The DOI matches its Crossref record; 43 of the 43 references it cites were found in a registry or an index.
Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs
Open accessAbstract
In response to infection, invertebrates process replicating viral RNA genomes into siRNAs of discrete sizes to guide virus clearance by RNA interference. Here, we show that viral siRNAs sequenced from fruit fly, mosquito, and nematode cells were all overlapping in sequence, suggesting a possibility of using siRNAs for viral genome assembly and virus discovery. To test this idea, we examined contigs assembled from published small RNA libraries and discovered five previously undescribed viruses from cultured Drosophila cells and adult mosquitoes, including three with a positive-strand RNA genome and two with a dsRNA genome. Notably, four of the identified viruses exhibited only low sequence similarities to known viruses, such that none could be assigned into an existing virus genus. We also report detection of virus-derived PIWI-interacting RNAs (piRNAs) in Drosophila melanogaster that have not been previously described in any other host species and demonstrate viral genome assembly from viral piRNAs in the absence of viral siRNAs. Thus, this study provides a powerful culture-independent approach for virus discovery in invertebrates by assembling viral genomes directly from host immune response products without prior virus enrichment or amplification. We propose that invertebrate viruses discovered by this approach may include previously undescribed human and vertebrate viral pathogens that are transmitted by arthropod vectors.
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MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0
Tamura, K., Dudley, J., Nei, M., & Kumar, S. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm092 · Cited by 28,730
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
Zerbino, D. R., & Birney, E. (2008) · Genome Research · doi:10.1101/gr.074492.107 · Cited by 9,491
Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment
Ewing, B., Hillier, L., Wendl, M. C., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.175 · Cited by 6,967
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
Ewing, B., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.186 · Cited by 5,439
Consed: A Graphical Tool for Sequence Finishing
Gordon, D., Abajian, C., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.195 · Cited by 3,302
A Species of Small Antisense RNA in Posttranscriptional Gene Silencing in Plants
Hamilton, A. J., & Baulcombe, D. C. (1999) · Science · doi:10.1126/science.286.5441.950 · Cited by 3,041
Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila
Brennecke, J., Aravin, A. A., Stark, A., Dus, M., Kellis, M., Sachidanandam, R., & Hannon, G. J. (2007) · Cell · doi:10.1016/j.cell.2007.01.043 · Cited by 2,524
Small silencing RNAs: an expanding universe
Ghildiyal, M., & Zamore, P. D. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2504 · Cited by 2,325
A Metagenomic Survey of Microbes in Honey Bee Colony Collapse Disorder
Cox-Foster, D. L., Conlan, S., Holmes, E. C., Palacios, G., Evans, J. D., Moran, N. A., Quan, P.-L., Briese, T., Hornig, M., Geiser, D. M., et al. (2007) · Science · doi:10.1126/science.1146498 · Cited by 1,759
Antiviral Immunity Directed by Small RNAs
Ding, S.-W., & Voinnet, O. (2007) · Cell · doi:10.1016/j.cell.2007.07.039 · Cited by 1,521
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Cited by
Small RNA-based antimicrobial immunity
Guo, Z., Li, Y., & Ding, S.-W. (2019) · Nature Reviews Immunology · doi:10.1038/s41577-018-0071-x · Cited by 391
Self-citationTransgenerational Inheritance of an Acquired Small RNA-Based Antiviral Response in C. elegans
Rechavi, O., Minevich, G., & Hobert, O. (2011) · Cell · doi:10.1016/j.cell.2011.10.042 · Cited by 351
C6/36 Aedes albopictus Cells Have a Dysfunctional Antiviral RNA Interference Response
Brackney, D. E., Scott, J. C., Sagawa, F., Woodward, J. E., Miller, N. A., Schilkey, F. D., Mudge, J., Wilusz, J., Olson, K. E., Blair, C. D., et al. (2010) · PLoS Neglected Tropical Diseases · doi:10.1371/journal.pntd.0000856 · Cited by 326
Goic, B., Vodovar, N., Mondotte, J. A., Monot, C., Frangeul, L., Blanc, H., Gausson, V., Vera-Otarola, J., Cristofari, G., & Saleh, M.-C. (2013) · Nature Immunology · doi:10.1038/ni.2542 · Cited by 265
R2D2 Organizes Small Regulatory RNA Pathways in Drosophila∇†
Okamura, K., Robine, N., Liu, Y., Liu, Q., & Lai, E. C. (2011) · Molecular and Cellular Biology · doi:10.1128/mcb.01141-10 · Cited by 70
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Metadata
- Authors
- Wu, Q., Luo, Y., Lu, R., Lau, N., Lai, E. C., Li, W.-X., & Ding, S.-W.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2010-01-04
- Volume
- 107
- Issue
- 4
- Pages
- 1606-1611
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2047738921
- Cited by
- 468
- References
- 43
- FWCI
- 38.76
- Type
- journal article
- Language
- en
- Open access
- green
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