M. Libault, L. Pingault, P. Zogli, and J. Schiefelbein, Plant systems biology at the single-cell level, Trends Plant Sci, vol.22, pp.949-960, 2017.

A. E. Moor and S. Itzkovitz, Spatial transcriptomics: Paving the way for tissue-level systems biology, Curr. Opin. Biotechnol, vol.46, pp.126-133, 2017.

S. Zeilinger, Friends or foes? Emerging insights from fungal interactions with plants, FEMS Microbiol. Rev, vol.40, pp.182-207, 2016.

E. Kemen and J. D. Jones, Obligate biotroph parasitism: Can we link genomes to lifestyles?, Trends Plant Sci, vol.17, p.5, 2012.

A. R. Buxbaum, G. Haimovich, and R. H. Singer, In the right place at the right time: Visualizing and understanding mRNA localization, Nat. Rev. Mol. Cell Biol, vol.16, pp.95-109, 2015.

A. Schuller, J. Kehr, and J. Ludwig-muller, Laser microdissection coupled to transcriptional profiling of Arabidopsis roots inoculated by Plasmodiophora brassicae indicates a role for brassinosteroids in clubroot formation, Plant Cell Physiol, vol.55, pp.392-411, 2014.

D. B. Müller, C. Vogel, Y. Bai, and J. A. Vorholt, The plant microbiota: Systems-level insights and perspectives, Annu. Rev. Genet, vol.50, pp.211-234, 2016.

P. Vandenkoornhuyse, A. Quaiser, M. Duhamel, A. Le-van, and A. Dufresne, 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. Egan, The seaweed holobiont: Understanding seaweed-bacteria interactions, FEMS Microbiol. Rev, vol.37, pp.462-476, 2013.

B. B. Misra, S. M. Assmann, and S. X. Chen, Plant single-cell and single-cell-type metabolomics, Trends Plant Sci, vol.19, pp.637-646, 2014.

D. J. Wang and S. Bodovitz, Single cell analysis: The new frontier in "omics, Trends Biotechnol, vol.28, pp.281-290, 2010.

I. Weibrecht, In situ detection of individual mRNA molecules and protein complexes or post-translational modifications using padlock probes combined with the in situ proximity ligation assay, Nat. Protoc, vol.8, pp.355-372, 2013.

T. Trcek, T. Lionnet, H. Shroff, and R. Lehmann, mRNA quantification using single-molecule FISH in Drosophila embryos, Nat. Protoc, vol.12, pp.1326-1348, 2017.

D. Niessing, R. P. Jansen, T. Pohlmann, and M. Feldbrugge, mRNA transport in fungal top models, 2018.

,

S. Duncan, T. S. Olsson, M. Hartley, C. Dean, and S. Rosa, A method for detecting single mRNA molecules in Arabidopsis thaliana, Plant Methods, 2016.

E. Francoz, Complementarity of medium-throughput in situ RNA hybridization and tissue-specific transcriptomics: Case study of Arabidopsis seed development kinetics, Sci. Rep, 2016.

L. Bruno, Multi-probe in situ hybridization to whole mount Arabidopsis seedlings, Int. J. Dev. Biol, vol.55, pp.197-203, 2011.

K. H. Chen, A. N. Boettiger, J. R. Moffitt, S. Y. Wang, and X. W. Zhuang, Spatially resolved, highly multiplexed RNA profiling in single cells, Science, 2015.

E. Baroja-fernandez, Sucrose synthase activity in the sus1/sus2/sus3/sus4 Arabidopsis mutant is sufficient to support normal cellulose and starch production, Proc. Natl. Acad. Sci. USA, vol.109, pp.321-326, 2012.

A. Schwelm, Not in your usual Top 10: Protists that infect plants and algae, Mol. Plant Pathol, vol.19, pp.1029-1044, 2018.

P. Murúa, Maullinia braseltonii sp nov (Rhizaria, Phytomyxea, Phagomyxida): A cyst-forming parasite of the bull kelp Durvillaea spp. (Stramenopila, Phaeophyceae, Fucales), Protist, vol.168, pp.468-480, 2017.

S. Neuhauser, L. Huber, and M. Kirchmair, Is Roesleria subterranea a primary pathogen or a minor parasite of grapevines? Risk assessment and a diagnostic decision scheme, Eur. J. Plant Pathol, vol.130, pp.503-510, 2011.

I. Maier, E. Parodi, R. Westermeier, and D. G. Muller, Maullinia ectocarpii gen. et sp. nov. (Plasmodiophorea), an intracellular parasite in Ectocarpus siliculosus (Ectocarpales, Phaeophyceae) and other filamentous brown algae, Protist, vol.151, pp.225-238, 2000.

A. Schwelm, The Plasmodiophora brassicae genome reveals insights in its life cycle and ancestry of chitin synthases, Sci. Rep, vol.5, p.11153, 2015.

S. A. Rolfe, The compact genome of the plant pathogen Plasmodiophora brassicae is adapted to intracellular interactions with host Brassica spp, BMC Genomics, vol.17, p.272, 2016.

S. Irani, Transcriptome analysis of response to Plasmodiophora brassicae infection in the Arabidopsis shoot and root, BMC Genomics, vol.19, p.23, 2018.

S. Bulman, Arabidopsis thaliana expressing PbBSMT, a gene encoding a SABATH-type methyltransferase from the plant pathogenic protist Plasmodiophora brassicae, show leaf chlorosis and altered host susceptibility, Plant Biol. (Stuttg), vol.21, issue.1, pp.120-130, 2019.

K. Singh, G. Tzelepis, M. Zouhar, P. Ry?ánek, and C. Dixelius, The immunophilin repertoire of Plasmodiophora brassicae and functional analysis of PbCYP3 cyclophilin, Mol. Genet. Genomics, vol.293, pp.381-390, 2018.

A. Cormier, Re-annotation, improved large-scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus, New Phytol, vol.214, pp.219-232, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01402123

N. Ye, Saccharina genomes provide novel insight into kelp biology, Nat. Commun, vol.6, 2015.

G. Farnham, M. Strittmatter, S. Coelho, J. M. Cock, and C. Brownlee, Gene silencing in Fucus embryos: Developmental consequences of RNAi-mediated cytoskeletal disruption, J. Phycol, vol.49, pp.819-829, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01806438

J. M. Archibald and P. J. Keeling, Actin and ubiquitin protein sequences support a cercozoan/foraminiferan ancestry for the plasmodiophorid plant pathogens, J. Eukaryot. Microbiol, vol.51, pp.113-118, 2004.

J. Ludwig-müller, A novel methyltransferase from the intracellular pathogen Plasmodiophora brassicae methylates salicylic acid, Mol. Plant Pathol, vol.16, pp.349-364, 2015.

C. Leblanc, Vanadium haloperoxidases: From the discovery 30 years ago to X-ray crystallographic and V K-edge absorption spectroscopic studies, Coord. Chem. Rev, vol.301, pp.134-146, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01121900

M. Strittmatter, Infection of the brown alga Ectocarpus siliculosus by the oomycete Eurychasma dicksonii induces oxidative stress and halogen metabolism, Plant Cell Environ, vol.39, pp.259-271, 2016.

J. A. West and D. L. Mcbride, Long-term and diurnal carpospore discharge patterns in the Ceramiaceae, Rhodomelaceae and Delesseriaceae (Rhodophyta), Hydrobiologia, vol.398, pp.101-114, 1999.

C. A. Schneider, W. S. Rasband, K. W. Eliceiri, and . Nih, Image to ImageJ: 25 years of image analysis, Nat. Methods, vol.9, 2012.

M. Stettler, Blocking the metabolism of starch breakdown products in Arabidopsis leaves triggers chloroplast degradation, Mol. Plant, vol.2, pp.1233-1246, 2009.

A. Schuller and J. Ludwig-müller, Histological methods to detect the clubroot pathogen Plasmodiophora brassicae during its complex life cycle, Plant. Pathol, vol.65, pp.1223-1237, 2016.

A. Cosse, P. Potin, and C. Leblanc, Patterns of gene expression induced by oligoguluronates reveal conserved and environmentspecific molecular defense responses in the brown alga Laminaria digitata, New Phytol, vol.182, pp.239-250, 2009.

A. H. Robin, M. R. Hossain, H. Kim, I. Nou, and J. Park, Role of cytokinins in clubroot disease development, Plant Breed. Biotechnol, vol.7, pp.73-82, 2019.

I. Gaspar and A. Ephrussi, Strength in numbers: Quantitative single-molecule RNA detection assays, Wiley Interdiscip. Rev. Dev. Biol, vol.4, pp.135-150, 2015.

C. Lee, S. E. Roberts, and A. S. Gladfelter, Quantitative spatial analysis of transcripts in multinucleate cells using single-molecule FISH, Methods, vol.98, pp.124-133, 2016.

C. Medioni and F. Besse, The secret life of RNA: Lessons from emerging methodologies, RNA Detection: Methods and Protocols, vol.1, 2018.

L. A. Van-gijtenbeek and J. Kok, Illuminating messengers: An update and outlook on RNA visualization in bacteria, Front. Microbiol, vol.8, p.1161, 2017.

S. W. Foley, M. C. Kramer, and B. D. Gregory, RNA structure, binding, and coordination in Arabidopsis, Wiley Interdiscip. Rev. RNA, vol.8, 1426.

Y. Ding, In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features, Nature, vol.505, 2013.

M. Djavaheri, Mimicking the host regulation of salicylic acid: A virulence strategy by the clubroot pathogen Plasmodiophora brassicae, Mol. Plant Microbe Interact, vol.32, pp.296-305, 2019.

S. Bulman, J. Siemens, H. J. Ridgway, C. Eady, and A. J. Conner, Identification of genes from the obligate intracellular plant pathogen, Plasmodiophora brassicae, FEMS Microbiol. Lett, vol.264, pp.198-204, 2006.

S. Bulman, Genomics of biotrophic, plant-infecting plasmodiophorids using in vitro dual cultures, Protist, vol.162, pp.449-461, 2011.

E. C. Donald, G. Jaudzems, and I. J. Porter, Pathology of cortical invasion by Plasmodiophora brassicae in clubroot resistant and susceptible Brassica oleracea hosts, Plant. Pathol, vol.57, pp.201-209, 2008.

I. Mühlenberg, A. Schuller, J. Siemens, P. Kobelt, and J. Ludwig-müller, Plasmodiophora brassicae, the causal agent of clubroot disease, may penetrate plant cell walls via cellulase, Plant Prot. Sci. Prague, vol.38, pp.69-72, 2003.

D. Riascos, E. Ortiz, D. Quintero, L. Montoya, and L. Hoyos-carvajal, Histopathological and morphological alterations caused by plasmodiophora brassicae in Brassica oleracea, Agron. Colomb, vol.29, pp.57-67, 2011.

, Scientific RepoRtS |, vol.10, p.14269, 2020.

T. Cavalier-smith and E. E. Chao, Phylogeny of choanozoa, apusozoa, and other protozoa and early eukaryote megaevolution, J. Mol. Evol, vol.56, pp.540-563, 2003.

P. H. Fesel and A. Zuccaro, beta-glucan: Crucial component of the fungal cell wall and elusive MAMP in plants, Fungal Genet. Biol, vol.90, pp.53-60, 2016.

A. C. Vlot, E. Pabst, and M. Riedlmeier, Systemic signalling in plant defence, p.3, 2017.

J. Ludwig-müller, E. Prinsen, S. A. Rolfe, and J. D. Scholes, Metabolism and plant hormone action during clubroot disease, J. Plant Growth Regul, vol.28, pp.229-244, 2009.

C. Merchante, A. N. Stepanova, and J. M. Alonso, Translation regulation in plants: An interesting past, an exciting present and a promising future, Plant J, vol.90, pp.628-653, 2017.