Next-generation sequencing-based transcriptome analysis of Cryptolaemus montrouzieri under insecticide stress reveals resistance-relevant genes in ladybirds

Genomics

Volumn 100, Issue 1, 2012, Pages 35-41

  Zhang, Yuhong ^a   Jiang, Ruixin ^a   Wu, Hongsheng ^a   Liu, Ping ^a   Xie, Jiaqin ^a   He, Yunyu ^a   Pang, Hong ^a  

^a SUN YAT SEN UNIVERSITY   (China)

Author keywords

Biological control agents; Gene expression profiling; High throughput RNA sequencing; Insecticide resistance; Transcriptome analysis

Indexed keywords

TRANSCRIPTOME;

ANIMAL EXPERIMENT; ARTICLE; BIOLOGICAL CONTROL AGENT; COLEOPTERA; CONTROLLED STUDY; CRYPTOLAEMUS MONTROUZIERI; DOWN REGULATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE FUNCTION; GENETIC ANALYSIS; GENETIC RESISTANCE; GENETIC VARIABILITY; HIGH THROUGHPUT SEQUENCING; INSECT GENETICS; INSECTICIDE RESISTANCE; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; RNA ANALYSIS; RNA SEQUENCE; RNA TRANSCRIPTION; SEQUENCE ANALYSIS; TRANSCRIPTION REGULATION; UPREGULATION;

ANIMALS; BEETLES; BIOLOGICAL CONTROL AGENTS; DOWN-REGULATION; GENE EXPRESSION PROFILING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; INSECTICIDE RESISTANCE; INSECTICIDES; UP-REGULATION;

COCCINELLIDAE; CRYPTOLAEMUS MONTROUZIERI; PSEUDOCOCCIDAE;

EID: 84862768926     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2012.05.002     Document Type: Article

References (44)

1. Jiang R.X., Li S., Guo Z.P., Pang H. Research status of Cryptolaemus montrouzieri Mulsant and establishing its description criteria. J. Environ. Entomol. 2009, 31:238-247.
2. Li L.Y. The research and application prospects of Cryptolaemus montrouzieri in China. Nat. Enemies Insects 1993, 15:142-152.
3. Babu T.R., Ramanamurthy G. Residual toxicity of pesticides to the adults of Cryptolaemus montrouzieri Mulsant (Coccinellidae: Coleoptera). Int. Pest Control 1999, 41:137-138.
4. Cloyd R.A., Dickinson A. Effect of insecticides on mealybug destroyer (Coleoptera: Coccinellidae) and parasitoid Leptomastix dactylopii (Hymenoptera: Encyrtidae), natural enemies of citrus mealybug (Homoptera: Pseudococcidae). J. Econ. Entomol. 2006, 99:1596-1604.
5. Urbaneja A., et al. Efficacy of five selected acaricides against Tetranychus urticae (Acari: Tetranychidae) and their side effects on relevant natural enemies occurring in citrus orchards. Pest Manage. Sci. 2008, 64:834-842.
6. Mani M., Lakshmi V.J., Krishnamoorthy A. Side effects of some pesticides on the adult longevity, progeny production and prey consumption of Cryptolaemus montrouzieri Mulsant (Coccinellidae, Coleoptera). Indian J. Plant Prot. 1997, 25:48-51.
7. Cloonan N., Grimmond S.M. Transcriptome content and dynamics at single-nucleotide resolution. Genome Biol. 2008, 9:234.
8. Morozova O., Marra M.A. Applications of next-generation sequencing technologies in functional genomics. Genomics 2008, 92:255-264.
9. Wang Z., Gerstein M., Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 2009, 10:57-63.
10. Ozsolak F., Milos P.M. RNA sequencing: advances, challenges and opportunities. Nat. Rev. Genet. 2011, 12:87-98.
11. Huang W., Marth G. EagleView: a genome assembly viewer for next-generation sequencing technologies. Genome Res. 2008, 18:1538-1543.
12. Nagalakshmi U., et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 2008, 320:1344-1349.
13. Wilhelm B.T., et al. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 2008, 453:1239-1243.
14. Mortazavi A., Williams B.A., McCue K., Schaeffer L., Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 2008, 5:621-628.
15. Lister R., et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 2008, 133:523-536.
16. Marioni J., Mason C., Mane S., Stephens M., Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 2008, 18:1509-1517.
17. Morin R.D., et al. Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. Biotechniques 2008, 45:81-94.
18. Graveley B.R., et al. The developmental transcriptome of Drosophila melanogaster. Nature 2011, 471:473-479.
19. Feldmeyer B., Wheat C.W., Rezdorn N.K., Rotter B., Pfenninger M. Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance. BMC Genomics 2011, 12:317.
20. Xiang L.X., He D., Dong W.R., Zhang Y.W., Shao J.Z. Deep sequencing-based transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus reveals insight into the immune-relevant genes in marine fish. BMC Genomics 2010, 11:472.
21. Wang X.W., Luan J.B., Li J.M., Bao Y.Y., Zhang C.X., Liu S.S. De novo characterization of a whitefly transcriptome and analysis of its gene expression during development. BMC Genomics 2010, 11:400.
22. Anisimov S.V. Serial analysis of gene expression (SAGE): 13years of application in research. Curr. Pharm. Biotechnol. 2008, 9:338-350.
23. Zerbino D.R., Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008, 18:821-829.
24. Garg R., Patel R.K., Tyagi A.K., Jain M. De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res. 2011, 18:53-63.
25. Ye J., McGinnis S., Madden T.L. BLAST: improvements for better sequence analysis. Nucleic Acids Res. 2006, 34:W6-W9.
26. Iseli C., Jongeneel C.V., Bucher P. ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol. 1999, 138-148.
27. Ye J., et al. WEGO: a web tool for plotting GO annotations. Nucleic Acids Res. 2006, 34:W293-W297.
28. Tatusov R.L., Galperin M.Y., Natale D.A., Koonin E.V. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 2000, 28:33-36.
29. Kanehisa M., Goto S., Kawashima S., Okuno Y., Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res. 2004, 32:D277-D280.
30. Audic S., Claverie J.M. The significance of digital gene expression profiles. Genome Res. 1997, 7:986-995.
31. Richards S., et al. The genome of the model beetle and pest Tribolium castaneum. Nature 2008, 452:949-955.
32. Tomizawa M., Casida J.E. Neonicotinoid insecticide toxicology: mechanisms of selective action. Annu. Rev. Pharmacol. Toxicol. 2005, 45:247-268.
33. Zhou Q.X., Ding Y.J., Xiao J.P. Sensitive determination of thiamethoxam, imidacloprid and acetamiprid in environmental water samples with solid-phase extraction packed with multiwalled carbon nanotubes prior to high-performance liquid chromatography. Anal. Bioanal. Chem. 2006, 385:1520-1525.
34. Hanriot L., et al. A combination of LongSAGE with Solexa sequencing is well suited to explore the depth and the complexity of transcriptome. BMC Genomics 2008, 9:418.
35. Pan Q., Shai O., Lee L.J., Frey B.J., Blencowe B.J. Deep surveying of alternative splicing complexity in the human transcriptome by high throughput sequencing. Nat. Genet. 2008, 40:1413-1415.
36. Mattick J.S. The genetic signatures of noncoding RNAs. PLoS Genet. 2009, 5:e1000459.
37. Raymond-Delpech V., Matsuda K., Sattelle B.M., Rauh J.J., Sattelle D.B. Ion channels: molecular targets of neuroactive insecticides. Invert. Neurosci. 2005, 5:119-133.
38. David J., et al. Transcriptome response to pollutants and insecticides in the dengue vector Aedes aegypti using next-generation sequencing technology. BMC Genomics 2010, 11:216.
39. Djouaka R.F., et al. Expression of the cytochrome P450s, CYP6P3 and CYP6M2 are significantly elevated in multiple pyrethroid resistant populations of Anopheles gambiae s.s. from Southern Benin and Nigeria. BMC Genomics 2008, 9:538.
40. Vontas J., et al. Transcriptional analysis of insecticide resistance in Anopheles stephensi using cross-species microarray hybridization. Insect Mol. Biol. 2007, 16:315-324.
41. 't Hoen P.A., et al. Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res. 2008, 36:e141.
42. Morrissy A.S., et al. Next-generation tag sequencing for cancer gene expression profiling. Genome Res. 2009, 19:1825-1835.
43. Eisen M.B., Spellman P.T., Brown P.O., Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. U. S. A. 1998, 95:14863-14868.
44. Saldanha A.J. Java Treeview-extensible visualization of microarray data. Bioinformatics 2004, 20:3246-3248.