Expression of Small RNA in Aphis gossypii and Its Potential Role in the Resistance Interaction with Melon

PLoS ONE

Volumn 7, Issue 11, 2012, Pages

  Sattar, Sampurna ^a   Addo Quaye, Charles ^b   Song, Yan ^c   Anstead, James A ^a   Sunkar, Ramanjulu ^c   Thompson, Gary A ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

^c OKLAHOMA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; UNTRANSLATED RNA;

ARTICLE; CATABOLISM; CELL DIFFERENTIATION; CONTROLLED STUDY; COTTON APHID; HERBIVORY; MELON; MORPHOGENESIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHLOEM; POLYMERASE CHAIN REACTION; RNA SEQUENCE; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION;

ANIMALS; APHIDS; BASE SEQUENCE; CUCUMIS MELO; GENE EXPRESSION REGULATION; MICRORNAS; PLANT PROTEINS; RNA, PLANT; RNA, SMALL INTERFERING; SEQUENCE ANALYSIS, RNA;

APHIDIDAE; APHIS GOSSYPII; CUCUMIS; CUCUMIS MELO; GOSSYPIUM HIRSUTUM; HEXAPODA;

EID: 84869237346     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0048579     Document Type: Article

References (67)

1. Lee RC, Feinbaum RL, Ambros V, (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843-854.
2. Kim VN, Han J, Siomi MC, (2009) Biogenesis of small RNAs in animals. Nature Reviews Molecular Cell Biology 10: 126-139.
3. Lin H, Spradling AC, (1997) A novel group of pumilio mutations affects the asymmetric division of germline stem cells in the Drosophila ovary. Development 124: 2463-2476.
4. Aravin AA, Sachidanandam R, Girard A, Fejes-Toth K, Hannon GJ, (2007) Developmentally Regulated piRNA Clusters Implicate MILI in Transposon Control. Science 316: 744-747.
5. Hartig JV, Tomari Y, Förstemann K, (2007) piRNAs-the ancient hunters of genome invaders. Genes Dev 21: 1707-1713.
6. Rajasethupathy P, Antonov I, Sheridan R, Frey S, Sander C, et al. (2012) A Role for Neuronal piRNAs in the Epigenetic Control of Memory-Related Synaptic Plasticity. Cell 149: 693-707.
7. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ, (2007) miRBase: tools for microRNA genomics. Nucleic Acids Res 36: D154-D158.
8. Kozomara A, Griffiths-Jones S, (2010) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39: D152-D157.
9. Legeai F, Rizk G, Walsh T, Edwards O, Gordon K, et al. (2010) Bioinformatic prediction, deep sequencing of microRNAs and expression analysis during phenotypic plasticity in the pea aphid, Acyrthosiphon pisum. BMC Genomics 11: 281 doi:10.1186/1471-2164-11-281.
10. Chen Q, Lu L, Hua H, Zhou F, Lu L, et al. (2012) Characterization and Comparative Analysis of Small RNAs in Three Small RNA Libraries of the Brown Planthopper (Nilaparvata lugens). PLoS One 7doi:10.1371/journal.pone.0032860.
11. Foster SP, Tomiczek M, Thompson R, Denholm I, Poppy G, et al. (2007) Behavioural side-effects of insecticide resistance in aphids increase their vulnerability to parasitoid attack. Animal Behaviour 74: 621-632.
12. Dogimont C, Chovelon V, Tual S, Boissot N, Rittener V, et al. (2008) Molecular diversity at the Vat/Pm-W resistance locus in melon. In: Pitrat M, editors. Cucurbitaceae 2008.Proceedings of the IXth EUCARPIA meeting on genetics and breeding of Cucurbitaceae.
13. Kennedy G, Kishaba A, (1977) Response of alate melon aphids (Hemiptera-(Homoptera)-Aphididae) to resistant and susceptible muskmelon lines. J Econ Entomol 70: 407-410.
14. McCreight J, Bohn G, Kishaba A, (1992) Pedigree of PI 414723 melon. Cucurbit Genet Coop Rep 15: 51-52.
15. Soria C, Moriones E, Fereres A, Garzo E, Gómez-Guillamón ML, (2003) New source of resistance to mosaic virus transmission by Aphis gossypii in melon. Euphytica 133: 313-318 doi:10.1023/A:1025721329026.
16. Garzo E, Soria C, Gómez-Guillamón ML, Fereres A, (2002) Feeding behavior of Aphis gossypii on resistant accessions of different melon genotypes (Cucumis melo). Phytoparasitica 30: 129-140 doi:10.1007/BF02979695.
17. Pauquet J, Burget E, Hagen L, Chovelon V, Le Menn A, et al. (2004) Map-based cloning of Vat gene from melon conferring resistance to both aphid colonization and aphid transmission of several viruses. In: Lebeda A, Paris H, editors. Proceedings of Cucurbitaceae 2004, the 8th EUCARPIA meeting on Cucurbit genetics and breeding. Olomouc (CZ): Palaky University. pp. 325-329.
18. Bohn G, Kishaba A, Toba H, (1972) Mechanisms of resistance to melon aphid in a muskmelon line. Hortic Sci 7: 281-282.
19. Klingler J, Powell G, Thompson GA, Isaacs R, (1998) Phloem specific aphid resistance in Cucumis melo line AR 5: effects on feeding behaviour and performance of Aphis gossypii. Entomol Exp Appl 86: 79-88 doi:10.1046/j.1570-7458.1998.00267.x.
20. McCormick KP, Willmann MR, Meyers BC, (2011) Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments. Silence 2: 2 doi:10.1186/1758-907X-2-2.
21. Chen X, Li Q, Wang J, Guo X, Jiang X, et al. (2009) Identification and characterization of novel amphioxus microRNAs by Solexa sequencing. Genome Biol 10: R78 doi:10.1186/gb-2009-10-7-r78.
22. Friedländer MR, Chen W, Adamidi C, Maaskola J, Einspanier R, et al. (2008) Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol 26: 407-415.
23. Gonzalez-Ibeas D, Blanca J, Donaire L, Saladié M, Mascarell-Creus A, et al. (2011) Analysis of the melon (Cucumis melo) small RNAome by high-throughput pyrosequencing. BMC Genomics 12: 393 doi:10.1186/1471-2164-12-393.
24. Sattar S, Song Y, Anstead JA, Sunkar R, Thompson GA, (2012) Cucumis melo microRNA expression profile during aphid herbivory in a resistant and susceptible interaction. Mol Plant Microbe Interact 25: 839-848.
25. Bailey TL, (2011) DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics 27: 1653-1659 doi:10.1093/bioinformatics/btr261.
26. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, et al. (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37: W202-208 doi:10.1093/nar/gkp335.
27. Baumann P, Lai C, Baumann L, Rouhbakhsh D, Moran NA, et al. (1995) Mutualistic associations of aphids and prokaryotes: biology of the genus buchnera. Appl Environ Microbiol 61: 1-7.
28. Bartel DP, (2009) MicroRNAs: target recognition and regulatory functions. Cell 136: 215-233 doi:10.1016/j.cell.2009.01.002.
29. Belles X, Cristino AS, Tanaka ED, Rubio M, Piulachs M-D (2012) 2- Insect MicroRNAs: From Molecular Mechanisms to Biological Roles. Insect Molecular Biology and Biochemistry. San Diego: Academic Press. pp. 30-56.
30. Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E, (2007) The role of site accessibility in microRNA target recognition. Nat Genet 39: 1278-1284.
31. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, et al. (2000) The genome sequence of Drosophila melanogaster. Science 287: 2185-2195.
32. McQuilton P, St Pierre SE, Thurmond J, (2012) FlyBase 101-the basics of navigating FlyBase. Nucleic Acids Res 40: D706-714.
33. Rehmsmeier M, Steffen P, Höchsmann M, Giegerich R, (2004) Fast and effective prediction of microRNA/target duplexes. RNA 10: 1507-1517 doi:10.1261/rna.5248604.
34. Gomez-Orte E, Belles X, (2009) MicroRNA-dependent metamorphosis in hemimetabolan insects. Proc Natl Acad Sci USA 106: 21678-21682.
35. Wei Y, Chen S, Yang P, Ma Z, Kang L, (2009) Characterization and comparative profiling of the small RNA transcriptomes in two phases of locust. Genome Biol 10: R6 doi:10.1186/gb-2009-10-1-r6.
36. Zhang Y, Zhou X, Ge X, Jiang J, Li M, et al. (2009) Insect-Specific microRNA involved in the development of the silkworm Bombyx mori. PLoS ONE 4: e4677 doi:10.1371/journal.pone.0004677.
37. Jagadeeswaran G, Zheng Y, Sumathipala N, Jiang H, Arrese EL, et al. (2010) Deep sequencing of small RNA libraries reveals dynamic regulation of conserved and novel microRNAs and microRNA-stars during silkworm development. BMC Genomics 11: 52 doi:10.1186/1471-2164-11-52.
38. Klingler J, Thompson GA, Perl-Treves R, (2001) Mapping of cotton-melon aphid resistance in melon. J Amer Soc Hort Sci 126: 56-63.
39. Cristino AS, Tanaka ED, Rubio M, Piulachs M-D, Belles X, (2011) Deep sequencing of organ- and stage-specific microRNAs in the evolutionarily basal insect Blattella germanica (L.) (Dictyoptera, Blattellidae). PLoS ONE 6: e19350 doi:10.1371/journal.pone.0019350.
40. Skalsky RL, Vanlandingham DL, Scholle F, Higgs S, Cullen BR, (2010) Identification of microRNAs expressed in two mosquito vectors, Aedes albopictus and Culex quinquefasciatus. BMC Genomics 11: 119 doi:10.1186/1471-2164-11-119.
41. Behura SK, (2007) Insect microRNAs: Structure, function and evolution. Insect Biochem Mol Biol 37: 3-9.
42. Mishima Y, Stahlhut C, Giraldez AJ, (2007) miR-1-2 gets to the heart of the matter. Cell 129: 247-249.
43. Silver SJ, Hagen JW, Okamura K, Perrimon N, Lai EC, (2007) Functional screening identifies miR-315 as a potent activator of Wingless signaling. Proc Natl Acad Sci USA 104: 18151-18156.
44. Clop A, Marcq F, Takeda H, Pirottin D, Tordoir X, et al. (2006) A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep. Nat Genet 38: 813-818.
45. Chen J-F, Mandel EM, Thomson JM, Wu Q, Callis TE, et al. (2006) The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation. Nat Genet 38: 228-233 doi:10.1038/ng1725.
46. Müller CB, Williams IS, Hardie J, (2001) The role of nutrition, crowding and interspecific interactions in the development of winged aphids. Ecol Entomol 26: 330-340.
47. Iovino N, Pane A, Gaul U, (2009) miR-184 has multiple roles in Drosophila female germline development. Dev Cell 17: 123-133.
48. Walters KFA, Brough C, Dixon AFG, (1988) Habitat quality and reproductive investment in aphids. Ecol Entomology 13: 337-345.
49. Tsurudome K, Tsang K, Liao EH, Ball R, Penney J, et al. (2010) The Drosophila miR-310 cluster negatively regulates synaptic strength at the neuromuscular junction. Neuron 68: 879-893 doi:10.1016/j.neuron.2010.11.016.
50. Berezikov E, (2011) Evolution of microRNA diversity and regulation in animals. Nat Rev Genet 12: 846-860.
51. Pasquinelli AE, (2012) MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship. Nat Rev Genet 13: 271-282.
52. Yoo B-C, Kragler F, Varkonyi-Gasic E, Haywood V, Archer-Evans S, et al. (2004) A systemic small RNA signaling system in plants. Plant Cell 16: 1979-2000.
53. Varkonyi-Gasic E, Gould N, Sandanayaka M, Sutherland P, MacDiarmid RM, (2010) Characterisation of microRNAs from apple (Malus domestica "Royal Gala") vascular tissue and phloem sap. BMC Plant Biol 10: 159.
54. Buhtz A, Pieritz J, Springer F, Kehr J, (2010) Phloem small RNAs, nutrient stress responses, and systemic mobility. BMC Plant Biol 10: 64 doi:10.1186/1471-2229-10-64.
55. Rodriguez-Medina C, Atkins CA, Mann AJ, Jordan ME, Smith PM, (2011) Macromolecular composition of phloem exudate from white lupin (Lupinus albus L.). BMC Plant Biol 11: 36 doi:10.1186/1471-2229-11-36.
56. Chen J-Q, Delobel B, Rahbé Y, Sauvion N, (1996) Biological and chemical characteristics of a genetic resistance of melon to the melon aphid. Entomol Exp Appl 80: 250-253.
57. Lu C, Meyers BC, Green PJ, (2007) Construction of small RNA cDNA libraries for deep sequencing. Methods 43: 110-117.
58. Langmead B, Trapnell C, Pop M, Salzberg SL, (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25 doi:10.1186/gb-2009-10-3-r25.
59. Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, et al. (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33: 179-188.
60. Varkonyi-Gasic E, Wu R, Wood M, Walton EF, Hellens RP, (2007) Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs. Plant Methods 3: 12 doi:10.1186/1746-4811-3-12.
61. Pfaffl MW, (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29: 2002-2007.
62. Flutre T, Duprat E, Feuillet C, Quesneville H, (2011) Considering transposable element diversification in de novo annotation approaches. PLoS ONE 6: e16526 doi:10.1371/journal.pone.0016526.
63. Lee L, Hunter W, Hunnicutt L (2005) An expressed sequence tag (EST) cDNA library of Aphis gossypii alates. American phytopathological society annual meeting. Austin TX: American phytopathological society. p. P-579.
64. Gauthier J-P, Legeai F, Zasadzinski A, Rispe C, Tagu D, (2007) AphidBase: a database for aphid genomic resources. Bioinformatics 23: 783-784.
65. Quinlan AR, Hall IM, (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
66. Zhang Z, Schwartz S, Wagner L, Miller W, (2000) A Greedy Algorithm for Aligning DNA Sequences. Journal of Computational Biology 7: 203-214 doi:10.1089/10665270050081478.
67. 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.