Metagenomics of plant and fungal viruses reveals an abundance of persistent: Lifestyles

Frontiers in Microbiology

Volumn 5, Issue DEC, 2014, Pages

  Roossinck, Marilyn J ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED RNA; RIBOSOME RNA; TRANSCRIPTOME;

ANASTOMOSIS; CRYPHONECTRIA; ENDOPHYTIC FUNGUS; GENETIC ANALYSIS; HETEROBASIDIOMYCETES; LIFESTYLE; METAGENOMICS; MICROBIAL DIVERSITY; MYCOVIRUS; NONHUMAN; NOTE; PERSISTENT VIRUS INFECTION; PHYLOGENY; PLANT COMMUNITY; PLANT IMMUNITY; PLANT VIRUS; SCLEROTINIA SCLEROTIORUM; SEQUENCE ANALYSIS; TOTIVIRUS; VERTICAL TRANSMISSION; VIRUS VIRULENCE;

EID: 84920673553     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2014.00767     Document Type: Note

References (31)

1. Angly, F.E., Felts, B., Breitbart, M., Salamon, P., Edwards, R.A., Carlson, C., Chan, A.M., Haynes, M., Kelley, S., Liu, H., Mahaffy, J.M., Mueller, J.E., Nulton, J., Olson, R., Parsons, R., Rayhawk, S., Suttle, C.A., and Rohwer, F. (2006). The marine viromes of four oceanic regions. PLoS Biology 4 e368.
2. Blackwell, M. (2011). The fungi: 1, 2, 3... 5.1 million species? Am. J. Bot. 98, 426-438.
3. Boccardo, G., Lisa, V., Luisoni, E., and Milne, R.G. (1987). Cryptic plant viruses, in Adv. Virus Res. 32, 171-214.
4. Chiba, S., Kondo, H., Tani, A., Saisho, D., Sakamoto, W., Kanematsu, S., and Suzuki, N. 2011. Widespread endogenization of genome sequences of non-retroviral RNA viruses into plant genomes. PLoS Pathogens 7 e1002146.
5. Dawe, A.L., and Nuss, D.L. (2013). Hypovirus Molecular Biology: From Koch's Postulates to Host Self-Recognition Genes that Restrict Virus Transmission, Adv. Virus Res. 86, 110-147.
6. Feldman, T.S., Morsy, M.R., and Roossinck, M.J. (2012). Are communities of microbial symbionts more diverse than communitiies of macrobial hosts? Fungal Biology 116, 465-477.
7. Hyder, R., Pennanen, T., Hamberg, L., Vainio, E.J., Piri, T., and Hantula, J. (2013). Two viruses of Heterobasidion confer beneficial, cryptic, or detrimental effects to their hosts in different situations. Fungal Ecology 6, 387-396.
8. Jiang, L., Wijeratne, A.J., Wijeratne, S., Fraga, M., Meulia, T., Doohan, D., Li, Z., and Qu, F. (2013). Profiling mRNAs of two Cuscuta species reveals possible candidate transcripts shared by parasitic plants, in: PLoS One. 8 e81389.
9. King, A.M.Q., Adams, M.J., Carstens, E.B., and Lefkowitz, E.J. (eds.). (2012). Virus Taxonomy Ninth Report of the International Committee On Taxonomy of Viruses. San Diego, CA: Elsevier Academic Press.
10. Kreuze, J. (2014). siRNA deep sequencing and assembly: piecing together viral infections, in Detection and Diagnostics of Plant Pathogens, eds. M.L. Gullino & P.J.M. Bonants. Springer, 21-38.
11. Labonté, J.M., and Suttle, C.A. (2013). Previously unknown and highly divergent viruses populate the oceans. ISME J. 7, 2169-2177.
12. Li, L., Liu, J., Xu, A., Want, T., Chen, J., and Zhu, X. (2013). Molecular characterization of a trisegmented chrysovirus isolated from the radish Raphanus sativus. Vir. Res. 176, 169-178.
13. Liu, H., Fu, Y., Jiang, D., Li, G., Xie, J., Cheng, J., Pend, Y., Ghabriel, S.A., and Yi, X. (2010). Widespread horizontal gene transfer from double-stranded RNA viruses to eukaryotic nuclear genomes. J. Virol. 84, 11879-11887.
14. Liu, L., Xie, J., Cheng, J., Fu, Y., Li, G., Yi, X., and Jiang, D. (2014). Fungal negativestranded RNA virus that is related to bornavirus and nyavirus. Proc. Natl. Acad. Sci. USA 111, 12205-12210.
15. Liu, Y.-C., Linder-Basso, D., Hillman, B.I., Kaneso, S., and Milgroom, M.G. (2003). Evidence for interspecies transmission of viruses in natural populations of filamentous fungi in the genus Cryphonectria. Molecular Ecology 12, 1619-1628.
16. 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.
17. Márquez, L.M., and Roossinck, M.J. (2012). Do persistent RNA viruses fit the trade-off hypothesis of virulence evolution? Curr. Op. Virol. 2, 556-560.
18. Milgroom, M.G., and Hillman, B.I. (2011). The Ecology and Evolution of Fungal Viruses, in Studies in Viral Ecology: Microbial and Botanical Host Systems, ed. C.J. Hurst. John Wiley & Sons, 217-253.
19. Nakatsukasa-Akune, M., Yamashita, K., Shimoda, Y., Uchiumi, T., Abe, M., Aoki, T., Kamizawa, A., Ayabe, S.-I., Higashi, S., and Suzuki, A. (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.
20. Roossinck, M.J. (2010). Lifestyles of plant viruses. Phil. Trans. R. Soc. B 365, 1899-1905.
21. Roossinck, M.J. (2012). Plant virus metagenomics: Biodiversity and ecology. Annu. Rev. Genet. 46, 357-367.
22. Roossinck, M.J., Sabanadzovic, S., Okada, R., and Valverde, R.A. (2011). The remarkable evoluntionary history of endornaviruses. J. Gen. Virol. 92, 2674-2678.
23. Safari, M., and Roossinck, M.J. (2014). How does the genome structure and lifestyle of a virus affect its population variation? Curr. Op. Virol. 9, 39-44.
24. Seifert, K.A. (2009). Progress towards DNA barcoding of fungi. Mol. Ecol. Res. 9, 83-89.
25. Sela, N., Luria, N., and Dombrovsky, A. (2012). Genome assembly of Bell pepper endornavirus from small RNA. J. Virol. 86, 7721.
26. Stobbe, A.H., and Roossinck, M.J. 2014. Plant virus metagenomics: what we know and why we need to know more. Frontiers in Plant Science 5: 150.
27. Vainio, E.J., Hakanpää, J., Dai, Y.-C., Hansen, E., Korhonen, K., and Hantula, J. (2011). Species of Heterobasidion host a diverse pool of partitiviruses with global distribution and interspecies transmission. Fungal Biol. 115, 1234-1243.
28. Valverde, R.A., and Gutierrez, D.L. (2007). Transmission of a dsRNA in bell pepper and evidence that it consists of the genome of an endornavirus. Virus Genes 35, 399-403.
29. Villarreal, L.P. (2007). Virus-host symbiosis mediated by persistence. Symbiosis 44, 1-9.
30. Yu, X., Li, B., Fu, Y., Jiang, D., Ghabrial, S.A., Peng, Y., Xie, J., Cheng, J., Huang, J., and Yi, X. (2010). A geminivirus-related DNA mycovirus that confers hypovirulence to a plant pathogenic fungus. Proc. Natl. Acad. Sci. USA 107, 8387-8392.
31. Yu, X., Li, B., Fu, Y., Xie, J., Cheng, J., Ghabrial, S.A., Li, G., Yi, X., and Jiang, D. (2013). Extracellular transmission of a DNA mycovirus and its use as a natural fungicide. Proc. Natl. Acad. Sci. USA 110, 1452-1457.