76 Runckel C, Flenniken M L, Engel J C, et al. Temporal analysis of the honey bee microbiome reveals four novel viruses and seasonal prevalence of known viruses, Nosema, and Crithidia. PLoS One, 2011, 6: e20656
[2]
77 Zirkel F, Kurth A, Quan P L, et al. An insect nidovirus emerging from a primary tropical rainforest. MBio, 2011, 2: e00077
[3]
78 Xu Y, Huang L Z, Fu S, et al. Population diversity of rice stripe virus-derived siRNAs in three different hosts and RNAi-based antiviral immunity in Laodelphgax striatellus. PLoS One, 2012, 7: e46238
[4]
79 Li J M, Andika I B, Shen J F, et al. Characterization of rice black-streaked dwarf virus- and rice stripe virus-derived siRNAs in singly and doubly infected insect vector Laodelphax striatellus. PLoS One, 2013, 8: e66007
[5]
80 Ge L M, Zhang J T, Zhou X P, et al. Genetic structure and population variability of Tomato yellow leaf curl China virus. J Virol, 2007, 81: 5902-5907
[6]
81 Borucki M K, Allen J E, Chen-Harris H, et al. The role of viral population diversity in adaptation of bovine coronavirus to new host environments. PLoS One, 2013, 8: e52752
[7]
82 Wright C F, Morelli M J, Thebaud G, et al. Beyond the consensus: dissecting within-host viral population diversity of foot-and-mouth disease virus by using next-generation genome sequencing. J Virol, 2011, 85: 2266-2275
[8]
94 Manrao E A, Derrington I M, Laszlo A H, et al. Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase. Nat Biotechnol, 2012, 30: 349-353
[9]
1 Strange R N, Scott P R. Plant disease: a threat to global food security. Annu Rev Phytopathol, 2005, 43: 83-116
[10]
2 Coutts R. Plant-viruses—new threats to crops from changing farming practices. Nature, 1986, 322: 594
[11]
3 Goldsmith C S, Miller S E. Modern uses of electron microscopy for detection of viruses. Clin Microbiol Rev, 2009, 22: 552-563
[12]
4 Grover V, Pierce M L, Melcher U. Microarray hybridization for detection of plant viruses from natural settings. Phytopathology, 2007, 97: S43
[13]
5 Grover V, Pierce M L, Hoyt P, et al. Oligonucleotide-based microarray for detection of plant viruses employing sequence-independent amplification of targets. J Virol Methods, 2010, 163: 57-67
[14]
6 Bentley D R. The human genome project—an overview. Med Res Rev, 2000, 20: 189-196
[15]
7 Collins F. Has the revolution arrived? Nature, 2010, 464: 674-675
[16]
8 Ansorge W J. Next-generation DNA sequencing techniques. New Biotechnol, 2009, 25: 195-203
[17]
9 Mardis E R. The impact of next-generation sequencing technology on genetics. Trends Genet, 2008, 24: 133-141
[18]
10 Whitfeld P R. A Method for the determination of nucleotide sequence in polyribonucleotides. Biochem J, 1954, 58: 390-396
[19]
11 Sanger F, Nicklen S, Coulson A R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA, 1977, 74: 5463-5467
[20]
12 Maxam A M, Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci USA, 1977, 74: 560-564
[21]
13 Metzker M L. Applications of next-generation sequencing sequencing technologies—the next generation. Nat Rev Genet, 2010, 11: 31-46
[22]
14 Margulies M, Egholm M, Altman W E, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature, 2005, 437: 376-380
[23]
15 Fedurco M, Romieu A, Williams S, et al. BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies. Nucleic Acids Res, 2006, 34: e22
[24]
16 Turcatti G, Romieu A, Fedurco M, et al. A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis. Nucleic Acids Res, 2008, 36: e25
[25]
17 Shendure J, Porreca G J, Reppas N B, et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science, 2005, 309: 1728-1732
[26]
18 Liu S J, Vijayendran D, Bonning B C. Next generation sequencing technologies for insect virus discovery. Viruses, 2011, 3: 1849-1869
[27]
19 Olson S A. EMBOSS opens up sequence analysis. European Molecular Biology Open Software Suite. Brief Bioinform, 2002, 3: 87-91
[28]
20 Li R Q, Zhu H M, Ruan J, et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res, 2010, 20: 265-272
[29]
21 Zerbino D R, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res, 2008, 18: 821-829
[30]
22 Wu Q F, Wang Y, Cao M J, et al. Homology-independent discovery of replicating pathogenic circular RNAs by deep sequencing and a new computational algorithm. Proc Natl Acad Sci USA, 2012, 109: 3938-3943
[31]
23 Lecoq H. Discovery of the first virus, Tobacco mosaic virus: 1892 or 1898? C R Acad Sci Ⅲ, 2001, 324: 929-933
[32]
24 Roossinck M J. The big unknown: plant virus biodiversity. Curr Opin Virol, 2011, 1: 63-67
[33]
25 Wren J D, Roossinck M J, Nelson R S, et al. Plant virus biodiversity and ecology. PLoS Biol, 2006, 4: 314-315
[34]
26 Mokili J L, Rohwer F, Dutilh B E. Metagenomics and future perspectives in virus discovery. Curr Opin Virol, 2012, 2: 63-77
[35]
27 Riesenfeld C S, Schloss P D, Handelsman J. Metagenomics: genomic analysis of microbial communities. Annu Rev Genet, 2004, 38: 525-552
[36]
28 Alavandi S V, Poornima M. Viral metagenomics: a tool for virus discovery and diversity in aquaculture. Indian J Virol, 2012, 23: 88-98
[37]
29 Breitbart M, Salamon P, Andresen B, et al. Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci USA, 2002, 99: 14250-14255
[38]
30 Zhang T, Breitbart M, Lee W H, et al. RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol, 2006, 4: 108-118
[39]
31 Culley A I, Lang A S, Suttle C A. Metagenomic analysis of coastal RNA virus communities. Science, 2006, 312: 1795-1798
[40]
32 Muthukumar V, Wiley G B, Pierce M L, et al. Metagenomics for identification of novel plant viruses. Phytopathology, 2007, 97: S81-S82
[41]
33 Cox-Foster D L, Conlan S, Holmes E C, et al. A metagenomic survey of microbes in honey bee colony collapse disorder. Science, 2007, 318: 283-287
[42]
34 Palacios G, Druce J, Du L, et al. A new arenavirus in a cluster of fatal transplant-associated diseases. New Engl J Med, 2008, 358: 991-998
[43]
35 Adams I P, Glover R H, Monger W A, et al. Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology. Mol Plant Pathol, 2009, 10: 537-545
[44]
36 Monger W A, Adams I P, Glover R H, et al. The complete genome sequence of Canna yellow streak virus. Arch Virol, 2010, 155: 1515-1518
[45]
37 Monger W A, Alicai T, Ndunguru J, et al. The complete genome sequence of the Tanzanian strain of Cassava brown streak virus and comparison with the Ugandan strain sequence. Arch Virol, 2010, 155: 429-433
[46]
38 Al Rwahnih M, Daubert S, Golino D, et al. Deep sequencing analysis of RNAs from a grapevine showing Syrah decline symptoms reveals a multiple virus infection that includes a novel virus. Virology, 2009, 387: 395-401
[47]
39 Coetzee B, Freeborough M J, Maree H J, et al. Deep sequencing analysis of viruses infecting grapevines: virome of a vineyard. Virology, 2010, 400: 157-163
[48]
40 Al Rwahnih M, Daubert S, Urbez-Torres J R, et al. Deep sequencing evidence from single grapevine plants reveals a virome dominated by mycoviruses. Arch Virol, 2011, 156: 397-403
[49]
41 Adams I P, Miano D W, Kinyua Z M, et al. Use of next-generation sequencing for the identification and characterization of Maize chlorotic mottle virus and Sugarcane mosaic virus causing maize lethal necrosis in Kenya. Plant Pathol, 2013, 62: 741-749
[50]
42 Verbeek M, Dullemans A M, van Bekkum P J, et al. Evidence for Lettuce big-vein associated virus as the causal agent of a syndrome of necrotic rings and spots in lettuce. Plant Pathol, 2013, 62: 444-451
[51]
43 Wylie S J, Jones M G K. Complete genome sequences of seven carlavirus and potyvirus isolates from Narcissus and Hippeastrum plants in Australia, and proposals to clarify their naming. Arch Virol, 2012, 157: 1471-1480
[52]
44 Pardina P E R, Bejerman N, Luque A V, et al. Complete nucleotide sequence of an Argentinean isolate of sweet potato virus G. Virus Genes, 2012, 45: 593-595
[53]
45 Fauquet C M, Bisaro D M, Briddon R W, et al. Revision of taxonomic criteria for species demarcation in the family Geminiviridae, and an updated list of begomovirus species. Arch Virol, 2003, 148: 405-421
[54]
46 Hagen C, Frizzi A, Gabriels S, et al. Accurate and sensitive diagnosis of geminiviruses through enrichment, high-throughput sequencing and automated sequence identification. Arch Virol, 2012, 157: 907-915
[55]
47 Roossinck M J, Saha P, Wiley G B, et al. Ecogenomics: using massively parallel pyrosequencing to understand virus ecology. Mol Ecol, 2010, 19: 81-88
[56]
48 Wylie S J, Luo H, Li H, et al. Multiple polyadenylated RNA viruses detected in pooled cultivated and wild plant samples. Arch Virol, 2012, 157: 271-284
[57]
49 Voinnet O. RNA silencing as a plant immune system against viruses. Trends Genet, 2001, 17: 449-459
[58]
50 Ding S W. RNA silencing. Curr Opin Biotech, 2000, 11: 152-156
[59]
51 Chapman E J, Carrington J C. Specialization and evolution of endogenous small RNA pathways. Nat Rev Genet, 2007, 8: 884-896
[60]
52 Ding S W, Lu R. Virus-derived siRNAs and piRNAs in immunity and pathogenesis. Curr Opin Virol, 2011, 1: 533-544
[61]
53 Hamilton A J, Baulcombe D C. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science, 1999, 286: 950-952
[62]
54 Donaire L, Wang Y, Gonzalez-Ibeas D, et al. Deep-sequencing of plant viral small RNAs reveals effective and widespread targeting of viral genomes. Virology, 2009, 392: 203-214
[63]
55 Yang X L, Wang Y, Guo W, et al. Characterization of small interfering RNAs derived from the geminivirus/betasatellite complex using deep sequencing. PLoS One, 2011, 6: e16928
[64]
56 Sahu P P, Rai N K, Chakraborty S, et al. Tomato cultivar tolerant to Tomato leaf curl New Delhi virus infection induces virus-specific short interfering RNA accumulation and defence-associated host gene expression. Mol Plant Pathol, 2010, 11: 531-544
[65]
57 Lin K Y, Cheng C P, Chang B C H, et al. Global analyses of small interfering RNAs derived from Bamboo mosaic virus and its associated satellite RNAs in different plants. PLoS One, 2010, 5: e11928
[66]
58 Yan F, Zhang H M, Adams M J, et al. Characterization of siRNAs derived from Rice stripe virus in infected rice plants by deep sequencing. Arch Virol, 2010, 155: 935-940
[67]
59 Ruiz-Ruiz S, Navarro B, Gisel A, et al. Citrus tristeza virus infection induces the accumulation of viral small RNAs (21-24-nt) mapping preferentially at the 3′-terminal region of the genomic RNA and affects the host small RNA profile. Plant Mol Biol, 2011, 75: 607-619
[68]
60 Hu Q A, Hollunder J, Niehl A, et al. Specific impact of Tobamovirus infection on the Arabidopsis small RNA profile. PLoS One, 2011, 6: e19549
[69]
61 Molnar A, Csorba T, Lakatos L, et al. Plant virus-derived small interfering RNAs originate predominantly from highly structured single-stranded viral RNAs. J Virol, 2005, 79: 7812-7818
[70]
62 Blevins T, Rajeswaran R, Shivaprasad P V, et al. Four plant Dicers mediate viral small RNA biogenesis and DNA virus induced silencing. Nucleic Acids Res, 2006, 34: 6233-6246
[71]
63 Kreuze J F, Perez A, Untiveros M, et al. Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: a generic method for diagnosis, discovery and sequencing of viruses. Virology, 2009, 388: 1-7
[72]
64 Hagen C, Frizzi A, Kao J, et al. Using small RNA sequences to diagnose, sequence, and investigate the infectivity characteristics of vegetable-infecting viruses. Arch Virol, 2011, 156: 1209-1216
[73]
65 Wu Q F, Luo Y J, Lu R, et al. Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs. Proc Natl Acad Sci USA, 2010, 107: 1606-1611
[74]
66 Pallett D W, Ho T, Cooper I, et al. Detection of Cereal yellow dwarf virus using small interfering RNAs and enhanced infection rate with Cocksfoot streak virus in wild cocksfoot grass (Dactylis glomerata). J Virol Methods, 2010, 168: 223-227
[75]
67 Pantaleo V, Saldarelli P, Miozzi L, et al. Deep sequencing analysis of viral short RNAs from an infected Pinot Noir grapevine. Virology, 2010, 408: 49-56
[76]
68 Li R G, Gao S, Hernandez A G, et al. Deep sequencing of small RNAs in tomato for virus and viroid identification and strain differentiation. PLoS One, 2012, 7: e37127
[77]
69 Zhang Y, Singh K, Kaur R, et al. Association of a novel DNA virus with the grapevine vein-clearing and vine decline syndrome. Phytopathology, 2011, 101: 1081-1090
[78]
70 Giampetruzzi A, Roumi V, Roberto R, et al. A new grapevine virus discovered by deep sequencing of virus- and viroid-derived small RNAs in Cv Pinot gris. Virus Res, 2012, 163: 262-268
[79]
71 Alabi O J, Zheng Y, Jagadeeswaran G, et al. High-throughput sequence analysis of small RNAs in grapevine (Vitis vinifera L.) affected by grapevine leafroll disease. Mol Plant Pathol, 2012, 13: 1060-1076
[80]
72 Poojari S, Alabi O J, Fofanov V Y, et al. A leafhopper-transmissible DNA virus with novel evolutionary lineage in the family geminiviridae implicated in grapevine redleaf disease by next-generation sequencing. PLoS One, 2013, 8: e64194
[81]
73 Studholme D J, Glover R H, Boonham N. Application of high-throughput DNA sequencing in phytopathology. Annu Rev Phytopathol, 2011, 49: 87-105
[82]
74 Mansoor S, Zafar Y, Briddon R W. Geminivirus disease complexes: the threat is spreading. Trends Plant Sci, 2006, 11: 209-212
[83]
75 Ng T F F, Duffy S, Polston J E, et al. Exploring the diversity of plant DNA viruses and their satellites using vector-enabled metagenomics on whiteflies. PLoS One, 2011, 6: e19050
[84]
83 Ramakrishnan M A, Tu Z J, Singh S, et al. The feasibility of using high resolution genome sequencing of influenza a viruses to detect mixed infections and quasispecies. PLoS One, 2009, 4: e7105
[85]
84 Varghese V, Shahriar R, Rhee S Y, et al. Minority variants associated with transmitted and acquired HIV-1 nonnucleoside reverse transcriptase inhibitor resistance: implications for the use of second-generation nonnucleoside reverse transcriptase inhibitors. Jaids-J Acq Imm Def, 2009, 52: 309-315
[86]
85 Cornman R S, Boncristiani H, Dainat B, et al. Population-genomic variation within RNA viruses of the Western honey bee, Apis mellifera, inferred from deep sequencing. BMC Genomics, 2013, 14: 154
[87]
86 Garcia-Arenal F, Fraile A, Malpica J M. Variability and genetic structure of plant virus populations. Annu Rev Phytopathol, 2001, 39: 157-186
[88]
87 Martinez F, Lafforgue G, Morelli M J, et al. Ultradeep sequencing analysis of population dynamics of virus escape mutants in RNAi-mediated resistant plants. Mol Biol Evol, 2012, 29: 3297-3307
[89]
88 Lu Y D, Gan Q H, Chi X Y, et al. Roles of microRNA in plant defense and virus offense interaction. Plant Cell Rep, 2008, 27: 1571-1579
[90]
89 Simon-Mateo C, Garcia J A. MicroRNA-guided processing impairs Plum pox virus replication, but the virus readily evolves to escape this silencing mechanism. J Virol, 2006, 80: 2429-2436
[91]
90 Guo W X, Wu G T, Yan F, et al. Identification of novel Oryza sativa miRNAs in deep sequencing-based small RNA libraries of rice infected with Rice stripe virus. PLoS One, 2012, 7: e46443
[92]
91 Singh K, Talla A, Qiu W P. Small RNA profiling of virus-infected grapevines: evidences for virus infection-associated and variety-specific miRNAs. Funct Integr Genomic, 2012, 12: 659-669
[93]
92 Yin X C, Wang J, Cheng H, et al. Detection and evolutionary analysis of soybean miRNAs responsive to soybean mosaic virus. Planta, 2013, 237: 1213-1225
[94]
93 King A M Q, Adams M J, Carstens E B, et al. Virus Taxonomy Ninth Report of the International Committee on Taxonomy of Viruses. Waltham: Academic Press, Elsevier, 2012. 1327
