Plant virus metagenomics: What we know and why we need to know more

Frontiers in Plant Science

Volumn 5, Issue APR, 2014, Pages

  Stobbe, Anthony H ^a   Roossinck, Marilyn J ^a,b  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b MURDOCH UNIVERSITY   (Australia)

Author keywords

Bioinformatics; Ecogenomics; Virus biodiversity; Virus ecology; Wild plant viruses

Indexed keywords

EID: 84901047975     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2014.00150     Document Type: Article

References (35)

1. Albertsen, M., Hugenholtz, P., Sharskewski, A., Nielsen, K. L., Tyson, G. W., and Nielsen, P. H. (2013). Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat. Biotech. 31, 533-541. doi: 10.1038/nbt.2579
2. Ames, S. K., Hysom, D. A., Gardner, S. N., Lloyd, G. S., Gokhale, M. B., and Allen, J. E. (2013). Scalable metagenomic taxonomy classification using a reference genome database. Bioinformatics 29, 2253-2260. doi: 10.1093/bioinformatics/btt389
3. Ashby, M. K., Warry, A., Bejarano, E. R., Khashoggi, A., Burrell, M., and Lichtenstein, C. P. (1997). Analysis of multiple copies of geminiviral DNA in the genome of four closely related Nicotiana species suggest a unique integration event. Plant Mol. Biol. 35, 313-321. doi: 10.1023/A:1005885200550
4. Beijerinck, M. W. (1898). "Concerning a contagium vivum fluidum as cause of the spot disease of tobacco leaves, " in Phylopathological Classics, No. 7, ed J. Johnson (St. Paul, MN: American Phytopathological Society), 33-52.
5. Bejarano, E. R., Khashoggi, A., Witty, M., and Lichenstein, C. (1996). Integration of multiple repeats of geminiviral DNA into nuclear genome of tobacco during evolution. Proc. Natl. Acad. Sci. U.S.A. 93, 759-764. doi: 10.1073/pnas.93.2.759
6. Bock, R. (2010). The give-and-take of DNA: horizontal gene transfer in plants. Trends Plant Sci. 15, 11-22. doi: 10.1016/j.tplants.2009.10.001
7. Chiba, S., Kondo, H., Tani, A., Saisho, D., Sakamoto, W., Kanematsu, S., et al. (2011). Widespread endogenization of genome sequences of non-retroviral RNA viruses into plant genomes. PLoS Pathog. 7:e1002146. doi: 10.1371/journal.ppat.1002146
8. Danovaro, R., Corinaldesi, C., Dell'anno, A., Fuhrman, J. A., Middelburg, J. J., Noble, R. T., et al. (2011). Marine viruses and global climate change. FEMS Microbiol. Rev. 35, 993-1034. doi: 10.1111/j.1574-6976.2010.00258.x
9. Fraser, R. S. S. (1998). "Introduction to classical cross protection, " in Plant Virology Protocols, eds G. D. Foster, and S. C. Taylor (Totowa, NJ: Humana Press), 13-24. doi: 10.1385/0-89603-385-6:13
10. Goremykin, V. V., Salamini, F., Velasco, R., and Viola, R. (2009). Mitochondrial DNA of Vitis vinifera and the issue of rampant horizontal gene transfer. Mol. Biol. Evol. 26, 99-110. doi: 10.1093/molbev/msn226
11. Hohn, T., Richert-Pöggeler, K. R., Staginnus, C., Harper, G., Schwarzacher, T., Teo, C. H., et al. (2008). "Evolution of integrated plant viruses, " in Plant Virus Evolution, ed M. J. Roossinck (Heidelberg: Springer), 53-81.
12. Kreuze, J. F., Perez, A., Untiveros, M., Quispe, D., Fuentes, S., Barker, I., et al. (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, 1-7. doi: 10.1016/j.virol.2009.03.024
13. Kristensen, D. M., Mushegian, A. R., Dolja, V. V., and Koonin, E. V. (2010). New dimensions of the virus world discovered through metagenomics. Trends Microbiol. 18, 11-19. doi: 10.1016/j.tim.2009.11.003
14. Labonté, J. M., and Suttle, C. A. (2013). Previously unknown and highly divergent viruses populate the oceans. ISME J. 7, 2169-2177. doi: 10.1038/ismej.2013.110
15. Lebouvier, M., Laparie, M., Hullé, M., Marais, A., Cozic, Y., Lalouette, L., et al. (2011). The significance of the sub-Antarctric Kerguellen Islands for the assessment of the vulneraqbility of native communities to climate change, alian insect invastions and plant viruses. Biol. Invasions 13, 1195-1208. doi: 10.1007/s10530-011-9946-5
16. Liu, H., Fu, Y., Jiang, D., Li, G., Xie, J., Cheng, J., et al. (2010). Widespread horizontal gene transfer from double-stranded RNA viruses to eukaryotic nuclear genomes. J. Virol. 84, 11879-11887. doi: 10.1128/JVI.00955-10
17. MacDiarmid, R., Rodoni, B., Melcher, U., Ochoa-Corona, F., and Roossinck, M. (2013). Biosecurity implications of new technology and discovery in plant virus research. PLoS Pathog. 9:e1003337. doi: 10.1371/journal.ppat.1003337
18. Malmstrom, C. M., McCullough, A. J., Johnson, H. A., Newton, L. A., and Borer, E. T. (2005). Invasive annual grasses indirectly increase virus incidence in California native perennial bunchgrasses. Oecologia 145, 153-164. doi: 10.1007/s00442-005-0099-z
19. Márquez, L. M., Redman, R. S., Rodriguez, R. J., and Roossinck, M. J. (2007). A virus in a fungus in a plant-three way symbiosis required for thermal tolerance. Science 315, 513-515. doi: 10.1126/science.1136237
20. Muthukumar, V., Melcher, U., Pierce, M., Wiley, G. B., Roe, B. A., Palmer, M. W., et al. (2009). Non-cultivated plants of the Tallgrass Prairie Preserve of northeastern Oklahoma frequently contain virus-like sequences in particulate fractions. J. Virol. Methods 141, 169-173. doi: 10.1016/j.virusres.2008.06.016
21. Nakatsukasa-Akune, M., Yamashita, K., Shimoda, Y., Uchiumi, T., Abe, M., Aoki, T., et al. (2005). Suppression of root nodule formation by artificial expression of the TrEnodDR1 (coat protein of White clover cryptic virus 2) gene in Lotus japonicus. Mol. Plant Microbe Interact. 18, 1069-1080. doi: 10.1094/MPMI-18-1069
22. Ng, T. F. F., Duffy, S., Polston, J. E., Bixby, E., Vallad, G. E., and Breitbart, M. (2011). Exploring the diversity of plant DNA viruses and their satellites using vector-enabled metagenomics on whiteflies. PLoS ONE 6:e19050. doi: 10.1371/journal.pone.0019050
23. Pimentel, D., Zuniga, R., and Morrison, D. (2005). Update on the environmental and economic costs associated with alien-invasive species in the United States. Ecol. Econ. 52, 273-288. doi: 10.1016/j.ecolecon.2004.10.002
24. Roossinck, M. J. (2011). The good viruses: viral mutualistic symbioses. Nat. Rev. Microbiol. 9, 99-108. doi: 10.1038/nrmicro2491
25. Roossinck, M. J. (2012). Plant virus metagenomics: biodiversity and ecology. Annu. Rev. Genet. 46, 357-367. doi: 10.1146/annurev-genet-110711-155600
26. Roossinck, M. J. (2013). Plant virus ecology. PLoS Pathog. 9:e1003304. doi: 10.1371/journal.ppat.1003304
27. Roossinck, M. J., Saha, P., Wiley, G. B., Quan, J., White, J. D., Lai, H., et al. (2010). Ecogenomics: using massively parallel pyrosequencing to understand virus ecology. Mol. Ecol. 19, 81-88. doi: 10.1111/j.1365-294X.2009.04470.x
28. Schneider, G. F., and Dekker, C. (2012). DNA sequencing with nanopores. Nat. Biotech. 30, 326-329. doi: 10.1038/nbt.2181
29. Staginnus, C., Gregor, W., Mette, M. F., Teo, C. H., Borroto-Fernández, E. G., Machado, M. L. D. C., et al. (2007). Endogenous pararetroviral sequences in tomato (Solanum lycopersicum) and related species. BMC Plant Biol. 7:24. doi: 10.1186/1471-2229-7-24
30. Stobbe, A. H., Daniels, J., Espindola, A. S., Verma, R., Melcher, U., Ochoa-Corona, F., et al. (2013). E-probe diagnostic nucleic acid analysis (EDNA): a theoretical approach for handling of next generation sequencing data for diagnostics. J. Mirobiol. Methods 94, 356-366. doi: 10.1016/j.mimet.2013.07.002
31. Williamson, S. J., Rusch, D. B., Yooseph, S., Halpern, A. L., Heidelberg, K. B., Glass, J. I., et al. (2008). The Sorcerer II global ocean sampling expedition: metagenomic characterization of viruses within aquatic microbial samples. PLoS ONE 3:e1456. doi: 10.1371/journal.pone.0001456
32. Wren, J. D., Roossinck, M. J., Nelson, R. S., Sheets, K., Palmer, M. W., and Melcher, U. (2006). Plant virus biodiversity and ecology. PLoS Biol. 4:e80. doi: 10.1371/journal.pbio.0040080
33. Wu, D.-D., and Zhang, Y.-P. (2011). Eukaryotic origin of a metabolic pathway in virus by horizontal gene transfer. Genomics 98, 367-369. doi: 10.1016/j.ygeno.2011.08.006
34. Wu, Q., Luo, Y., Lu, R., Lau, N., Lai, E. C., Li, W.-X., et al. (2010). Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs. Proc. Natl. Acad. Sci. U.S.A. 107, 1606-1611. doi: 10.1073/pnas.0911353107
35. Xu, P., Chen, F., Mannas, J. P., Feldman, T., Sumner, L. W., and Roossinck, M. J. (2008). Virus infection improves drought tolerance. New Phytol. 180, 911-921. doi: 10.1111/j.1469-8137.2008.02627.x