De novo assembly and characterization of the global transcriptome for Rhyacionia leptotubula using illumina paired-end sequencing

PLoS ONE

Volumn 8, Issue 11, 2013, Pages

  Zhu, Jia Ying ^a   Li, Yong He ^a   Yang, Song ^a   Li, Qin Wen ^a  

^a SOUTHWEST FORESTRY UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CARBOXYLESTERASE; CYTOCHROME P450; HEAT SHOCK PROTEIN; TRANSCRIPTOME; INSECT PROTEIN; MICROSATELLITE DNA;

AMPLICON; ARTICLE; CONTROLLED STUDY; GENE; GENE IDENTIFICATION; HIGH THROUGHPUT SEQUENCING; HSP GENE; INSECTICIDE RESISTANCE; LEPIDOPTERA; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN FAMILY; RHYACIONIA LEPTOTUBULA; SIMPLE SEQUENCE REPEAT; ANIMAL; BIOLOGY; CHEMISTRY; GENE EXPRESSION PROFILING; GENETICS; MOLECULAR GENETICS; MOTH; PHYLOGENY; REPRODUCIBILITY;

ANIMALS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; INSECT PROTEINS; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE ANNOTATION; MOTHS; PHYLOGENY; REPRODUCIBILITY OF RESULTS; TRANSCRIPTOME;

EID: 84896738509     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0081096     Document Type: Article

References (68)

1. Zhu JY, Wei SJ, Li QW, Yang S, Li YH (2012) Mitochondrial genome of the pine tip moth Rhyacionia leptotubula (Lepidoptera: Tortricidae). Mitochondrial DNA 23: 376-378.
2. Zhu JY, Yang S, Li QW, Li YH (2011) Isolation and characterization of microsatellite loci for Rhyacionia leptotubula (Lepidoptera: Tortricidae). African J Microbiol Res 5: 4026-4028.
3. Wu XP, Qian Y, Ma WM, Ma X, Zhang JH (2008) A preliminary study on the biology of Rhyacionia leptotubula. J Southwest Forest Coll 28: 58-59.
4. Yang S, Ma MY, Li QW, Chai SQ (2012) Distribution and damage of Rhyacionia leptotubula in Northeastern Yunnan. Forest Pest Dis 31: 20-21, 41.
5. Gibbons JG, Janson EM, Hittinger CT, Johnston M, Abbot P, et al. (2009) Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics. Mol Biol Evol 26: 2731-2744.
6. Bai X, Mamidala P, Rajarapu SP, Jones SC, Mittapalli O (2011) Transcriptomics of the bed bug (Cimex lectularius). PLoS One 6: e16336.
7. Zhu JY, Yang P, Zhang Z, Wu GX, Yang B (2013) Transcriptomic immune response of Tenebrio molitor pupae to parasitization by Scleroderma guani . PLoS One 8: e54411.
8. 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 Biotechnol 29: 644-652.
9. Iseli C, Jongeneel CV, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol pp. 138-48.
10. Gotz S, Garcia-Gomez 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. (Pubitemid 351859009)
11. Finn RD, Clements J, Eddy SR (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39: W29-37.
12. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acid Res 25: 4876-4882. (Pubitemid 28022245)
13. 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.
14. Wang S, Wang X, He Q, Liu X, Xu W, et al. (2012) Transcriptome analysis of the roots at early and late seedling stages using Illumina paired-end sequencing and development of EST-SSR markers in radish. Plant Cell Rep 31: 1437-1447.
15. Price DP, Nagarajan V, Churbanov A, Houde P, Milligan B, et al. (2011) The fat body transcriptomes of the yellow fever mosquito Aedes aegypti, pre- and postblood meal. PLoS One 6: e22573.
16. Xue J, Bao YY, Li BL, Cheng YB, Peng ZY, et al. (2010) Transcriptome analysis of the brown planthopper Nilaparvata lugens . PLoS One 5: e14233.
17. Salem M, Rexroad CE, Wang J, Thorgaard GH, Yao J (2010) Characterization of the rainbow trout transcriptome using Sanger and 454-pyrosequencing approaches. BMC Genomics 11: 564.
18. 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.
19. Zhu JY, Zhao N, Yang B (2012) Global transcriptome profiling of the pine shoot beetle, Tomicus yunnanensis (Coleoptera: Scolytinae). PLoS One 7: e32291.
20. Fu N, Wang Q, Shen HL (2013) De novo assembly, gene annotation and marker development using Illumina paired-end transcriptome sequences in celery (Apium graveolens L.). PLoS One 8: e57686.
21. Zdobnov EM, Bork P (2007) Quantification of insect genome divergence. Trends Genet 23: 16-20. (Pubitemid 44960528)
22. Ewen-Campen B, Shaner N, Panfilio KA, Suzuki Y, Roth S, et al. (2011) The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus . BMC Genomics 12: 61.
23. Shi CY, Yang H, Wei CL, Yu O, Zhang ZZ, et al. (2011) Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds. BMC Genomics 12:131.
24. Zhan S, Merlin C, Boore JL, Reppert SM (2011) The monarch butterfly genome yields insights into long-distance migration. Cell 147: 1171-1185.
25. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29. (Pubitemid 30257031)
26. Wang XW, Luan JB, Li JM, Bao YY, Zhang CX, et al. (2010) De novo characterization of a whitefly transcriptome and analysis of its gene expression during development. BMC Genomics 11: 400.
27. Liang C, Liu X, Yiu SM, Lin BL (2013) De novo assembly and characterization of Camelina sativa transcriptome by paired-end sequencing. BMC Genomics 14: 146.
28. Shi CY, Yang H, Wei CL, Yu O, Zhang ZZ, et al. (2011) Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds. BMC Genomics 12: 131.
29. Feyereisen R (1999) Insect P450 enzymes. Annu Rev Entomol 44: 507-33.
30. Durand N, Carot-Sans G, Chertemps T, Bozzolan F, Party V, et al. (2010) Characterization of an antennal carboxylesterase from the pest moth Spodoptera littoralis degrading a host plant odorant. PLoS One 5: e15026.
31. Liu N, Li T, Reid WR, Yang T, Zhang L (2011) Multiple Cytochrome P450 genes: their constitutive overexpression and permethrin induction in insecticide resistant mosquitoes, Culex quinquefasciatus . PLoS One 6: e23403.
32. Karatolos N, Williamson MS, Denholm I, Gorman K, Ffrench-Constant RH, et al. (2012) Over-expression of a cytochrome P450 is associated with resistance to pyriproxyfen in the greenhouse whitefly Trialeurodes vaporariorum. PLoS One 7: e31077.
33. Hemingway J, Ranson H (2000) Insecticide resistance in insect vectors of human disease. Annu Rev Entomol 45: 371-391. (Pubitemid 30187866)
34. Gu J, Huang LX, Shen Y, Huang LH, Feng QL (2012) Hsp70 and small Hsps are the major heat shock protein members involved in midgut metamorphosis in the common cutworm, Spodoptera litura. Insect Mol Biol 21: 535-543.
35. Liu Z, Xi D, Kang M, Guo X, Xu B (2012) Molecular cloning and characterization of Hsp27.6: the first reported small heat shock protein from Apis cerana cerana. Cell Stress Chaperones 17: 539-551.
36. Gething MJ (1997) Guidebook to Molecular Chaperones and Protein-Folding Catalysts. Oxford, UK, Oxford Univ. Press. pp. 384.
37. Zhu JY, G Wu GX, Ye GY, Hu C (2013) Heat shock protein genes (hsp20, hsp75 and hsp90) from Pieris rapae: Molecular cloning and transcription in response to parasitization by Pteromalus puparum. Insect Sci 20: 183-193.
38. Manjunatha HB, Rajesh RK, Aparna HS (2010) Silkworm thermal biology: a review of heat shock response, heat shock proteins and heat acclimation in the domesticated silkworm, Bombyx mori. J Insect Sci 10: 204.
39. 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. Int J Biochem Mol Biol 2: 47-57.
40. Fiaux J, Bertelsen EB, Horwich AL, Wüthrich K (2002) NMR analysis of a 900K GroEL GroES complex. Nature 418: 207-211. (Pubitemid 34773778)
41. Hull JJ, Geib SM, Fabrick JA, Brent CS (2013) Sequencing and de novo assembly of the western tarnished plant bug (Lygus hesperus) transcriptome. PLoS One 8: e55105.
42. Czarnecka AM, Campanella C, Zummo G, Cappello F (2006) Heat shock protein 10 and signal transduction: a "capsula eburnean" of carcinogenesis? Cell Stress Chaperones 11: 287-294. (Pubitemid 46905763)
43. Haslbeck M, Franzmann T, Weinfurtner D, Buchner J (2005) Some like it hot: the structure and function of small heat shock proteins. Nat Struct Mol. Biol 12: 842-846. (Pubitemid 41486706)
44. Sun Y, MacRae TH (2005) Small heat shock proteins: molecular structure and chaperone function. Cell Mol Life Sci 62: 2460-2476. (Pubitemid 41801099)
45. Huang LH, Wang CZ, Kang L (2009) Cloning and expression of five heat shock protein genes in relation to cold hardening and development in the leafminer, Liriomyza sativa. J Insect Physiol 55: 279-285.
46. Li ZW, Li X, Yu QY, Xiang ZH, 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.
47. Franck E, Madsen O, van Rheede T, Ricard G, Huynen MA, et al. (2004) Evolutionary diversity of vertebrate small heat shock proteins. J Mol Evol 59: 792-805. (Pubitemid 40100875)
48. Qiu XB, Shao YM, Miao S, Wang L (2006) The diversity of the DnaJ/Hsp40 family, the crucial partners for Hsp70 chaperones. Cell Mol Life Sci 63: 2560-2570. (Pubitemid 44800711)
49. Shi M, Wang YN, Zhu N, Chen XX (2013) Four heat shock protein genes of the endoparasitoid wasp, Cotesia vestalis, and their transcriptional profiles in relation to developmental stages and temperature. PLoS One 8: e59721.
50. Bork P, Sander C, Valencia A, Bukau B (1992) A module of the DnaJ heat shock proteins found in malaria parasites. Trends Biochem Sci 17: 129.
51. Ohtsuka K, Hata M (2000) Mammalian HSP40/DNAJ homologs: cloning of novel cDNAs and a proposal for their classification and nomenclature. Cell Stress Chaperones 5: 98-112.
52. Toursel C, Dzierszinski F, Bernigaud A, Mortuaire M, Tomavo S (2000) Molecular cloning, organellar targeting and developmental expression of mitochondrial chaperone HSP60 in Toxoplasma gondii. Mol Biochem Parasitol 111: 319-332. (Pubitemid 32121675)
53. Zhou J, Wang WN, He WY, Zheng Y, Wang L, et al. (2010) Expression of HSP60 and HSP70 in white shrimp, Litopenaeus vannamei in response to bacterial challenge. J Invertebr Pathol 103: 170-178.
54. Quintana FJ, Cohen IR (2005) Heat shock proteins as endogenous adjuvants in sterile and septic inflammation. J Immunol 175: 2777-2782. (Pubitemid 41170492)
55. Wu Y, Egerton G, Ball A, Tanguay RM, Bianco AE (2000) Characterization of the heat-shock protein 60 chaperonin from Onchocerca volvulus. Mol Biochem Parasitol 107: 155-168. (Pubitemid 30211632)
56. Karlin S, Brocchieri L (1998) Heat shock protein 70 family: multiple sequence comparisons, function, and evolution. J Mol Evol 47: 565-577. (Pubitemid 28507477)
57. Tammariello SP, Rinehart JP, Denlinger DL (1999) Desiccation elicits heat shock protein transcription in the flesh fly, Sarcophaga crassipalpis, but does not enhance tolerance to high or low temperatures. J Insect Physiol 45: 933-938. (Pubitemid 29379004)
58. Xu P, Xiao J, Liu L, Li T, Huang D (2010) Molecular cloning and characterization of four heat shock protein genes from Macrocentrus cingulum (Hymenoptera: Braconidae). Mol Biol Rep 37: 2265-2272.
59. Tariq M, Nussbaumer U, Chen Y, Beisel C, Paro R (2009) Trithorax requires Hsp90 for maintenance of active chromatin at sites of gene expression. Proc Natl Acad Sci USA 106: 1157-1162.
60. Picard D (2002) Heat-shock protein 90, a chaperone for folding and regulation. Cell Mol Life Sci 59: 1640-1648.
61. Wang H, Li K, Zhu JY, Fang Q, Ye GY (2012) Cloning and expression pattern of heat shock protein genes from the endoparasitoid wasp, Pteromalus puparum in response to environmental stresses. Arch Insect Biochem Physiol 79: 247-63.
62. Yamagishi N, Ishihara K, Saito Y, Hatayama T (2003) Hsp105 but not Hsp70 family proteins suppress the aggregation of heat-denatured protein in the presence of ADP. FEBS Lett 555: 390-396. (Pubitemid 37486062)
63. Saito Y, Yamagishi N, Hatayama T (2007) Different localization of Hsp105 family proteins in mammalian cells. Exp Cell Res 313: 3707-3717. (Pubitemid 47464229)
64. Yasuda K, Ishihara K, Nakashima K, Hatayama T (1999) Genomic cloning and promoter analysis of the mouse 105-kDa heat shock protein (HSP105) gene. Biochem Biophys Res Commun 256: 75-80. (Pubitemid 29298919)
65. Li YC, Korol AB, Fahima T, Beiles A, Nevo E (2002) Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Mol Ecol 11: 2453-2465. (Pubitemid 35436668)
66. Xu Y, Zhou W, Zhou Y, Wu J, Zhou X (2012) Transcriptome and comparative gene expression analysis of Sogatella furcifera (Horváth) in response to southern rice black-streaked dwarf virus. PLoS One 7: e36238.
67. Keyghobadi N, Roland J, Strobeck C (2002). Isolation of novel microsatellite loci in the Rocky Mountain apollo butterfly, Parnassius smintheus. Hereditas 136: 247-250. (Pubitemid 35345367)
68. Zhao X, Tan Z, Feng H, Yang R, Li M, et al. (2002) Microsatellites in different Potyvirus genomes: survey and analysis. Gene 488: 52-56.