A Survey on Plant Viruses in Natural Brassicaceae Communities Using RNA-Seq

Tomlinson JA, Carter AL, Dale WT, Simpson CJ (1970) Weed plants as sources of cucumber mosaic virus. Ann Appl Biol 66:11–16. https://doi.org/10.1111/j.1744-7348.1970.tb04597.x

Mueller EE, Groves RL, Gratton C (2011) Crop and non-crop plants as potential reservoir hosts of alfalfa mosaic virus and cucumber mosaic virus for spread to commercial snap bean. Plant Dis 96:506–514. https://doi.org/10.1094/PDIS-02-11-0089

Roossinck MJ (2012) Plant virus metagenomics: biodiversity and ecology. Annu Rev Genet 46:359–369. https://doi.org/10.1146/annurev-genet-110711-155600

Aranda MA, Freitas-Astúa J (2017) Ecology and diversity of plant viruses, and epidemiology of plant virus-induced diseases. Ann Appl Biol 171:1–4. https://doi.org/10.1111/aab.12361

Islam W, Zhang J, Adnan M, Noman A, Zainab M, Jian W (2017) Plant virus ecology: a glimpse of recent accomplishments. Appl Ecol Environ Res 15:691–705. https://doi.org/10.15666/aeer/1501_691705

May RM, Anderson RM (1983) Epidemiology and genetics in the coevolution of parasites and hosts. Proc R Soc Lond B Biol Sci 219:281–313. https://doi.org/10.1098/rspb.1983.0075

Prendeville HR, Ye X, Morris TJ, Pilson D (2012) Virus infections in wild plant populations are both frequent and often unapparent. Am J Bot 99:1033–1042. https://doi.org/10.3732/ajb.1100509

Li L, Liu J, Zhang Q, Fu R, Zhu X, Li C, Chen J (2016) Seed-borne viral dsRNA elements in three cultivated Raphanus and Brassica plants suggest three cryptoviruses. Can J Microbiol 62:287–295. https://doi.org/10.1139/cjm-2015-0788

Alexander HM, Bruns E, Schebor H, Malmstrom CM (2017) Crop-associated virus infection in a native perennial grass: reduction in plant fitness and dynamic patterns of virus detection. J Ecol 105:1021–1031. https://doi.org/10.1111/1365-2745.12723

Pagán I, Montes N, Milgroom MG, García-Arenal F (2014) Vertical transmission selects for reduced virulence in a plant virus and for increased resistance in the host. PLoS Pathog 10:e1004293. https://doi.org/10.1371/journal.ppat.1004293

Bottenberg H, Irwin ME (1992) Using mixed cropping to limit seed mottling induced by soybean mosaic virus. Plant Dis 76:304–306. https://doi.org/10.1094/PD-76-0304

Jones RAC, Ferris DG (2000) Suppressing spread of alfalfa mosaic virus in grazed legume pasture swards using insecticides and admixture with grass, and effects of insecticides on numbers of aphids and three other pasture pests. Ann Appl Biol 137:259–271. https://doi.org/10.1111/j.1744-7348.2000.tb00067.x

Hooks CRR, Fereres A (2006) Protecting crops from non-persistently aphid-transmitted viruses: a review on the use of barrier plants as a management tool. Virus Res 120:1–16. https://doi.org/10.1016/j.virusres.2006.02.006

Pedersen AB, Fenton A (2007) Emphasizing the ecology in parasite community ecology. Trends Ecol Evol 22:133–139. https://doi.org/10.1016/j.tree.2006.11.005

Callaway RM (1995) Positive interactions among plants. Bot Rev 61:306–349. https://doi.org/10.1007/BF02912621

Seabloom EW, Borer ET, Gross K, Kendig AE, Lacroix C, Mitchell CE, Mordecai EA, Power AG (2015) The community ecology of pathogens: coinfection, coexistence and community composition. Ecol Lett 18:401–415. https://doi.org/10.1111/ele.12418

Filipe J, Maule M (2004) Effects of dispersal mechanisms on spatio-temporal development of epidemics. J Theor Biol 226:125–141. https://doi.org/10.1016/S0022-5193(03)00278-9

Gibson G (1997) Investigating mechanisms of spatiotemporal epidemic spread using stochastic models. Phytopathology 87:139–146. https://doi.org/10.1094/PHYTO.1997.87.2.139

Barba M, Czosnek H, Hadidi A (2014) Historical perspective, development and applications of next-generation sequencing in plant virology. Viruses 6:106–136. https://doi.org/10.3390/v6010106

Kamitani M, Nagano AJ, Honjo MN, Kudoh H (2016) RNA-Seq reveals virus-virus and virus-plant interactions in nature. FEMS Microbiol Ecol 92. https://doi.org/10.1093/femsec/fiw176

Palukaitis P, Roossinck MJ, Dietzgen RG, Francki RI (1992) Cucumber mosaic virus. Adv Virus Res 41:281–348

Ohshima K, Yamaguchi Y, Hirota R, Hamamoto T, Tomimura K, Tan Z, Sano T, Azuhata F, Walsh JA, Fletcher J, Chen J, Gera A, Gibbs A (2002) Molecular evolution of turnip mosaic virus: evidence of host adaptation, genetic recombination and geographical spread. J Gen Virol 83:1511–1521. https://doi.org/10.1099/0022-1317-83-6-1511

Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652. https://doi.org/10.1038/nbt.1883

Morlan JD, Qu K, Sinicropi DV (2012) Selective depletion of rRNA enables whole transcriptome profiling of archival fixed tissue. PLoS One 7:e42882. https://doi.org/10.1371/journal.pone.0042882

Rice P, Longden I, Bleasby A (2000) EMBOSS: the European molecular biology open software suite. Trends Genet 16:276–277. https://doi.org/10.1016/s0168-9525(00)02024-2

Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O’Hara R, Simpson GL, Solymos P, Stevens MHH, Wagner H (2015) Vegan: community ecology package. R package version 2.3-5. 2016

Roossinck MJ, Zhang L, Hellwald KH (1999) Rearrangements in the 5′ nontranslated region and phylogenetic analyses of cucumber mosaic virus RNA 3 indicate radial evolution of three subgroups. J Virol 73:6752–6758

Bashir NS, Kalhor MR, Zarghani SN (2006) Detection, differentiation and phylogenetic analysis of cucumber mosaic virus isolates from cucurbits in the northwest region of Iran. Virus Genes 32:277–288. https://doi.org/10.1007/s11262-005-6912-2

Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874. https://doi.org/10.1093/molbev/msw054

Pallett D, Thurston M, Cortina-Borja M, Edwards ML, Alexander M, Mitchell E, Raybould A, Cooper J (2002) The incidence of viruses in wild Brassica rapa ssp. sylvestris in southern England. Ann Appl Biol 141:163–170. https://doi.org/10.1111/j.1744-7348.2002.tb00209.x

Rist DL, Lorbeer JW (1989) Occurrence and overwintering of cucumber mosaic virus and broad bean wilt virus in weeds growing near commercial lettuce fields in New York. Phytopathology 79:65–69. https://doi.org/10.1094/Phyto-79-65

Kamitani M, Nagano AJ, Honjo MN, Kudoh H (2017) First report of Pelargonium zonate spot virus from wild Brassicaceae plants in Japan. J Gen Plant Pathol 83:329–332. https://doi.org/10.1007/s10327-017-0727-6

Lapidot M, Guenoune-Gelbart D, Leibman D, Holdengreber V, Davidovitz M, Machbash Z, Klieman-Shoval S, Cohen S, Gal-On A (2010) Pelargonium zonate spot virus is transmitted vertically via seed and pollen in tomato. Phytopathology 100:798–804. https://doi.org/10.1094/phyto-100-8-0798

Roossinck MJ (2010) Lifestyles of plant viruses. Philos Trans R Soc Lond Ser B Biol Sci 365:1899–1905. https://doi.org/10.1098/rstb.2010.0057

Schliephake E, Graichen K, Rabenstein FF (1999) Investigations on the vector transmission of the Beet mild yellowing virus (BMYV) and the Turnip yellows virus (TuYV). Journal of Plant Diseases and Protection 107(1):81–87. http://www.jstor.org/stable/43215342.

Whitfield AE, Falk BW, Rotenberg D (2015) Insect vector-mediated transmission of plant viruses. Virology 479-480:278–289. https://doi.org/10.1016/j.virol.2015.03.026

Choi SK, Yoon JY, Ryu KH, Choi JK, Palukaitis P, Park WM (2002) Systemic movement of a movement-deficient strain of cucumber mosaic virus in zucchini squash is facilitated by a cucurbit-infecting potyvirus. J Gen Virol 83:3173–3178. https://doi.org/10.1099/0022-1317-83-12-3173

Pruss G, Ge X, Shi XM, Carrington JC, Bowman Vance V (1997) Plant viral synergism: the potyviral genome encodes a broad-range pathogenicity enhancer that transactivates replication of heterologous viruses. Plant Cell 9:859–868

Kondo H, Hirano S, Chiba S, Andika IB, Hirai M, Maeda T, Tamada T (2013) Characterization of burdock mottle virus, a novel member of the genus Benyvirus, and the identification of benyvirus-related sequences in the plant and insect genomes. Virus Res 177:75–86. https://doi.org/10.1016/j.virusres.2013.07.015

Nibert ML, Ghabrial SA, Maiss E, Lesker T, Vainio EJ, Jiang D, Suzuki N (2014) Taxonomic reorganization of family Partitiviridae and other recent progress in partitivirus research. Virus Res 188:128–141. https://doi.org/10.1016/j.virusres.2014.04.007

Boccardo G, Lisa V, Luisoni E, Milne RG (1987) Cryptic plant viruses. Adv Virus Res 32:171–214. https://doi.org/10.1016/S0065-3527(08)60477-7