc R Soc B 280: 20131021. doi: 10.1098/rspb.2013.1021
|
[25] | Willis JD, Oppert B, Oppert C, Klingeman WE, Jurat-Fuentes JL (2011) Identification, cloning, and expression of a GHF9 cellulase from Tribolium castaneum (Coleoptera: Tenebrionidae). J Insect Physiol 57: 300–306. doi: 10.1016/j.jinsphys.2010.11.019
|
[26] | Valencia A, Alves AP, Siegfried BD (2013) Molecular cloning and functional characterization of an endogenous endoglucanase belonging to GHF45 from the western corn rootworm, Diabrotica virgifera virgifera. Gene 513: 260–267. doi: 10.1016/j.gene.2012.10.046
|
[27] | Siegfried BD, Waterfield N, Ffrench-Constant RH (2005) Expressed sequence tags from Diabrotica virgifera virgifera midgut identify a coleopteran cadherin and a diversity of cathepsins. Insect Mol Biol 14: 137–143. doi: 10.1111/j.1365-2583.2005.00538.x
|
[28] | Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotech 29: 644–652. doi: 10.1038/nbt.1883
|
[29] | Girard C, Jouanin L (1999) Molecular cloning of a gut-specific chitinase cDNA from the beetle Phaedon cochleariae. Insect Biochem Mol Biol 29: 549–556. doi: 10.1016/s0965-1748(99)00029-6
|
[30] | Eigenheer AL, Keeling CI, Young S, Tittiger C (2003) Comparison of gene representation in midguts from two phytophagous insects, Bombyx mori and Ips pini, using expressed sequence tags. Gene 316: 127–136. doi: 10.1016/s0378-1119(03)00749-2
|
[31] | Lee SJ, Kim SR, Yoon HJ, Kim I, Lee KS, et al. (2004) cDNA cloning, expression, and enzymatic activity of a cellulase from the mulberry longicorn beetle, Apriona germari. Comp Biochem Physiol B: Biochem Mol Biol 139: 107–116. doi: 10.1016/j.cbpc.2004.06.015
|
[32] | Gao Y, Bu Y, Luan Y-X (2008) Phylogenetic relationships of basal hexapods reconstructed from nearly complete 18S and 28S rRNA gene sequences. Zool Sci 25: 1139–1145. doi: 10.2108/zsj.25.1139
|
[33] | Davison A, Blaxter M (2005) Ancient origin of glycosyl hydrolase family 9 cellulase genes. Mol Biol Evol 22: 1273–1284. doi: 10.1093/molbev/msi107
|
[34] | Ohtoko K, Ohkuma M, Moriya S, Inoue T, Usami R, et al. (2000) Diverse genes of cellulase homologues of glycosyl hydrolase family 45 from the symbiotic protists in the hindgut of the termite Reticulitermes speratus. Extremophiles 4: 343–349. doi: 10.1007/s007920070003
|
[35] | Todaka N, Inoue T, Saita K, Ohkuma M, Nalepa CA, et al. (2010) Phylogenetic analysis of cellulolytic enzyme genes from representative lineages of termites and a related cockroach. PloS one 5: e8636. doi: 10.1371/journal.pone.0008636
|
[36] | Li L, Frohlich J, Pfeiffer P, Konig H (2003) Termite gut symbiotic archaezoa are becoming living metabolic fossils. Eukaryot Cell 2: 1091–1098. doi: 10.1128/ec.2.5.1091-1098.2003
|
[37] | Xu B, Janson J-C, Sellos D (2001) Cloning and sequencing of a molluscan endo-β-1,4-glucanase gene from the blue mussel, Mytilus edulis. Eur J Biochem 268: 3718–3727. doi: 10.1046/j.1432-1327.2001.02280.x
|
[38] | Harada Y, Hosoiri Y, Kuroda R (2004) Isolation and evaluation of dextral-specific and dextral-enriched cDNA clones as candidates for the handedness-determining gene in a freshwater gastropod, Lymnaea stagnalis. Dev Genes Evol 214: 159–169. doi: 10.1007/s00427-004-0392-6
|
[39] | Fujita K, Shimomura K, Yamamoto K, Yamashita T, Suzuki K (2006) A chitinase structurally related to the glycoside hydrolase family 48 is indispensable for the hormonally induced diapause termination in a beetle. Biochem Biophys Res Commun 345: 502–507. doi: 10.1016/j.bbrc.2006.04.126
|
[40] | Keeling CI, Henderson H, Li M, Yuen M, Clark EL, et al. (2012) Transcriptome and full-length cDNA resources for the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major insect pest of pine forests. Insect Biochem Mol Biol 42: 525–536. doi: 10.1016/j.ibmb.2012.03.010
|
[41] | Berger E, Zhang D, Zverlov VV, Schwarz WH (2007) Two noncellulosomal cellulases of Clostridium thermocellum, Cel9I and Cel48Y, hydrolyse crystalline cellulose synergistically. FEMS Microbiol Lett 268: 194–201. doi: 10.1111/j.1574-6968.2006.00583.x
|
[42] | Ljungdahl LG (2008) The cellulase/hemicellulase system of the anaerobic fungus orpinomyces PC-2 and aspects of its applied use. Ann N Y Acad Sci 1125: 308–321. doi: 10.1196/annals.1419.030
|
[43] | Garcia-Vallvé S, Romeu A, Palau J (2000) Horizontal gene transfer of glycosyl hydrolases of the rumen fungi. Mol Biol Evol 17: 352–361. doi: 10.1093/oxfordjournals.molbev.a026315
|
[44] | Hung YL, Chen HJ, Liu JC, Chen YC (2012) Catalytic efficiency diversification of duplicate beta-1,3–1,4-glucanases from Neocallimastix patriciarum J11. Appl Environ Microbiol 78: 4294–4300. doi: 10.1128/aem.07473-11
|
[45] | Keeling C, Yuen M, Liao N, Docking T, Chan S, et al. (2013) Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest. Genome Biology 14: R27. doi: 10.1186/gb-2013-14-3-r27
|
[46] | Celorio-Mancera MP, Allen ML, Powell AL, Ahmadi H, Salemi MR, et al. (2008) Polygalacturonase causes lygus-like damage on plants: cloning and identification of western tarnished plant bug (Lygus hesperus) polygalacturonases secreted during feeding. Arthropod-Plant Interactions 2: 215–225. doi: 10.1007/s11829-008-9050-7
|
[47] | Allen ML, Mertens JA (2008) Molecular cloning and expression of three polygalacturonase cDNAs from the tarnished plant bug, Lygus lineolaris. J Insect Sci 8: 1–14. doi: 10.1673/031.008.2701
|
[48] | Pauchet Y, Freitak D, Heidel-Fischer HM, Heckel DG, Vogel H (2009) Immunity or digestion: glucanase activity in a glucan-binding protein family from Lepidoptera. J Biol Chem 284: 2214–2224. doi: 10.1074/jbc.m806204200
|
[49] | Bragatto I, Genta FA, Ribeiro AF, Terra WR, Ferreira C (2010) Characterization of a β-1,3-glucanase active in the alkaline midgut of Spodoptera frugiperda larvae and its relation to β-glucan-binding proteins. Insect Biochem Mol Biol 40: 861–872. doi: 10.1016/j.ibmb.2010.08.006
|
[50] | Hughes AL (2012) Evolution of the betaGRP/GNBP/beta-1,3-glucanase family of insects. Immunogenetics 64: 549–558. doi: 10.1007/s00251-012-0610-8
|
[51] | Kovalchuk SN, Bakunina IY, Burtseva YV, Emelyanenko VI, Kim NY, et al. (2009) An endo-(1→3)-β-D-glucanase from the scallop Chlamys albidus: catalytic properties, cDNA cloning and secondary-structure characterization. Carbohydrate Research 344: 191–197. doi: 10.1016/j.carres.2008.10.028
|
[52] | Song JM, Nam K, Sun YU, Kang MH, Kim CG, et al. (2010) Molecular and biochemical characterizations of a novel arthropod endo-beta-1,3-glucanase from the Antarctic springtail, Cryptopygus antarcticus, horizontally acquired from bacteria. Comp Biochem Physiol B Biochem Mol Biol 155: 403–412. doi: 10.1016/j.cbpb.2010.01.003
|
[53] | Kim Y-S, Ryu J-H, Han S-J, Choi K-H, Nam K-B, et al. (2000) Gram-negative bacteria-binding protein, a pattern recognition receptor for lipopolysaccharide and β-1,3-glucan that mediates the signaling for the induction of innate immune genes in Drosophila melanogaster cells. J Biol Chem 275: 32721–32727. doi: 10.1074/jbc.m003934200
|
[54] | Pili-Floury S, Leulier F, Takahashi K, Saigo K, Samain E, et al. (2004) In vivo RNA interference analysis reveals an unexpected role for GNBP1 in the defense against Gram-positive bacterial infection in Drosophila adults. J Biol Chem 279: 12848–12853. doi: 10.1074/jbc.m313324200
|
[55] | Zhang R, Cho HY, Kim HS, Ma YG, Osaki T, et al. (2003) Characterization and properties of a 1,3-beta-D-glucan pattern recognition protein of Tenebrio molitor larvae that is specifically degraded by serine protease during prophenoloxidase activation. J Biol Chem 278: 42072–42079. doi: 10.1074/jbc.m307475200
|
[56] | Ma C, Kanost MR (2000) A beta1,3-glucan recognition protein from an insect, Manduca sexta, agglutinates microorganisms and activates the phenoloxidase cascade. J Biol Chem 275: 7505–7514. doi: 10.1074/jbc.275.11.7505
|
[57] | Ochiai M, Ashida M (2000) A pattern-recognition protein for beta-1,3-glucan. The binding domain and the cDNA cloning of beta-1,3-glucan recognition protein from the silkworm, Bombyx mori. J Biol Chem 275: 4995–5002. doi: 10.1074/jbc.275.7.4995
|
[58] | Bulmer MS, Bachelet I, Raman R, Rosengaus RB, Sasisekharan R (2009) Targeting an antimicrobial effector function in insect immunity as a pest control strategy. Proc Natl Acad Sci USA 106: 12652–12657. doi: 10.1073/pnas.0904063106
|
[59] | Kanagawa M, Satoh T, Ikeda A, Adachi Y, Ohno N, et al. (2011) Structural insights into recognition of triple-helical beta-glucans by an insect fungal receptor. J Biol Chem 286: 29158–29165. doi: 10.1074/jbc.m111.256701
|
[60] | Mishima Y, Quintin J, Aimanianda V, Kellenberger C, Coste F, et al. (2009) The N-terminal domain of Drosophila Gram-negative binding protein 3 (GNBP3) defines a novel family of fungal pattern recognition receptors. J Biol Chem 284: 28687–28697. doi: 10.1074/jbc.m109.034587
|
[61] | Genta FA, Bragatto I, Terra WR, Ferreira C (2009) Purification, characterization and sequencing of the major β-1,3-glucanase from the midgut of Tenebrio molitor larvae. Insect Biochem Mol Biol 39: 861–874. doi: 10.1016/j.ibmb.2009.10.003
|
[62] | Genta FA, Dumont AF, Marana SR, Terra WR, Ferreira C (2007) The interplay of processivity, substrate inhibition and a secondary substrate binding site of an insect exo-beta-1,3-glucanase. Biochim Biophys Acta 1774: 1079–1091. doi: 10.1016/j.bbapap.2007.07.006
|
[63] | Genta FA, Terra WR, Ferreira C (2003) Action pattern, specificity, lytic activities, and physiological role of five digestive beta-glucanases isolated from Periplaneta americana. Insect Biochem Mol Biol 33: 1085–1097. doi: 10.1016/s0965-1748(03)00121-8
|
[64] | Chen XY, Kim JY (2009) Callose synthesis in higher plants. Plant Signal Behav 4: 489–492. doi: 10.4161/psb.4.6.8359
|
[65] | Aspeborg H, Coutinho PM, Wang Y, Brumer H, Henrissat B (2012) Evolution, substrate specificity and subfamily classification of glycoside hydrolase family 5 (GH5). BMC Evol Biol 12: 186. doi: 10.1186/1471-2148-12-186
|
[66] | Acu?a R, Padilla BE, Flórez-Ramos CP, Rubio JD, Herrera JC, et al. (2012) Adaptive horizontal transfer of a bacterial gene to an invasive insect pest of coffee. Proc Natl Acad Sci USA 109: 4197–4202. doi: 10.1073/pnas.1121190109
|
[67] | Fischer R, Ostafe R, Twyman RM (2013) Cellulases from insects. Advances in biochemical engineering/biotechnology 136: 51–64. doi: 10.1007/10_2013_206
|
[68] | Hunt T, Bergsten J, Levkanicova Z, Papadopoulou A, John OS, et al. (2007) A comprehensive phylogeny of beetles reveals the evolutionary origins of a superradiation. Science 318: 1913–1916. doi: 10.1126/science.1146954
|
[69] | Van Belleghem SM, Roelofs D, Van Houdt J, Hendrickx F (2012) De novo transcriptome assembly and SNP discovery in the wing polymorphic salt marsh beetle Pogonus chalceus (Coleoptera, Carabidae). PloS one 7: e42605. doi: 10.1371/journal.pone.0042605
|
[70] | Tribolium Genome Sequencing Consortium (2008) The genome of the model beetle and pest Tribolium castaneum. Nature 452: 949–955.
|
[71] | Sinnott M (1990) Catalytic mechanisms of enzymatic glycosyl transfer. Chem Rev 90: 1171–1202. doi: 10.1021/cr00105a006
|
[72] | Ferreira AH, Marana SR, Terra WR, Ferreira C (2001) Purification, molecular cloning, and properties of a beta-glycosidase isolated from midgut lumen of Tenebrio molitor (Coleoptera) larvae. Insect Biochem Mol Biol 31: 1065–1076. doi: 10.1016/s0965-1748(01)00054-6
|
[73] | Marana SR, Jacobs-Lorena M, Terra WR, Ferreira C (2001) Amino acid residues involved in substrate binding and catalysis in an insect digestive beta-glycosidase. Biochim Biophys Acta 1545: 41–52. doi: 10.1016/s0167-4838(00)00260-0
|
[74] | Scharf ME, Kovaleva ES, Jadhao S, Campbell JH, Buchman GW, et al. (2010) Functional and translational analyses of a beta-glucosidase gene (glycosyl hydrolase family 1) isolated from the gut of the lower termite Reticulitermes flavipes. Insect Biochem Mol Biol 40: 611–620. doi: 10.1016/j.ibmb.2010.06.002
|
[75] | Mian IS (1998) Sequence, structural, functional, and phylogenetic analyses of three glycosidase families. Blood cells, molecules & diseases 24: 83–100. doi: 10.1006/bcmd.1998.9998
|
[76] | Marques AR, Coutinho PM, Videira P, Fialho AM, Sa-Correia I (2003) Sphingomonas paucimobilis beta-glucosidase Bgl1: a member of a new bacterial subfamily in glycoside hydrolase family 1. The Biochemical journal 370: 793–804. doi: 10.1042/bj20021249
|
[77] | Ferreira AH, Terra WR, Ferreira C (2003) Characterization of a beta-glycosidase highly active on disaccharides and of a beta-galactosidase from Tenebrio molitor midgut lumen. Insect Biochem Mol Biol 33: 253–265. doi: 10.1016/s0965-1748(02)00239-4
|
[78] | Ernst HA, Lo Leggio L, Willemoes M, Leonard G, Blum P, et al. (2006) Structure of the Sulfolobus solfataricus alpha-glucosidase: implications for domain conservation and substrate recognition in GH31. J Mol Biol 358: 1106–1124. doi: 10.1016/j.jmb.2006.02.056
|
[79] | Opota O, Charles JF, Warot S, Pauron D, Darboux I (2008) Identification and characterization of the receptor for the Bacillus sphaericus binary toxin in the malaria vector mosquito, Anopheles gambiae. Comp Biochem Physiol B Biochem Mol Biol 149: 419–427. doi: 10.1016/j.cbpb.2007.11.002
|
[80] | Zhang Q, Hua G, Bayyareddy K, Adang MJ (2013) Analyses of alpha-amylase and alpha-glucosidase in the malaria vector mosquito, Anopheles gambiae, as receptors of Cry11Ba toxin of Bacillus thuringiensis subsp. jegathesan. Insect Biochem Mol Biol 43: 907–915. doi: 10.1016/j.ibmb.2013.07.003
|
[81] | Wheeler D, Redding AJ, Werren JH (2013) Characterization of an ancient lepidopteran lateral gene transfer. PloS one 8: e59262. doi: 10.1371/journal.pone.0059262
|
[82] | Shen Z, Denton M, Mutti N, Pappan K, Kanost MR, et al. (2003) Polygalacturonase from Sitophilus oryzae: possible horizontal transfer of a pectinase gene from fungi to weevils. J Insect Sci 3: 24.
|
[83] | Kirsch R, Wielsch N, Vogel H, Svatos A, Heckel D, et al. (2012) Combining proteomics and transcriptome sequencing to identify active plant-cell-wall-degrading enzymes in a leaf beetle. BMC Genomics 13: 587. doi: 10.1186/1471-2164-13-587
|
[84] | Juge N (2006) Plant protein inhibitors of cell wall degrading enzymes. Trends Plant Sci 11: 359–367. doi: 10.1016/j.tplants.2006.05.006
|
[85] | Waller JM, Bigger M, Hillocks RJ (2007) Postharvest and processing pests and microbial problems. In: Waller JM, Bigger M, Hillocks RJ, editors. Coffee Pests, Diseases and Their Management. CABI, Wallingford, UK. 325–335.
|
[86] | Valentine BD (2005) The scientific name of the coffee bean weevil and some additional bibliography (Coleoptera: Anthribidae: Araecerus Sch?nherr). Insecta Mundi 19: 247–253.
|
[87] | Damon A (2000) A review of the biology and control of the coffee berry borer, Hypothenemus hampei (Coleoptera: Scolytidae). Bull Entomol Res 90: 453–465. doi: 10.1017/s0007485300000584
|
[88] | Vega FE, Davis AP, Jaramillo J (2012) From forest to plantation? Obscure articles reveal alternative host plants for the coffee berry borer, Hypothenemus hampei (Coleoptera: Curculionidae). Biol J Linn Soc 107: 86–94. doi: 10.1111/j.1095-8312.2012.01912.x
|
[89] | Dunning Hotopp JC (2011) Horizontal gene transfer between bacteria and animals. Trends Genet 27: 157–163. doi: 10.1016/j.tig.2011.01.005
|
[90] | Schmieder R, Edwards R (2011) Quality control and preprocessing of metagenomic datasets. Bioinformatics 27: 863–864. doi: 10.1093/bioinformatics/btr026
|
[91] | Joshi N. Sickle - A windowed adaptive trimming for fastq files using quality. Available: https://github.com/najoshi/sickle. Accessed 2013 May 30.
|
[92] | Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WEG, et al. (2004) Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res 14: 1147–1159. doi: 10.1101/gr.1917404
|
[93] | Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821–829. doi: 10.1101/gr.074492.107
|
[94] | Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389–3402. doi: 10.1093/nar/25.17.3389
|
[95] | Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, et al. (2009) BLAST+: architecture and applications. BMC Bioinformatics 10: 421. doi: 10.1186/1471-2105-10-421
|
[96] | The UniProt Consortium (2013) Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res 41: D43–D47. doi: 10.1093/nar/gks1068
|
[97] | Zhao QY, Wang Y, Kong YM, Luo D, Li X, et al. (2011) Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. BMC Bioinformatics 12 Suppl 14S2. doi: 10.1186/1471-2105-12-s14-s2
|
[98] | Li R, Yu C, Li Y, Lam TW, Yiu SM, et al. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25: 1966–1967. doi: 10.1093/bioinformatics/btp336
|
[99] | Birol I, Jackman SD, Nielsen CB, Qian JQ, Varhol R, et al. (2009) De novo transcriptome assembly with ABySS. Bioinformatics 25: 2872–2877. doi: 10.1093/bioinformatics/btp367
|
[100] | Langmead B, Trapnell C, Pop M, Salzberg S (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10: R25. doi: 10.1186/gb-2009-10-3-r25
|
[101] | Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat Methods 5: 621–628. doi: 10.1038/nmeth.1226
|
[102] | Ramsk?ld D, Wang ET, Burge CB, Sandberg R (2009) An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput Biol 5: e1000598. doi: 10.1371/journal.pcbi.1000598
|
[103] | Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30: 772–780. doi: 10.1093/molbev/mst010
|
[104] | Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688–2690. doi: 10.1093/bioinformatics/btl446
|
[105] | Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406–425.
|
[106] | Felsenstein J (2013) PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.
|
[107] | Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783–791. doi: 10.2307/2408678
|