S. Massart, A. Olmos, H. Jijakli, and T. Candresse, Current impact and future directions of high throughput sequencing in plant virus diagnostics, vol.188, pp.90-96, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02635445

S. Massart, T. Candresse, J. Gil, C. Lacomme, L. Predajna et al., A Framework for the Evaluation of Biosecurity, Commercial, Regulatory and Scientific Impacts of Plant Viruses and Viroids Identified by NGS Technologies, Front Microbiol, vol.8, p.45, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01606670

M. J. Roossinck, D. P. Martin, and P. Roumagnac, Plant virus metagenomics: advances in virus discovery, Phytopathology, vol.105, pp.716-727, 2015.

I. P. Adams, R. H. Glover, W. A. Monger, R. Mumford, E. Jackeviciene et al., Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology, Mol Plant Pathol, vol.10, p.19523106, 2009.

Q. Wu, S. W. Ding, Y. Zhang, and S. Zhu, Identification of viruses and viroids by next-generation sequencing and homology-dependent and homology-independent algorithms, Annu Rev Phytopathol, vol.53, pp.425-444, 2015.

H. J. Maree, A. Fox, A. Rwahnih, M. Boonham, and N. , Application of HTS for Routine Plant Virus Diagnostics: State of the Art and Challenges, Front. Plant Science, vol.9, pp.1-4, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02625816

Y. Jo, S. Lian, and H. Chu, Peach RNA viromes in six different peach cultivars, Sci Rep, vol.8, issue.1, p.29382911, 2018.

B. M. Coetzee, J. Freeborough, H. Maree, M. Celton, J. G. Rees et al., Deep sequencing analysis of viruses infecting grapevines: virome of a vineyard, Virology, vol.400, pp.157-163, 2010.

J. M. Hily, T. Candresse, S. Garcia, E. Vigne, M. Tannière et al., High-Throughput Sequencing and the Viromic Study of Grapevine Leaves: From the Detection of Grapevine-Infecting Viruses to the Description of a, New Environmental Tymovirales Member. Front. Microbiol, vol.9, p.1782, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02626175

M. Beuve, J. M. Hily, A. Alliaume, C. Reinbold, L. Maguet et al., A complex virome unveiled by deep sequencing analysis of RNAs from a French Pinot Noir grapevine exhibiting strong leafroll symptoms, Arch. Virol, vol.163, issue.11, p.30033497, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02628897

A. Rumbou, T. Candresse, A. Marais, S. Theil, J. Langer et al., A novel badnavirus discovered from Betula sp. affected by birch leaf-roll disease, PLoS ONE, vol.13, issue.3, p.193888, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02624650

R. Jalkanen, C. Büttner, and S. Von-bargen, Cherry leaf roll virus abundant on Betula pubescens in Finland, Silva Fennica, vol.41, pp.755-762, 2007.

A. Rumbou, S. Von-bargen, R. Demiral, J. Langer, M. Rott et al., High genetic diversity at the inter-/intra-host level of Cherry leaf roll virus population associated with the birch leaf-roll disease in Fennoscandia, Scand J For Res, vol.31, issue.6, pp.546-560, 2016.

J. Langer, A. Rumbou, A. Fauter, S. Von-bargen, and . Bü, High genetic variation in a small population of Cherry leaf roll virus in Betula sp., of montane origin in Corsica, For Pathol, vol.46, issue.6, pp.595-599, 2016.

S. Von-bargen, E. Grubits, B. Jalkanen, and C. Ttner, Cherry leaf roll virus-an emerging virus in Finland?, Silva Fennica, vol.43, pp.727-738, 2009.

C. Bü-ttner, V. Bargen, S. Bandte, and M. , Mü hlbach HP. Forests diseases caused by viruses, Infectious forest diseases, pp.97-110, 2013.

D. H. Huson, S. Beier, I. Flade, A. Górska, M. El-hadidi et al., Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data, PLoS Comput Biol, vol.12, issue.6, p.1004957, 2016.

W. A. Kibbe, OligoCalc: an online oligonucleotide properties calculator', Nucleic Acids Res, vol.35, 2007.

F. Youssef, A. Marais, C. Faure, P. Gentit, and T. Candresse, Strategies to facilitate the development of uncloned or cloned infectious full-length viral cDNAs: Apple chlorotic leaf spot virus as a case study, Virol J, vol.8, p.488, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02644133

A. Larsson, AliView: a fast and lightweight alignment viewer and editor for large datasets, Bioinformatics, vol.30, issue.22, pp.3276-3278, 2014.

K. Tamura, G. Stecher, D. Peterson, A. Filipski, and S. Kumar, MEGA6: Molecular Evolutionary Genetics Analysis version 6.0, Molecular Biology and Evolution, vol.30, pp.2725-2729, 2013.

D. James and J. Phelan, Complete genome sequence and analysis of blackcurrant leaf chlorosis associated virus, a new member of the genus Idaeovirus, Arch Virol, vol.162, p.28190194, 2017.

T. Thekke-veetil and T. Ho, Characterization and detection of a novel idaeovirus infecting blackcurrant, Eur J Plant Pathol, vol.149, pp.751-757, 2017.

E. B. Opoku, M. Landgraf, K. Pack, M. Bandte, S. Von-bargen et al., Emerging viruses in urban green-detection of the virome in birch (Betula sp, J Horticulture, Biological Sciences, vol.5, issue.2, 2018.

, Virus Taxonomy, Committee on Taxonomy of Viruses (ICTV), 2016.

M. Landgraf, J. Gehlsen, A. Rumbou, M. Bandte, S. Von-bargen et al., Absterbende Birken im urbanen Grün Berlins-eine Studie zur Virusinfektion, Jahrbuch der Baumpflege 2016, pp.276-283

M. Vayssier-taussat, A. E. Citti, C. J. Cosson, F. M. Jacques, A. M. Candresse et al., Shifting the paradigm from pathogens to pathobiome: new concepts in the light of metaomics, Front. Cell. Infect.Microbiol, vol.4, p.29, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01153583

E. Rosenberg and I. Zilber-rosenberg, The hologenome concept: Human, animal and plant microbiota, 2013.

P. Vandenkoornhuyse, A. Quaiser, M. Duhamel, L. Van, A. Dufresne et al., The importance of the microbiome of the plant holobiont, New Phytol, vol.206, pp.1196-1206, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01115639

S. Hacquard, Disentangling the factors shaping microbiota composition across the plant holobiont, New Phytol, vol.209, pp.454-457, 2016.

O. E. Mckenna, G. Posselt, G. Gadermaier, and S. Wessler, Multi-Approach Analysis for the Identification of Proteases within Birch Pollen, vol.18, p.1433, 2017.

M. Landgraf, J. Langer, J. Grö, L. Zinnert, M. Bandte et al., Viruserkrankungen im urbanen Grün-eine Studie an Birken im Berliner Bezirk Steglitz-Zehlendorf Viral diseases in urban areas-a study on birch in Berlin Steglitz-Zehlendorf Jahrbuch der Baumpflege, 21, pp.327-332, 2017.