Sequencing and De Novo Assembly of the Western Tarnished Plant Bug (Lygus hesperus) Transcriptome

PLoS ONE

Volumn 8, Issue 1, 2013, Pages

  Hull, J Joe ^a   Geib, Scott M ^a   Fabrick, Jeffrey A ^a   Brent, Colin S ^a  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHAPERONIN 60; EARLY PREGNANCY FACTOR; HEAT SHOCK PROTEIN 40; HEAT SHOCK PROTEIN 70; HEAT SHOCK PROTEIN 90; SMALL HEAT SHOCK PROTEIN; TRANSCRIPTOME;

ADULT ANIMAL; ARTICLE; COMPARATIVE STUDY; CONTROLLED STUDY; DNA LIBRARY; DROSOPHILA MELANOGASTER; FEMALE; GENE EXPRESSION PROFILING; GENETIC VARIABILITY; HEAT TOLERANCE; HEMIPTERA; LYGUS HESPERUS; MALE; MOLECULAR DYNAMICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PEA APHID; PEDICULUS; PHYLOGENETIC TREE; POLYMERASE CHAIN REACTION; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN EXPRESSION; PYROSEQUENCING; SEMI QUANTITATIVE POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; TEMPERATURE STRESS; TRANSCRIPTOMICS; TRIBOLIUM CASTANEUM; UPREGULATION; VALIDATION PROCESS;

ANIMALS; BASE SEQUENCE; DNA PRIMERS; FEMALE; HEAT-SHOCK PROTEINS; HEMIPTERA; MALE; PHYLOGENY; POLYMERASE CHAIN REACTION; TRANSCRIPTOME;

ARTHROPODA; GOSSYPIUM HIRSUTUM; HEMIPTERA; HEXAPODA; LYGUS HESPERUS; LYGUS LINEOLARIS; MEDICAGO SATIVA; MIRIDAE;

EID: 84872831700     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0055105     Document Type: Article

References (72)

1. Beards GW, Strong FE, (1966) Photoperiod in relation to diapause in Lygus hesperus Knight. Hilgardia 37: 345-362.
2. Leigh TF, (1966) A reproductive diapause in Lygus hesperus Knight. J Econ Entomol 59: 1280-1281.
3. Spurgeon DW, Brent CS, (2010) Morphological characters of diapause in Lygus hesperus Knight (Hemiptera: Miridae). J Entomol Sci 45: 303-316.
4. Kelton LA, (1975) The Lygus Bugs (Genus Lygus Hahn) of North America (Heteroptera: Miridae). Mem Entomol Soc Can 95: 1-101.
5. Scott DR, (1977) An annotated listing of host plants of Lygus hesperus Knight. Entomo Soc Am Bull 23: 19-22.
6. Wheeler AG (2001) Biology of the plant bugs (Hemiptera: Miridae): pests, predators, opportunists. Ithaca: Comstock Publishing Associates.
7. Butts R, Lamb R, (1990) Injury to oilseed rape caused by mirid bugs (Lygus)(Heteroptera: Miridae) and its effect on seed production. Ann Appl Biol 117: 253-266.
8. Turnock WJ, Gerber GH, Timlick BH, Lamb RJ, (1995) Losses of canola seeds from feeding by Lygus species [Heteroptera: Miridae] in Manitoba. Can J Plant Sci 75: 731-736.
9. Naranjo SE, Dierig D, Ellsworth PC, (2008) Survery and evaluation of Lygus bugs on lesquerella and guayule, two new desert crops in the western USA. J Insect Sci 8: 49.
10. Ritter RA, Lenssen A, Blodgett S, Taper MA, (2010) Regional assemblages of Lygus (Heteroptera: Miridae) in Montana canola fields. J Kansas Entomol Soc 83: 297-305.
11. Naranjo SE, Ellsworth PC, Dierig D, (2011) Impact of Lygus spp. (Hemiptera: Miridae) on damage, yield, and quality of lesquerella (Physaria fendleri), a potential new oil-seed crop. J Econ Entomol 104: 1575-1583.
12. Snodgrass G, (1996) Insecticide resistance in field populations of the tarnished plant bug (Heteroptera: Miridae) in cotton in the Mississippi Delta. J Econ Entomol 89: 783-790.
13. Snodgrass GL, Scott WP, (2000) Seasonal changes in pyrethroid resistance in tarnished plant bug (Heteroptera: Miridae) populations during a three-year period in the delta area of Arkansas, Louisiana, and Mississippi. J Econ Entomol 93: 441-446.
14. Snodgrass G, Gore J, Abel C, Jackson R, (2009) Acephate resistance in populations of the tarnished plant bug (Heteroptera: Miridae) from the Mississippi River Delta. J Econ Entomol 102: 699-707.
15. Feder ME, Hofmann GE, (1999) Heat-shock proteins, molecluar chaperones, and the stress response: Evolutionary and ecological physiology. Ann Rev Physiol 61: 243-282.
16. Sorensen JG, Kristensen TN, Loeschcke V, (2003) The evolutionary and ecological role of heat shock proteins. Ecol Lett 6: 1025-1037.
17. Vermeulen CJ, Loeschcke V, (2007) Longevity and the stress response in Drosophila. Exp Gerontol 42: 153-159.
18. Pauchet Y, Wilkinson P, van Munster M, Augustin S, Pauron D, et al. (2009) Pyrosequencing of the midgut transcriptome of the poplar leaf beetle Chrysomela tremulae reveals new gene families in Coleoptera. Insect Biochem Mol Biol 39: 403-413.
19. Pauchet Y, Wilkinson P, Vogel H, Nelson DR, Reynolds SE, et al. (2010) Pyrosequencing the Manduca sexta larval midgut transcriptome: messages for digestion, detoxification and defence. Insect Mol Biol 19: 61-75.
20. Bai X, Zhang W, Orantes L, Jun T-H, Mittapalli O, et al. (2010) Combining next-generation sequencing strategies for rapid molecular resource development from an invasive aphid species, Aphis glycines. PLoS ONE 5: e11370.
21. Wang X-W, Luan J-B, Li J-M, Bao Y-Y, Zhang C-X, et al. (2010) De novo characterization of a whitefly transcriptome and analysis of its gene expression during development. BMC Genomics 11: 400.
22. Karatolos N, Pauchet Y, Wilkinson P, Chauhan R, Denholm I, et al. (2011) Pyrosequencing the transcriptome of the greenhouse whitefly, Trialeurodes vaporariorum reveals multiple transcripts encoding insecticide targets and detoxifying enzymes. BMC Genomics 12: 56.
23. Shen G-M, Dou W, Niu J-Z, Jiang H-B, Yang W-J, et al. (2011) Transcriptome analysis of the oriental fruit fly (Bactrocera dorsalis). PLoS ONE 6: e29127.
24. Peng X, Zha W, He R, Lu T, Zhu L, et al. (2011) Pyrosequencing the midgut transcriptome of the brown planthopper, Nilaparvata lugens. Insect Mol Biol 20: 745-762.
25. Comeault AA, Sommers M, Schwander T, Buerkle CA, Farkas TE, et al. (2012) De novo characterization of the Timema cristinae transcriptome facilitates marker discovery and inference of genetic divergence. Mol Ecol Resour 12: 549-561.
26. Sze S-H, Dunham JP, Carey B, Chang PL, Li F, et al. (2012) A de novo transcriptome assembly of Lucilia sericata (Diptera: Calliphoridae) with predicted alternative splices, single nucleotide polymorphisms and transcript expression estimates. Insect Mol Biol 21: 205-221.
27. Liu F, Tang T, Sun L, Jose Priya TA, (2012) Transcriptomic analysis of the housefly (Musca domestica) larva using massively parallel pyrosequencing. Mol Biol Rep 39: 1927-1934.
28. 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.
29. Xue J, Bao Y-Y, Li B-L, Cheng Y-B, Peng Z-Y, et al. (2010) Transcriptome analysis of the brown planthopper Nilaparvata lugens. PLoS ONE 5: e14233.
30. Zhu J-Y, Zhao N, Yang B, (2012) Global transcriptome profiling of the pine shoot beetle, Tomicus yunnanensis (Coleoptera: Scolytinae). PLoS ONE 7: e32291.
31. Mittapalli O, Bai X, Mamidala P, Rajarapu SP, Bonello P, et al. (2010) Tissue-specific transcriptomics of the exotic invasive insect pest Emerald Ash Borer (Agrilus planipennis). PLoS ONE 5: e13708.
32. Bai X, Mamidala P, Rajarapu SP, Jones SC, Mittapalli O, (2011) Transcriptomics of the bed bug (Cimex lectularius). PLoS ONE 6: e16336.
33. Zhang F, Guo H, Zheng H, Zhou T, Zhou Y, et al. (2010) Massively parallel pyrosequencing-based transcriptome analyses of small brown planthopper (Laodelphax striatellus), a vector insect transmitting rice stripe virus (RSV). BMC Genomics 11: 303.
34. Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, et al. (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676.
35. Götz S, García-Gómez JM, Terol J, Williams TD, Nagaraj SH, et al. (2008) High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 36: 3420-3435.
36. Hsu J-C, Chien T-Y, Hu C-C, Chen M-JM, Wu W-J, et al. (2012) Discovery of genes related to insecticide resistance in Bactrocera dorsalis by functional genomic analysis of a de novo assembled transcriptome. PLoS ONE 7: e40950.
37. Davidson JF, Whyte B, Bissinger PH, Schiestl RH, (1996) Oxidative stress is involved in heat-induced cell death in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 93: 5116-5121.
38. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36: D480-484.
39. Kanehisa M, Goto S, (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28: 27-30.
40. Bale JS, Masters GJ, Hodkinson ID, (2002) Herbivory in global climate change research: direct effects of rising temperature on insect herbivores. Glob Change Biol 8: 1-16.
41. Law CJ, Maloney PC, Wang D-N, (2008) Ins and outs of major facilitator superfamily antiporters. Ann Rev Microbiol 62: 289-305.
42. Werck-Reichhart D, Feyereisen R, (2000) Cytochromes P450: a success story. Genome Biol 1: 1-9.
43. Wheelock CE, Shan G, Ottea J, (2005) Overview of carboxylesterases and their role in the metabolism of insecticides. J Pestic Sci 30: 75-83.
44. Zhu YC, Guo Z, He Y, Luttrell R, (2012) Microarray analysis of gene regulations and potential association with acephate-resistance and fitness cost in Lygus lineolaris. PLoS ONE 7: e37586.
45. Richter K, Haslbeck M, Buchner J, (2010) The heat shock response: life on the verge of death. Mol Cell 40: 253-266.
46. Horwich AL, Farr GW, Fenton WA, (2006) GroEL-GroES-mediated protein folding. Chem Rev 106: 1917-1930.
47. Jia H, Halilou AI, Hu L, Cai W, Liu J, et al. (2011) Heat shock protein 10 (Hsp10) in immune-related diseases: one coin, two sides. Intl J Biochem Mol Biol 2: 47-57.
48. Garrido C, Paul C, Seigneuric R, Kampinga HH, (2012) The small heat shock proteins family: The long forgotten chaperones. Intl J Biochem Cell Biol 44: 1588-1592.
49. Frydenberg J, Hoffmann AA, Loeschcke V, (2003) DNA sequence variation and latitudinal associations in hsp23, hsp26 and hsp27 from natural populations of Drosophila melanogaster. Mol Ecol 12: 2025-2032.
50. Graham AM, Merrill JD, McGaugh SE, Noor MAF, (2012) Geographic selection in the small heat shock gene complex differentiating populations of Drosophila pseudoobscura. J Hered 103: 400-407.
51. Li Z-W, Li X, Yu Q-Y, Xiang Z-H, Kishino H, et al. (2009) The small heat shock protein (sHSP) genes in the silkworm, Bombyx mori, and comparative analysis with other insect sHSP genes. BMC Evol Biol 9: 215.
52. Qiu XB, Shao YM, Miao S, Wang L, (2006) The diversity of the DnaJ/Hsp40 family, the crucial partner for Hsp70 chaperones. Cell Mol Life Sci 63: 2560-2570.
53. Cheetham ME, Caplan AJ, (1998) Structure, function and evolution of DnaJ: conservation and adaptation of chaperone function. Cell Stress Chaperones 3: 28-36.
54. Ranford JC, Henderson B, (2002) Chaperonins in disease: mechanisms, models, and treatments. Mol Pathol 55: 209-213.
55. Yébenes H, Mesa P, Muñoz IG, Montoya G, Valpuesta JM, (2011) Chaperonins: two rings for folding. Trends in Biochem Sci 36: 424-432.
56. Claros MG, Vincens P, (1996) Computational method to predict mitochondrially imported proteins and their targeting sequences. Eur J Biochem 241: 779-786.
57. Daugaard M, Rohde M, Jäättelä M, (2007) The heat shock protein 70 family: Highly homologous proteins with overlapping and distinct functions. FEBS Lett 581: 3702-3710.
58. Picard D, (2002) Heat-shock protein 90, a chaperone for folding and regulation. Cell Mol Life Sci 59: 1640-1648.
59. Borkovich KA, Farrelly FW, Finkelstein DB, Taulien J, Lindquist S, (1989) hsp82 is an essential protein that is required in higher concentrations for growth of cells at higher temperatures. Mol Cell Biol 9: 3919-3930.
60. Nathan DF, Lindquist S, (1995) Mutational analysis of Hsp90 function: interactions with a steroid receptor and a protein kinase. Mol Cell Biol 15: 3917-3925.
61. Nakai A, Ishikawa T, (2001) Cell cycle transition under stress conditions controlled by vertebrate heat shock factors. EMBO J 20: 2885-2895.
62. Benoit JB, Lopez-Martinez G, Phillips ZP, Patrick KR, Denlinger DL, (2010) Heat shock proteins contribute to mosquito dehydration tolerance. J Insect Physiol 56: 151-156.
63. Colinet H, Lee SF, Hoffmann A, (2010) Knocking down expression of Hsp22 and Hsp23 by RNA interference affects recovery from chill coma in Drosophila melanogaster. J Exp Biol 213: 4146-4150.
64. Lü Z-C, Wan F-H, (2011) Using double-stranded RNA to explore the role of heat shock protein genes in heat tolerance in Bemisia tabaci (Gennadius). J Exp Biol 214: 764-769.
65. Debolt JW, (1982) Meridic diet for rearing successive generations of Lygus hesperus. Ann Entomol Soc Am 75: 119-122.
66. Patana R, (1982) Disposable diet packet for feeding and oviposition of Lygus hesperus (Hemiptera: Miridae). J Econ Entomol 75: 668-669.
67. Altschul SF, Madden TL, Schäffer 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.
68. Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, et al. (2008) The Pfam protein families database. Nucleic Acids Res 36: D281-288.
69. Finn RD, Clements J, Eddy SR, (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39: W29-37.
70. Katoh K, Kuma K-i, Toh H, Miyata T, (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33: 511-518.
71. Katoh K, Misawa K, Kuma K-i, Miyata T, (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30: 3059-3066.
72. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.