Identification and characterization of microRNAs in small brown planthopper (Laodephax striatellus) by next-generation sequencing

PLoS ONE

Volumn 9, Issue 7, 2014, Pages

  Zhou, Guoyan ^a   Wang, Tingzhang ^a   Lou, Yonggen ^a   Cheng, Jia'an ^a   Zhang, Hengmu ^b   Xu, Jian Hong ^a  

^a ZHEJIANG UNIVERSITY   (China)

^b INSTITUTE OF PLANT PROTECTION AND MICROBIOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; TRANSFER RNA;

ARTICLE; CONTROLLED STUDY; DEVELOPMENTAL STAGE; FEMALE; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE LIBRARY; GENE ONTOLOGY; GENE SEQUENCE; GENE TARGETING; GENETIC CONSERVATION; INSECT DEVELOPMENT; LAODEPHAX STRIATELLUS; MALE; METABOLIC REGULATION; NEXT GENERATION SEQUENCING; NONHUMAN; PLANTHOPPER; PREDICTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; RNA SEQUENCE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; ANIMAL; CONFORMATION; CROP; GENETICS; HEMIPTERA; HIGH THROUGHPUT SEQUENCING; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PARASITOLOGY;

ANIMALS; BASE SEQUENCE; CONSERVED SEQUENCE; CROPS, AGRICULTURAL; GENE EXPRESSION REGULATION; GENE LIBRARY; HEMIPTERA; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICRORNAS; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION;

EID: 84904796981     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0103041     Document Type: Article

References (65)

1. Carthew RW, Sontheimer EJ (2009) Origins and Mechanisms of miRNAs and siRNAs. Cell 136: 642-655.
2. Zamore PD, Haley B (2005) Ribo-gnome: the big world of small RNAs. Science 309: 1519-1524. (Pubitemid 41266468)
3. Lee R, Feinbaum R, Ambros V (2004) A Short History of a Short RNA. Cell S116: S89-S92.
4. Ruvkun G, Wightman B, Ha I (2004) The 20 years it took to recognize the importance of tiny RNAs. Cell S116: S93-S96.
5. Lin H (2007) piRNAs in the germ line. Science 316: 397.
6. Bartel DP (2004) MicroRNAs Genomics, Biogenesis, Mechanism, and Function. Cell 116: 281-297.
7. Pasquinelli AE, Hunter S, Bracht J (2005) MicroRNAs: a developing story. Curr Opin Genet Dev 15: 200-205. (Pubitemid 40410666)
8. Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, et al. (2005) Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 434: 338-345. (Pubitemid 40469170)
9. Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136: 215-233.
10. Miska EA (2005) How microRNAs control cell division, differentiation and death. Curr Opin Genet Dev 15: 563-568.
11. Makeyev EV, Zhang J, Carrasco MA, Maniatis T (2007) The MicroRNA miR-124 promotes neuronal differentiation by triggering brain-specific alternative pre-mRNA splicing. Mol Cell 27: 435-448. (Pubitemid 47126944)
12. Liu F, Peng W, Li Z, Li W, Li L, et al. (2012) Next-generation small RNA sequencing for microRNAs profiling in Apis mellifera: comparison between nurses and foragers. Insect Mol Biol 21: 297-303.
13. Wang Y, Fan HW, Huang HJ, Xue J, Wu WJ, et al. (2012) Chitin synthase 1 gene and its two alternative splicing variants from two sap-sucking insects, Nilaparvata lugens and Laodelphax striatellus (Hemiptera: Delphacidae). Insect Biochem Mol Biol 42: 637-646.
14. 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.
15. 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.
16. Lijun C, Xizhi M, Lin K, Kejing D, Shouyuan Z, et al. (2003) Detecting Rice stripe virus (RSV) in the small brown planthopper (Laodelphax striatellus) with high specificity by RT-PCR. Journal of Virological Methods 112: 115-120. (Pubitemid 37338264)
17. Toriyama S (1986) Rice stripe virus: prototype of a new group of viruses that replicate in plants and insects. Microbiol Sci 3: 347-351.
18. Fu BX, Bellis GA, Hong J, Wang JR, Wu Q, et al. (2012) Morphology, distribution, and abundance of antennal sensilla of male and female macropterous and brachypterous small brown planthopper, Laodelphax striatellus (Fallen) (Hemiptera: Delphacidae). Microsc Res Tech 75: 1492-1512.
19. Hao Z, Wang L, He Y, Liang J, Tao R (2011) Expression of defense genes and activities of antioxidant enzymes in rice resistance to rice stripe virus and small brown planthopper. Plant Physiol Biochem 49: 744-751.
20. Hoshizaki S (1997) Allozyme polymorphism and geographic variation in the small brown planthopper, Laodelphax striatellus (Homoptera: Delphacidae). Biochem Genet 35: 383-393.
21. Lee RCF, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14.pdf. Cell 75: 843-854. (Pubitemid 24014542)
22. Basyuk E, Suavet F, Doglio A, Bordonne R, Bertrand E (2003) Human let-7 stem-loop precursors harbor features of RNase III cleavage products. Nucleic Acids Res 31: 6593-6597. (Pubitemid 37508765)
23. Mallory AC, Vaucheret H (2006) Functions of microRNAs and related small RNAs in plants. Nat Genet 38 Suppl: S31-36.
24. Molnar A, Bassett A, Thuenemann E, Schwach F, Karkare S, et al. (2009) Highly specific gene silencing by artificial microRNAs in the unicellular alga Chlamydomonas reinhardtii. Plant J 58: 165-174.
25. Chen QH, Lu L, Hua HX, Zhou F, Lu LX, et al. (2012) Characterization and Comparative Analysis of Small RNAs in Three Small RNA Libraries of the Brown Planthopper (Nilaparvata lugens). PLoS One 7: e32860-e32871.
26. 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.
27. Liu S, Li D, Li Q, Zhao P, Xiang Z, et al. (2010) MicroRNAs of Bombyx mori identified by Solexa sequencing. BMC Genomics 11: 148.
28. Marco A, Hui JH, Ronshaugen M, Griffiths-Jones S (2010) Functional shifts in insect microRNA evolution. Genome Biol Evol 2: 686-696.
29. Mead EA, Tu Z (2008) Cloning, characterization, and expression of microRNAs from the Asian malaria mosquito, Anopheles stephensi. BMC Genomics 9: 244.
30. Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, et al. (2007) Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450: 219-232. (Pubitemid 350100553)
31. Weaver DB, Anzola JM, Evans JD, Reid JG, Reese JT, et al. (2007) Computational and transcriptional evidence for microRNAs in the honey bee genome. Genome Biol 8: R97.
32. 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.
33. Yang M, Lee JE, Padgett RW, Edery I (2008) Circadian regulation of a limited set of conserved microRNAs in Drosophila. BMC Genomics 9: 83.
34. Wei Z, Liu X, Feng T, Chang Y (2011) Novel and conserved micrornas in Dalian purple urchin (Strongylocentrotus nudus) identified by next generation sequencing. Int J Biol Sci 7: 180-192.
35. 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.
36. Wei C, Salichos L, Wittgrove CM, Rokas A, Patton JG (2012) Transcriptome-wide analysis of small RNA expression in early zebrafish development. RNA 18: 915-929.
37. Surridge AK, Lopez-Gomollon S, Moxon S, Maroja LS, Rathjen T, et al. (2011) Characterisation and expression of microRNAs in developing wings of the neotropical butterfly Heliconius melpomene. BMC Genomics 12: 62.
38. Ro S, Ma HY, Park C, Ortogero N, Song R, et al. (2013) The mitochondrial genome encodes abundant small noncoding RNAs. Cell Res 23: 759-774.
39. Zhang KJ, Zhu WC, Rong X, Zhang YK, Ding XL, et al. (2013) The complete mitochondrial genomes of two rice planthoppers, Nilaparvata lugens and Laodelphax striatellus: conserved genome rearrangement in Delphacidae and discovery of new characteristics of atp8 and tRNA genes. BMC Genomics 14: 417.
40. Du T, Zamore PD (2007) Beginning to understand microRNA function. Cell Res 17: 661-663. (Pubitemid 47255935)
41. Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, et al. (2008) Criteria for annotation of plant MicroRNAs. Plant Cell 20: 3186-3190.
42. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, et al. (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326: 1112-1115.
43. Gao ZH, Wei JH, Yang Y, Zhang Z, Xiong HY, et al. (2012) Identification of conserved and novel microRNAs in Aquilaria sinensis based on small RNA sequencing and transcriptome sequence data. Gene 505: 167-175.
44. Chen X, Yu X, Cai Y, Zheng H, Yu D, et al. (2010) Next-generation small RNA sequencing for microRNAs profiling in the honey bee Apis mellifera. Insect Mol Biol 19: 799-805.
45. Du P, Wu J, Zhang J, Zhao S, Zheng H, et al. (2011) Viral infection induces expression of novel phased microRNAs from conserved cellular microRNA precursors. PLoS Pathog 7: e1002176.
46. Li T, Li H, Zhang YX, Liu JY (2011) Identification and analysis of seven H(2)O(2)-responsive miRNAs and 32 new miRNAs in the seedlings of rice (Oryza sativa L. ssp. indica). Nucleic Acids Res 39: 2821-2833.
47. Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, et al. (2007) Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res 17: 1850-1864. (Pubitemid 351360008)
48. Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, et al. (2003) A uniform system for microRNA annotation. RNA 9: 277-279. (Pubitemid 36246165)
49. 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: e179.
50. Kramer MF (2011) Stem-loop RT-qPCR for miRNAs. Curr Protoc Mol Biol Chapter 15: Unit 15 10.
51. 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.
52. Yang J, Chen D, He Y, Melendez A, Feng Z, et al. (2013) MiR-34 modulates Caenorhabditis elegans lifespan via repressing the autophagy gene atg9. Age (Dordr) 35: 11-22.
53. Glazov EA, Cottee PA, Barris WC, Moore RJ, Dalrymple BP, et al. (2008) A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome Res 18: 957-964. (Pubitemid 351793068)
54. Wheat CW, Wahlberg N (2013) Phylogenomic insights into the cambrian explosion, the colonization of land and the evolution of flight in arthropoda. Syst Biol 62: 93-109.
55. Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, et al. (2008) Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452: 745-749. (Pubitemid 351522763)
56. Tehler D, Hoyland-Kroghsbo NM, Lund AH (2011) The miR-10 microRNA precursor family. RNA Biol 8: 728-734.
57. Hertel J, Bartschat S, Wintsche A, Otto C, Students of the Bioinformatics Computer L, et al. (2012) Evolution of the let-7 microRNA family. RNA Biol 9: 231-241.
58. Pelaez P, Trejo MS, Iniguez LP, Estrada-Navarrete G, Covarrubias AA, et al. (2012) Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing. BMC Genomics 13: 83.
59. Stark A, Brennecke J, Russell RB, Cohen SM (2003) Identification of Drosophila MicroRNA targets. PLoS Biol 1: E60.
60. Enright AJ, John B, Gaul U, Tuschl T, Sander C, et al. (2003) MicroRNA targets in Drosophila. Genome Biol 5: R1.
61. Yu X, Wang H, Lu Y, de Ruiter M, Cariaso M, et al. (2012) Identification of conserved and novel microRNAs that are responsive to heat stress in Brassica rapa. J Exp Bot 63: 1025-1038.
62. Song C, Wang C, Zhang C, Korir NK, Yu H, et al. (2010) Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata). BMC Genomics 11: 431.
63. German MA, Pillay M, Jeong DH, Hetawal A, Luo S, et al. (2008) Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol 26: 941-946.
64. Yekta S, Shih IH, Bartel DP (2004) MicroRNA-directed cleavage of HOXB8 mRNA. Science 304: 594-596. (Pubitemid 38541919)
65. Bushati N, Cohen SM (2007) microRNA functions. Annu Rev Cell Dev Biol 23: 175-205.