A. Agrawal, J. Lau, and P. Hamback, Community heterogeneity and the evolution of interactions between plants and insect herbivores, The Quarterly Review of Biology, vol.81, issue.4, pp.349-376, 2006.
DOI : 10.1086/511529
URL : https://www.msu.edu/~jenlau/pdf/publications/Agrawal et al. QRB 2006.pdf

H. Alexander, K. Mauck, A. Whitfield, K. Garrett, and C. Malmstrom, Plant-virus interactions and the agro-ecological interface, European Journal of Plant Pathology, vol.180, issue.4, pp.529-547, 2014.
DOI : 10.1111/j.1469-8137.2008.02627.x

B. Allan, F. Keesing, and R. Ostfeld, Effect of Forest Fragmentation on Lyme Disease Risk, Conservation Biology, vol.25, issue.1, pp.267-272, 2003.
DOI : 10.1093/jmedent/25.4.224

S. Altschul, W. Gish, W. Miller, E. Myers, and D. Lipman, Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990.
DOI : 10.1016/S0022-2836(05)80360-2

P. Anderson, A. Cunningham, N. Patel, F. Morales, P. Epstein et al., Emerging infectious diseases of plants: pathogen pollution, climate change and agrotechnology drivers, Trends in Ecology & Evolution, vol.19, issue.10, pp.535-544, 2004.
DOI : 10.1016/j.tree.2004.07.021

Y. Benjamini and Y. Hochberg, Controlling the false discovery rate -a practical and powerful approach to multiple testing, J R Stat Soc Ser B-Methodol, vol.57, pp.289-300, 1995.

P. Bernardo, M. Golden, M. Akram, . Naimuddin, N. Nadarajan et al., Identification and characterisation of a highly divergent geminivirus: Evolutionary and taxonomic implications, Virus Research, vol.177, issue.1, pp.35-45, 2013.
DOI : 10.1016/j.virusres.2013.07.006
URL : https://doi.org/10.1016/j.virusres.2013.07.006

E. Borer, P. Hosseini, E. Seabloom, and A. Dobson, Pathogen-induced reversal of native dominance in a grassland community, Proceedings of the National Academy of Sciences, vol.8, issue.6923, pp.5473-5478, 2007.
DOI : 10.1038/nature01346
URL : http://www.pnas.org/content/104/13/5473.full.pdf

J. Brum, J. Ignacio-espinoza, E. Kim, G. Trubl, R. Jones et al., Illuminating structural proteins in viral ???dark matter??? with metaproteomics, Proceedings of the National Academy of Sciences, vol.5, issue.9, pp.2436-2441, 2016.
DOI : 10.1109/TVCG.2011.56
URL : http://www.pnas.org/content/113/9/2436.full.pdf

J. Burdon, P. Thrall, and A. Ericson, The Current and Future Dynamics of Disease in Plant Communities, Annual Review of Phytopathology, vol.44, issue.1, pp.19-39, 2006.
DOI : 10.1146/annurev.phyto.43.040204.140238

I. Cooper and R. Jones, Wild plants and viruses: underinvestigated ecosystems, AdvVirus Res, vol.67, pp.1-47, 2006.
DOI : 10.1016/s0065-3527(06)67001-2

P. Dixon, VEGAN, a package of R functions for community ecology, Journal of Vegetation Science, vol.8, issue.6, pp.927-930, 2003.
DOI : 10.1890/1051-0761(1998)008[0300:DTISC]2.0.CO;2

S. Doledec, D. Chessel, C. Terbraak, and S. Champely, Matching species traits to environmental variables: a new three-table ordination method, Environmental and Ecological Statistics, vol.39, issue.270, pp.143-166, 1996.
DOI : 10.1007/978-94-011-3198-8_3

S. Dray and P. Legendre, TESTING THE SPECIES TRAITS???ENVIRONMENT RELATIONSHIPS: THE FOURTH-CORNER PROBLEM REVISITED, Ecology, vol.46, issue.4, pp.3400-3412, 2008.
DOI : 10.2307/2937189
URL : https://hal.archives-ouvertes.fr/hal-00428249

R. Edgar, Muscle: a multiple sequence alignment method with reduced time and space complexity, BMC Bioinformatics, vol.5, issue.1, p.113, 2004.
DOI : 10.1186/1471-2105-5-113

S. Flory and K. Clay, Pathogen accumulation and long-term dynamics of plant invasions, Journal of Ecology, vol.72, issue.3, pp.607-613, 2013.
DOI : 10.1073/pnas.72.6.2116
URL : http://onlinelibrary.wiley.com/doi/10.1111/1365-2745.12078/pdf

M. Hill and A. Smith, Principal Component Analysis of Taxonomic Data with Multi-State Discrete Characters, Taxon, vol.25, issue.2/3, pp.249-255, 1976.
DOI : 10.2307/1219449

X. Huang and A. Madan, CAP3: A DNA Sequence Assembly Program, Genome Research, vol.9, issue.9, pp.868-877, 1999.
DOI : 10.1101/gr.9.9.868
URL : http://genome.cshlp.org/content/9/9/868.full.pdf

R. Jones, Plant virus emergence and evolution: Origins, new encounter scenarios, factors driving emergence, effects of changing world conditions, and prospects for control, Virus Research, vol.141, issue.2, pp.113-130, 2009.
DOI : 10.1016/j.virusres.2008.07.028

R. Jones and B. Coutts, Spread of introduced viruses to new plants in natural ecosystems and the threat this poses to plant biodiversity, Molecular Plant Pathology, vol.56, issue.3, pp.541-545, 2015.
DOI : 10.1111/j.1365-3059.2007.01653.x

F. Keesing, L. Belden, P. Daszak, A. Dobson, C. Harvell et al., Impacts of biodiversity on the emergence and transmission of infectious diseases, Nature, vol.52, issue.7324, pp.647-652, 2010.
DOI : 10.3201/eid1112.040789

V. Taxonomy, Classification and Nomenclature of Viruses, Ninth Report of the International Committee on Taxonomy of Viruses

C. Lacroix, A. Jolles, E. Seabloom, A. Power, C. Mitchell et al., Non-random biodiversity loss underlies predictable increases in viral disease prevalence, Journal of The Royal Society Interface, vol.13, issue.2, 2014.
DOI : 10.1111/j.1461-0248.2009.01418.x
URL : http://rsif.royalsocietypublishing.org/content/royinterface/11/92/20130947.full.pdf

P. Legendre and L. Legendre, Numerical Ecology, 2012.
DOI : 10.1016/B978-0-12-409548-9.10595-0
URL : https://hal.archives-ouvertes.fr/hal-00530195

C. Malmstrom, C. Hughes, L. Newton, and C. Stoner, Virus infection in remnant native bunchgrasses from invaded California grasslands, New Phytologist, vol.96, issue.1, pp.217-230, 2005.
DOI : 10.1111/j.1438-8677.1990.tb00152.x
URL : http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2005.01479.x/pdf

C. Malmstrom, A. Mccullough, H. Johnson, L. Newton, and E. Borer, Invasive annual grasses indirectly increase virus incidence in California native perennial bunchgrasses, Oecologia, vol.8, issue.1, pp.153-164, 2005.
DOI : 10.1093/ee/22.1.149

M. Martin, Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet.journal, vol.17, issue.1, p.10, 2011.
DOI : 10.14806/ej.17.1.200

C. Mitchell, D. Tilman, and J. Groth, EFFECTS OF GRASSLAND PLANT SPECIES DIVERSITY, ABUNDANCE, AND COMPOSITION ON FOLIAR FUNGAL DISEASE, Ecology, vol.83, issue.6, pp.1713-1726, 2002.
DOI : 10.1038/35021046

V. Muthukumar, U. Melcher, M. Pierce, G. Wiley, B. Roe et al., Non-cultivated plants of the Tallgrass Prairie Preserve of northeastern Oklahoma frequently contain virus-like sequences in particulate fractions, Virus Research, vol.141, issue.2, pp.169-173, 2009.
DOI : 10.1016/j.virusres.2008.06.016

V. Muthukumar, G. Wiley, M. Pierce, B. Roe, and U. Melcher, Metagenomics for identification of novel plant viruses, Phytopathology, vol.97, pp.81-82, 2007.

N. Myers, R. Mittermeier, C. Mittermeier, G. Da-fonseca, and K. J. , Biodiversity hotspots for conservation priorities, Nature, vol.401, issue.6772, pp.853-858, 2000.
DOI : 10.1038/32761

M. Nibert, S. Ghabrial, E. Maiss, T. Lesker, E. Vainio et al., Taxonomic reorganization of family Partitiviridae and other recent progress in partitivirus research, Virus Research, vol.188, pp.128-141, 2014.
DOI : 10.1016/j.virusres.2014.04.007

I. Pagan, P. Gonzalez-jara, A. Moreno-letelier, M. Rodelo-urrego, A. Fraile et al., Effect of Biodiversity Changes in Disease Risk: Exploring Disease Emergence in a Plant-Virus System, PLoS Pathogens, vol.3, issue.7, p.1002796, 2012.
DOI : 10.1371/journal.ppat.1002796.s003

E. Palanga, D. Filloux, D. Martin, E. Fernandes, D. Gargani et al., Metagenomic-based screening And molecular characterization of cowpeainfecting viruses in Burkina Faso, PLoS One, vol.11, p.165188, 2016.
DOI : 10.1371/journal.pone.0165188
URL : https://doi.org/10.1371/journal.pone.0165188

M. Roossinck, The big unknown: plant virus biodiversity, Current Opinion in Virology, vol.1, issue.1, pp.63-67, 2011.
DOI : 10.1016/j.coviro.2011.05.022

M. Roossinck, Plant Virus Metagenomics: Biodiversity and Ecology, Annual Review of Genetics, vol.46, issue.1, pp.359-369, 2012.
DOI : 10.1146/annurev-genet-110711-155600

M. Roossinck and F. Garcia-arenal, Ecosystem simplification, biodiversity loss and plant virus emergence, Current Opinion in Virology, vol.10, pp.56-62, 2015.
DOI : 10.1016/j.coviro.2015.01.005

M. Roossinck, D. Martin, and P. Roumagnac, Plant Virus Metagenomics: Advances in Virus Discovery, Phytopathology, vol.105, issue.6, pp.716-727, 2015.
DOI : 10.1094/PHYTO-12-14-0356-RVW

M. Roossinck, P. Saha, G. Wiley, J. Quan, J. White et al., Ecogenomics: using massively parallel pyrosequencing to understand virus ecology, Molecular Ecology, vol.437, pp.81-88, 2010.
DOI : 10.1111/j.1365-294X.2009.04470.x

K. Rosario and M. Breitbart, Exploring the viral world through metagenomics, Current Opinion in Virology, vol.1, issue.4, pp.1-9, 2011.
DOI : 10.1016/j.coviro.2011.06.004

T. Rottstock, J. Joshi, V. Kummer, and M. Fischer, Higher plant diversity promotes higher diversity of fungal pathogens, while it decreases pathogen infection per plant, Ecology, vol.95, issue.7, pp.1907-1917, 2014.
DOI : 10.1890/09-0863.1
URL : https://boris.unibe.ch/58172/1/13-2317%252E1.pdf

S. Scherr and J. Mcneely, Biodiversity conservation and agricultural sustainability: towards a new paradigm of 'ecoagriculture' landscapes, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.12, issue.1, pp.477-494, 2008.
DOI : 10.1104/pp.125.1.174
URL : http://rstb.royalsocietypublishing.org/content/royptb/363/1491/477.full.pdf

K. Tamura, G. Stecher, D. Peterson, A. Filipski, and S. Kumar, MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0, Molecular Biology and Evolution, vol.87, issue.12, pp.2725-2729, 2013.
DOI : 10.1128/JVI.02478-12
URL : https://academic.oup.com/mbe/article-pdf/30/12/2725/19498310/mst197.pdf

J. Thresh, Pests, Pathogens, and Vegetation, 1981.

B. Van-wilgen, The evolution of fire and invasive alien plant management practices in fynbos, South African Journal of Science, vol.105, issue.9/10, pp.335-342, 2009.
DOI : 10.4102/sajs.v105i9/10.106

A. Varsani, D. Shepherd, A. Monjane, B. Owor, J. Erdmann et al., Recombination, decreased host specificity and increased mobility may have driven the emergence of maize streak virus as an agricultural pathogen, Journal of General Virology, vol.92, issue.1-2, pp.2063-2074, 2008.
DOI : 10.1016/S0166-0934(00)00299-8

C. Webster, B. Coutts, R. Jones, M. Jones, and S. Wylie, Virus impact at the interface of an ancient ecosystem and a recent agroecosystem: studies on three legume-infecting potyviruses in the southwest Australian floristic region, Plant Pathology, vol.67, issue.5, pp.729-742, 2007.
DOI : 10.1007/s00705-002-0805-7

J. Wren, M. Roossinck, R. Nelson, K. Scheets, M. Palmer et al., Plant Virus Biodiversity and Ecology, PLoS Biology, vol.30, issue.3, p.80, 2006.
DOI : 10.1371/journal.pbio.0040080.g001
URL : https://doi.org/10.1371/journal.pbio.0040080

S. Wu and U. Manber, Agrep?a fast approximate pattern-matching tool, pp.53-162, 1992.