메뉴 건너뛰기




Volumn 5, Issue DEC, 2014, Pages

Bioinformatics approaches for viral metagenomics in plants using short RNAs: Model case of study and application to a Cicer arietinum population

Author keywords

[No Author keywords available]

Indexed keywords

SMALL INTERFERING RNA;

EID: 84928238976     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2014.00790     Document Type: Article
Times cited : (30)

References (52)
  • 1
    • 58049196894 scopus 로고    scopus 로고
    • RNA-based viral immunity initiated by the Dicer family of host immune receptors
    • Aliyari R, Ding SW. 2009. RNA-based viral immunity initiated by the Dicer family of host immune receptors. Immunol Rev 227(1): 176-188.
    • (2009) Immunol Rev , vol.227 , Issue.1 , pp. 176-188
    • Aliyari, R.1    Ding, S.W.2
  • 3
    • 84891776696 scopus 로고    scopus 로고
    • Historical perspective, development and applications of next-generation sequencing in plant virology
    • Barba M, Czosnek H, Hadidi A. 2014. Historical perspective, development and applications of next-generation sequencing in plant virology. Viruses 6(1): 106-136.
    • (2014) Viruses , vol.6 , Issue.1 , pp. 106-136
    • Barba, M.1    Czosnek, H.2    Hadidi, A.3
  • 5
    • 84924608716 scopus 로고
    • The epidemiology of TMV
    • Broadbent L. 1965. The epidemiology of TMV. Annals of Applied Biology 56(2): 177-205.
    • (1965) Annals of Applied Biology , vol.56 , Issue.2 , pp. 177-205
    • Broadbent, L.1
  • 7
    • 84878568756 scopus 로고    scopus 로고
    • The complete nucleotide sequence of sweet potato C6 virus: a carlavirus lacking a cysteine-rich protein
    • De Souza J, Fuentes S, Savenkov EI, Cuellar W, Kreuze JF. 2013. The complete nucleotide sequence of sweet potato C6 virus: a carlavirus lacking a cysteine-rich protein. Archives of virology 158(6): 1393-1396.
    • (2013) Archives of virology , vol.158 , Issue.6 , pp. 1393-1396
    • De Souza, J.1    Fuentes, S.2    Savenkov, E.I.3    Cuellar, W.4    Kreuze, J.F.5
  • 8
    • 34547587566 scopus 로고    scopus 로고
    • Antiviral Immunity Directed by Small RNAs
    • Ding SW, Voinnet O. 2007. Antiviral Immunity Directed by Small RNAs. Cell 130(3): 413-426.
    • (2007) Cell , vol.130 , Issue.3 , pp. 413-426
    • Ding, S.W.1    Voinnet, O.2
  • 10
    • 43949109593 scopus 로고    scopus 로고
    • Structural and genetic requirements for the biogenesis of tobacco rattle virus-derived small interfering RNAs
    • Donaire L, Barajas D, Martinez-Garcia B, Martinez-Priego L, Pagan I, Llave C. 2008. Structural and genetic requirements for the biogenesis of tobacco rattle virus-derived small interfering RNAs. Journal of virology 82(11): 5167-5177.
    • (2008) Journal of virology , vol.82 , Issue.11 , pp. 5167-5177
    • Donaire, L.1    Barajas, D.2    Martinez-Garcia, B.3    Martinez-Priego, L.4    Pagan, I.5    Llave, C.6
  • 11
    • 84867405454 scopus 로고    scopus 로고
    • Ago hook and RNA helicase motifs underpin dual roles for SDE3 in antiviral defense and silencing of nonconserved intergenic regions
    • Garcia D, Garcia S, Pontier D, Marchais A, Renou JP, Lagrange T, Voinnet O. 2012. Ago hook and RNA helicase motifs underpin dual roles for SDE3 in antiviral defense and silencing of nonconserved intergenic regions. Molecular cell 48(1): 109-120.
    • (2012) Molecular cell , vol.48 , Issue.1 , pp. 109-120
    • Garcia, D.1    Garcia, S.2    Pontier, D.3    Marchais, A.4    Renou, J.P.5    Lagrange, T.6    Voinnet, O.7
  • 12
    • 77950367420 scopus 로고    scopus 로고
    • Arabidopsis RNA-dependent RNA polymerases and dicer-like proteins in antiviral defense and small interfering RNA biogenesis during Turnip Mosaic Virus infection
    • Garcia-Ruiz H, Takeda A, Chapman EJ, Sullivan CM, Fahlgren N, Brempelis KJ, Carrington JC. 2010. Arabidopsis RNA-dependent RNA polymerases and dicer-like proteins in antiviral defense and small interfering RNA biogenesis during Turnip Mosaic Virus infection. The Plant cell 22(2): 481-496.
    • (2010) The Plant cell , vol.22 , Issue.2 , pp. 481-496
    • Garcia-Ruiz, H.1    Takeda, A.2    Chapman, E.J.3    Sullivan, C.M.4    Fahlgren, N.5    Brempelis, K.J.6    Carrington, J.C.7
  • 16
    • 0034953458 scopus 로고    scopus 로고
    • Silencing on the spot. Induction and suppression of RNA silencing in the Agrobacterium-mediated transient expression system.
    • Johansen LK, Carrington JC. 2001. Silencing on the spot. Induction and suppression of RNA silencing in the Agrobacterium-mediated transient expression system. Plant Physiol 126(3): 930-938.
    • (2001) Plant Physiol , vol.126 , Issue.3 , pp. 930-938
    • Johansen, L.K.1    Carrington, J.C.2
  • 17
    • 0022344804 scopus 로고
    • Domains in viroids: evidence of intermolecular RNA rearrangements and their contribution to viroid evolution
    • Keese P, Symons RH. 1985. Domains in viroids: evidence of intermolecular RNA rearrangements and their contribution to viroid evolution. Proc Natl Acad Sci U S A 82(14): 4582-4586.
    • (1985) Proc Natl Acad Sci U S A , vol.82 , Issue.14 , pp. 4582-4586
    • Keese, P.1    Symons, R.H.2
  • 18
    • 84876837100 scopus 로고    scopus 로고
    • The complete genome sequences of a Peruvian and a Colombian isolate of Andean potato latent virus and partial sequences of further isolates suggest the existence of two distinct potato-infecting tymovirus species
    • Kreuze J, Koenig R, De Souza J, Vetten HJ, Muller G, Flores B, Ziebell H, Cuellar W. 2013. The complete genome sequences of a Peruvian and a Colombian isolate of Andean potato latent virus and partial sequences of further isolates suggest the existence of two distinct potato-infecting tymovirus species. Virus research 173(2): 431-435.
    • (2013) Virus research , vol.173 , Issue.2 , pp. 431-435
    • Kreuze, J.1    Koenig, R.2    De Souza, J.3    Vetten, H.J.4    Muller, G.5    Flores, B.6    Ziebell, H.7    Cuellar, W.8
  • 19
    • 67349170750 scopus 로고    scopus 로고
    • 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
    • Kreuze JF, Perez A, Untiveros M, Quispe D, Fuentes S, Barker I, Simon R. 2009. 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 388(1): 1-7.
    • (2009) Virology , vol.388 , Issue.1 , pp. 1-7
    • Kreuze, J.F.1    Perez, A.2    Untiveros, M.3    Quispe, D.4    Fuentes, S.5    Barker, I.6    Simon, R.7
  • 21
    • 84997830636 scopus 로고    scopus 로고
    • Complete genome sequence of a new tobamovirus naturally infecting tomatoes in Mexico.
    • Li R, Gao S, Fei Z, Ling KS. 2013. Complete genome sequence of a new tobamovirus naturally infecting tomatoes in Mexico. Genome Announc 1(5).
    • (2013) Genome Announc , vol.1 , Issue.5
    • Li, R.1    Gao, S.2    Fei, Z.3    Ling, K.S.4
  • 22
    • 84864019126 scopus 로고    scopus 로고
    • Identification of a single-stranded DNA virus associated with citrus chlorotic dwarf disease, a new member in the family Geminiviridae
    • Loconsole G, Saldarelli P, Doddapaneni H, Savino V, Martelli GP, Saponari M. 2012. Identification of a single-stranded DNA virus associated with citrus chlorotic dwarf disease, a new member in the family Geminiviridae. Virology 432(1): 162-172.
    • (2012) Virology , vol.432 , Issue.1 , pp. 162-172
    • Loconsole, G.1    Saldarelli, P.2    Doddapaneni, H.3    Savino, V.4    Martelli, G.P.5    Saponari, M.6
  • 23
    • 63249121217 scopus 로고    scopus 로고
    • Application of 'next-generation' sequencing technologies to microbial genetics
    • MacLean D, Jones JD, Studholme DJ. 2009. Application of 'next-generation' sequencing technologies to microbial genetics. Nat Rev Microbiol 7(4): 287-296.
    • (2009) Nat Rev Microbiol , vol.7 , Issue.4 , pp. 287-296
    • MacLean, D.1    Jones, J.D.2    Studholme, D.J.3
  • 24
    • 84919343878 scopus 로고    scopus 로고
    • Characterization by deep sequencing of Prunus virus T, a novel Tepovirus infecting Prunus species.
    • Marais A, Faure C, Mustafayev E, Barone M, Alioto D, Candresse T. 2015. Characterization by deep sequencing of Prunus virus T, a novel Tepovirus infecting Prunus species. Phytopathology 105 (1):135-140.
    • (2015) Phytopathology , vol.105 , Issue.1 , pp. 135-140
    • Marais, A.1    Faure, C.2    Mustafayev, E.3    Barone, M.4    Alioto, D.5    Candresse, T.6
  • 25
    • 84903714975 scopus 로고    scopus 로고
    • Current impact and future directions of high throughput sequencing in plant virus diagnostics.
    • Massart S, Olmos A, Jijakli H, Candresse T. 2014. Current impact and future directions of high throughput sequencing in plant virus diagnostics. Virus research 188: 90-96.
    • (2014) Virus research , vol.188 , pp. 90-96
    • Massart, S.1    Olmos, A.2    Jijakli, H.3    Candresse, T.4
  • 26
    • 84857371051 scopus 로고    scopus 로고
    • Metagenomics and future perspectives in virus discovery
    • Mokili JL, Rohwer F, Dutilh BE. 2012. Metagenomics and future perspectives in virus discovery. Curr Opin Virol 2(1): 63-77.
    • (2012) Curr Opin Virol , vol.2 , Issue.1 , pp. 63-77
    • Mokili, J.L.1    Rohwer, F.2    Dutilh, B.E.3
  • 27
    • 53549106068 scopus 로고    scopus 로고
    • Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening
    • Moxon S, Jing R, Szittya G, Schwach F, Rusholme Pilcher RL, Moulton V, Dalmay T. 2008. Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Res 18(10): 1602-1609.
    • (2008) Genome Res , vol.18 , Issue.10 , pp. 1602-1609
    • Moxon, S.1    Jing, R.2    Szittya, G.3    Schwach, F.4    Rusholme Pilcher, R.L.5    Moulton, V.6    Dalmay, T.7
  • 28
    • 84867397631 scopus 로고    scopus 로고
    • MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
    • Namiki T, Hachiya T, Tanaka H, Sakakibara Y. 2012. MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic acids research 40(20): e155.
    • (2012) Nucleic acids research , vol.40 , Issue.20
    • Namiki, T.1    Hachiya, T.2    Tanaka, H.3    Sakakibara, Y.4
  • 29
    • 70450214042 scopus 로고    scopus 로고
    • Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction.
    • Navarro B, Pantaleo V, Gisel A, Moxon S, Dalmay T, Bisztray G, Di Serio F, Burgyan J. 2009 Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction. PloS one 4(11): e7686.
    • (2009) PloS one , vol.4 , Issue.11
    • Navarro, B.1    Pantaleo, V.2    Gisel, A.3    Moxon, S.4    Dalmay, T.5    Bisztray, G.6    Di Serio, F.7    Burgyan, J.8
  • 30
    • 56449112131 scopus 로고    scopus 로고
    • Cymbidium ringspot virus harnesses RNA silencing to control the accumulation of virus parasite satellite RNA
    • Pantaleo V, Burgyan J. 2008. Cymbidium ringspot virus harnesses RNA silencing to control the accumulation of virus parasite satellite RNA. Journal of virology 82(23): 11851-11858.
    • (2008) Journal of virology , vol.82 , Issue.23 , pp. 11851-11858
    • Pantaleo, V.1    Burgyan, J.2
  • 32
    • 34247168131 scopus 로고    scopus 로고
    • Molecular Bases of Viral RNA Targeting by Viral Small Interfering RNA-Programmed RISC
    • Pantaleo V, Szittya G, Burgyan J. 2007. Molecular Bases of Viral RNA Targeting by Viral Small Interfering RNA-Programmed RISC. Journal of virology 81(8): 3797-3806.
    • (2007) Journal of virology , vol.81 , Issue.8 , pp. 3797-3806
    • Pantaleo, V.1    Szittya, G.2    Burgyan, J.3
  • 33
    • 33845688601 scopus 로고    scopus 로고
    • A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana
    • Rajagopalan R, Vaucheret H, Trejo J, Bartel DP. 2006. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev 20(24): 3407-3425.
    • (2006) Genes Dev , vol.20 , Issue.24 , pp. 3407-3425
    • Rajagopalan, R.1    Vaucheret, H.2    Trejo, J.3    Bartel, D.P.4
  • 35
    • 79960458506 scopus 로고    scopus 로고
    • Environmental viruses from biodiversity to ecology
    • Roossinck MJ. 2011. Environmental viruses from biodiversity to ecology. Curr Opin Virol 1(1): 50-51.
    • (2011) Curr Opin Virol , vol.1 , Issue.1 , pp. 50-51
    • Roossinck, M.J.1
  • 36
    • 84870159495 scopus 로고    scopus 로고
    • Plant virus metagenomics: biodiversity and ecology.
    • Roossinck MJ. 2012. Plant virus metagenomics: biodiversity and ecology. Annu Rev Genet 46: 359-369.
    • (2012) Annu Rev Genet , vol.46 , pp. 359-369
    • Roossinck, M.J.1
  • 37
  • 39
    • 68049086735 scopus 로고    scopus 로고
    • Monitoring of herpes simplex virus DNA types 1 and 2 viral load in cerebrospinal fluid by real-time PCR in patients with herpes simplex encephalitis
    • Schloss L, Falk KI, Skoog E, Brytting M, Linde A, Aurelius E. 2009. Monitoring of herpes simplex virus DNA types 1 and 2 viral load in cerebrospinal fluid by real-time PCR in patients with herpes simplex encephalitis. J Med Virol 81(8): 1432-1437.
    • (2009) J Med Virol , vol.81 , Issue.8 , pp. 1432-1437
    • Schloss, L.1    Falk, K.I.2    Skoog, E.3    Brytting, M.4    Linde, A.5    Aurelius, E.6
  • 40
    • 84859768479 scopus 로고    scopus 로고
    • Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels
    • Schulz MH, Zerbino DR, Vingron M, Birney E. 2012. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28(8): 1086-1092.
    • (2012) Bioinformatics , vol.28 , Issue.8 , pp. 1086-1092
    • Schulz, M.H.1    Zerbino, D.R.2    Vingron, M.3    Birney, E.4
  • 42
    • 80655144445 scopus 로고    scopus 로고
    • Viral induction and suppression of RNA silencing in plants.
    • Shimura H, Pantaleo V. 2011. Viral induction and suppression of RNA silencing in plants. Biochim Biophys Acta 1809(11-12): 601-612.
    • (2011) Biochim Biophys Acta , vol.1809 , Issue.11-12 , pp. 601-612
    • Shimura, H.1    Pantaleo, V.2
  • 44
    • 84901047975 scopus 로고    scopus 로고
    • Plant virus metagenomics: what we know and why we need to know more.
    • Stobbe AH, Roossinck MJ. 2014. Plant virus metagenomics: what we know and why we need to know more. Frontiers in plant science 5: 150.
    • (2014) Frontiers in plant science , vol.5 , pp. 150
    • Stobbe, A.H.1    Roossinck, M.J.2
  • 46
    • 63549109144 scopus 로고    scopus 로고
    • Compromised Virus-Induced Gene Silencing in RDR6-Deficient Plants
    • Vaistij FE, Jones L. 2009. Compromised Virus-Induced Gene Silencing in RDR6-Deficient Plants. Plant Physiol 149(3): 1399-1407.
    • (2009) Plant Physiol , vol.149 , Issue.3 , pp. 1399-1407
    • Vaistij, F.E.1    Jones, L.2
  • 47
    • 0022432038 scopus 로고
    • Eleven new sequence variants of citrus exocortis viroid and the correlation of sequence with pathogenicity
    • Visvader JE, Symons RH. 1985. Eleven new sequence variants of citrus exocortis viroid and the correlation of sequence with pathogenicity. Nucleic acids research 13(8): 2907-2920.
    • (1985) Nucleic acids research , vol.13 , Issue.8 , pp. 2907-2920
    • Visvader, J.E.1    Symons, R.H.2
  • 48
    • 76249093088 scopus 로고    scopus 로고
    • RNAi-mediated viral immunity requires amplification of virus-derived siRNAs in Arabidopsis thaliana
    • Wang XB, Wu Q, Ito T, Cillo F, Li WX, Chen X, Yu JL, Ding SW. 2010. RNAi-mediated viral immunity requires amplification of virus-derived siRNAs in Arabidopsis thaliana. Proc Natl Acad Sci U S A 107(1): 484-489.
    • (2010) Proc Natl Acad Sci U S A , vol.107 , Issue.1 , pp. 484-489
    • Wang, X.B.1    Wu, Q.2    Ito, T.3    Cillo, F.4    Li, W.X.5    Chen, X.6    Yu, J.L.7    Ding, S.W.8
  • 49
    • 33644850032 scopus 로고    scopus 로고
    • Nomenclature and functions of RNA-directed RNA polymerases
    • Wassenegger M, Krczal G. 2006. Nomenclature and functions of RNA-directed RNA polymerases. Trends Plant Sci 11(3): 142-151.
    • (2006) Trends Plant Sci , vol.11 , Issue.3 , pp. 142-151
    • Wassenegger, M.1    Krczal, G.2
  • 50
    • 76249103869 scopus 로고    scopus 로고
    • Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs
    • Wu Q, Luo Y, Lu R, Lau N, Lai EC, Li WX, Ding SW. 2010. Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs. Proc Natl Acad Sci U S A 107(4): 1606-1611.
    • (2010) Proc Natl Acad Sci U S A , vol.107 , Issue.4 , pp. 1606-1611
    • Wu, Q.1    Luo, Y.2    Lu, R.3    Lau, N.4    Lai, E.C.5    Li, W.X.6    Ding, S.W.7
  • 51
    • 84863229993 scopus 로고    scopus 로고
    • Homologyindependent discovery of replicating pathogenic circular RNAs by deep sequencing and a new computational algorithm
    • Wu Q, Wang Y, Cao M, Pantaleo V, Burgyan J, Li WX, Ding SW. 2012. Homologyindependent discovery of replicating pathogenic circular RNAs by deep sequencing and a new computational algorithm. Proc Natl Acad Sci U S A 109(10): 3938-3943.
    • (2012) Proc Natl Acad Sci U S A , vol.109 , Issue.10 , pp. 3938-3943
    • Wu, Q.1    Wang, Y.2    Cao, M.3    Pantaleo, V.4    Burgyan, J.5    Li, W.X.6    Ding, S.W.7
  • 52
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
    • Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18(5): 821-829.
    • (2008) Genome Res , vol.18 , Issue.5 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.