A. Lévesque and C. , Fifty years of oomycetes-from consolidation to evolutionary and genomic exploration, Fungal Divers, vol.50, pp.35-46, 2011.

G. W. Beakes, S. L. Glockling, and S. Sekimoto, The evolutionary phylogeny of the oomycete 'fungi', Protoplasma, vol.249, pp.3-19, 2012.

T. Cavalier-smith and E. Chao, Phylogeny and megasystematics of phagotrophic heterokonts (kingdom Chromista), J Mol Evol, vol.62, pp.388-420, 2006.

H. S. Judelson, Metabolic Diversity and Novelties in the Oomycetes, Annu Rev Microbiol, vol.71, pp.21-39, 2017.

S. L. Baldauf, A. J. Roger, I. Wenk-siefert, and W. F. Doolittle, A kingdom-level phylogeny of eukaryotes based on combined protein data, Science, vol.290, pp.972-977, 2000.

F. Burki, The eukaryotic tree of life from a global phylogenomic perspective, Cold Spring Harb Perspect Biol, vol.6, p.16147, 2014.

R. Derelle, P. López-garcía, H. Timpano, and D. Moreira, A Phylogenomic Framework to Study the Diversity and Evolution of Stramenopiles (=Heterokonts), Mol Biol Evol, vol.33, pp.2890-2898, 2016.

B. M. Tyler, Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis, Science (80-), vol.313, pp.1261-1266, 2006.

N. H. Matari and J. E. Blair, A multilocus timescale for oomycete evolution estimated under three distinct molecular clock models, BMC Evol Biol, vol.14, pp.1-11, 2014.

M. Krings, T. N. Taylor, and N. Dotzler, The fossil record of the Peronosporomycetes (Oomycota), Mycologia, vol.103, pp.445-457, 2011.

C. Strullu-derrien, P. Kenrick, J. P. Rioult, and D. G. Strullu, Evidence of parasitic Oomycetes (Peronosporomycetes) infecting the stem cortex of the Carboniferous seed fern Lyginopteris oldhamia, Proc R Soc B Biol Sci, vol.278, pp.675-680, 2011.

M. Thines and S. Kamoun, Oomycete-plant coevolution: Recent advances and future prospects, Curr Opin Plant Biol, vol.13, pp.427-433, 2010.

F. Savory, G. Leonard, and T. A. Richards, The Role of Horizontal Gene Transfer in the Evolution of the Oomycetes, PLoS Pathog, vol.11, pp.1-6, 2015.

R. Jiang and B. M. Tyler, Mechanisms and Evolution of Virulence in Oomycetes, Annu Rev Phytopathol, vol.50, pp.295-318, 2012.

A. J. Phillips, V. L. Anderson, E. J. Robertson, C. J. Secombes, and P. Van-west, New insights into animal pathogenic oomycetes, Trends Microbiol, vol.16, pp.13-19, 2008.

E. Gaulin, C. Jacquet, A. Bottin, and B. Dumas, Root rot disease of legumes caused by Aphanomyces euteiches, Mol Plant Pathol, vol.8, pp.539-548, 2007.

M. Thines, Phylogeny and evolution of plant pathogenic oomycetes-a global overview, Eur J Plant Pathol, vol.138, pp.431-447, 2014.

M. Latijnhouwers, D. Wit, P. Govers, and F. , Oomycetes and fungi: Similar weaponry to attack plants, Trends Microbiol, vol.11, pp.462-469, 2003.

S. Kamoun, Plant Pathogens: Oomycetes (water mold), Encyclopedia of Microbiology, pp.689-695, 2009.

P. Van-west, Saprolegnia parasitica, an oomycete pathogen with a fishy appetite: new challenges for an old problem, Mycologist, vol.20, pp.99-104, 2006.

S. Kamoun, O. Furzer, J. Jones, H. S. Judelson, G. S. Ali et al., The Top 10 oomycete pathogens in molecular plant pathology, Mol Plant Pathol, vol.16, pp.413-434, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01568630

L. Derevnina, B. Petre, R. Kellner, Y. F. Dagdas, M. N. Sarowar et al., Emerging oomycete threats to plants and animals, Philos Trans R Soc B Biol Sci, vol.371, 2016.

E. Randall, V. Young, H. Sierotzki, G. Scalliet, P. Birch et al., Sequence diversity in the large subunit of RNA polymerase I contributes to Mefenoxam insensitivity in Phytophthora infestans, Mol Plant Pathol, vol.15, pp.664-676, 2014.

U. Gisi and H. Sierotzki, Oomycete Fungicides: Phenylamides, Quinone Outside Inhibitors, and Carboxylic Acid Amides, Fungicide Resistance in Plant Pathogens, pp.145-174, 2015.

M. C. Fisher, D. A. Henk, C. J. Briggs, J. S. Brownstein, L. C. Madoff et al., Emerging fungal threats to animal, plant and ecosystem health, Nature, vol.484, pp.186-194, 2012.

G. N. Agrios, Plant pathology, 2005.

M. Pais, J. Win, K. Yoshida, G. J. Etherington, L. M. Cano et al., From pathogen genomes to host plant processes: the power of plant parasitic oomycetes, Genome Biol, vol.14, pp.211-221, 2013.

F. N. Martin, J. E. Blair, and M. D. Coffey, A combined mitochondrial and nuclear multilocus phylogeny of the genus Phytophthora, Fungal Genet Biol, vol.66, pp.19-32, 2014.

Y. Meng, Q. Zhang, W. Ding, and W. Shan, Phytophthora parasitica: a model oomycete plant pathogen, Mycology, vol.5, pp.43-51, 2014.

F. Panabières, G. S. Ali, M. B. Allagui, R. Dalio, N. C. Gudmestad et al., Phytophthora nicotianae diseases worldwide: New knowledge of a long-recognised pathogen, Phytopathol Mediterr, vol.55, pp.20-40, 2016.

A. Attard, M. Gourgues, N. Callemeyn-torre, and H. Keller, The immediate activation of defense responses in Arabidopsis roots is not sufficient to prevent Phytophthora parasitica infection, New Phytol, vol.187, pp.449-460, 2010.

A. Attard, M. Gourgues, E. Galiana, F. Panabières, M. Ponchet et al., Strategies of attack and defense in plant-oomycete interactions, accentuated for Phytophthora parasitica Dastur (syn. P. Nicotianae Breda de Haan), J Plant Physiol, vol.165, pp.83-94, 2008.

H. S. Judelson and F. A. Blanco, The spores of Phytophthora: Weapons of the plant destroyer, Nat Rev Microbiol, vol.3, pp.47-58, 2005.

C. A. Walker and P. Van-west, Zoospore development in the oomycetes, Fungal Biol Rev, vol.21, pp.10-18, 2007.

A. R. Hardham, The cell biology behind Phytophthora pathogenicity, Australas Plant Pathol, vol.30, pp.91-98, 2001.

A. R. Hardham, Cell biology of plant-oomycete interactions, Cell Microbiol, vol.9, pp.31-39, 2007.

D. C. Erwin and O. K. Ribeiro, Phytophthora diseases worldwide, 1996.

L. Berre, J. Y. Engler, G. Panabières, and F. , Exploration of the late stages of the tomato-Phytophthora parasitica interactions through histological analysis and generation of expressed sequence tags, New Phytol, vol.177, pp.480-492, 2008.

W. Shan and A. R. Hardham, Construction of a bacterial artificial chromosome library, determination of genome size, and characterization of an Hsp70 gene family in Phytophthora nicotianae, Fungal Genet Biol, vol.41, pp.369-380, 2004.

P. Parasitica and . Genome,

F. Panabieres, J. Amselem, E. Galiana, L. Berre, and J. Y. , Gene identification in the oomycete pathogen Phytophthora parasitica during in vitro vegetative growth through expressed sequence tags, Fungal Genet Biol, vol.42, pp.611-623, 2005.

D. ?kalamera, A. P. Wasson, and A. R. Hardham, Genes expressed in zoospores of Phytophthora nicotianae, Mol Genet Genomics, vol.270, pp.549-557, 2004.

N. Kebdani, L. Pieuchot, E. Deleury, F. Panabières, L. Berre et al., Cellular and molecular characterization of Phytophthora parasitica appressorium-mediated penetration, New Phytol, vol.185, pp.248-257, 2010.

A. Attard, E. Evangelisti, N. Kebdani-minet, F. Panabières, E. Deleury et al., Transcriptome dynamics of Arabidopsis thaliana root penetration by the oomycete pathogen Phytophthora parasitica, BMC Genomics, vol.15, pp.538-557, 2014.

L. Berre, J. Gourgues, M. Samans, B. Keller, H. Panabières et al., Transcriptome dynamic of Arabidopsis roots infected with Phytophthora parasitica identifies VQ29, a gene induced during the penetration and involved in the restriction of infection, PLoS One, vol.12, p.190341, 2017.

S. Kamoun, Groovy times: filamentous pathogen effectors revealed, Curr Opin Plant Biol, vol.10, pp.358-365, 2007.

S. Dong, S. Raffaele, and S. Kamoun, The two-speed genomes of filamentous pathogens: Waltz with plants, Curr Opin Genet Dev, vol.35, pp.57-65, 2015.

J. Jones and J. L. Dangl, The plant immune system, Nature, vol.444, pp.323-329, 2006.

C. Zipfel, Pattern-recognition receptors in plant innate immunity, Curr Opin Immunol, vol.20, pp.10-16, 2008.

F. Brunner, S. Rosahl, J. Lee, J. J. Rudd, C. Geiler et al., Pep-13, a plant defense-inducing pathogen-associated pattern from Phytophthora transglutaminases, EMBO J, vol.21, pp.6681-6688, 2002.

D. Nennstiel, D. Scheel, and T. Nürnberger, Characterization and partial purification of an oligopeptide elicitor receptor from parsley (Petroselium crispum), FEBS Lett, vol.431, pp.405-410, 1998.

G. Fellbrich, A. Romanski, A. Varet, B. Blume, F. Brunner et al., NPP1, a Phytophthora-associated trigger of plant defense in parsley and Arabidopsis, Plant J, vol.32, pp.375-390, 2002.

S. Wawra, R. Belmonte, L. Löbach, M. Saraiva, A. Willems et al., Secretion, delivery and function of oomycete effector proteins, Curr Opin Microbiol, vol.15, pp.685-691, 2012.

J. Stassen and G. Van-den-ackerveken, How do oomycete effectors interfere with plant life?, Curr Opin Plant Biol, vol.14, pp.407-414, 2011.

M. Ponchet, F. Panabières, M. L. Milat, V. Mikes, J. L. Montillet et al., Are elicitins cryptograms in plant-Oomycete communications?, Cell Mol Life Sci, vol.56, pp.1020-1047, 1999.

H. Osman, V. Mikes, M. L. Milat, M. Ponchet, D. Marion et al., Fatty acids bind to the fungal elicitor cryptogein and compete with sterols, FEBS Lett, vol.489, pp.55-58, 2001.

R. G. Anderson, D. Deb, K. Fedkenheuer, and J. M. Mcdowell, Recent Progress in RXLR Effector Research, Mol Plant-Microbe Interact, vol.28, pp.1063-1072, 2015.

T. Amaro, G. Thilliez, G. B. Motion, and E. Huitema, A Perspective on CRN Proteins in the Genomics Age: Evolution, Classification, Delivery and Function Revisited, Front Plant Sci, vol.8, pp.99-111, 2017.

A. P. Rehmany, Differential Recognition of Highly Divergent Downy Mildew Avirulence Gene Alleles by RPP1 Resistance Genes from Two Arabidopsis Lines, Plant Cell Online, vol.17, pp.1839-1850, 2005.

P. R. Birch, P. C. Boevink, E. M. Gilroy, I. Hein, L. Pritchard et al., Oomycete RXLR effectors: delivery, functional redundancy and durable disease resistance, Curr Opin Plant Biol, vol.11, pp.373-379, 2008.

S. Kamoun, A Catalogue of the Effector Secretome of Plant Pathogenic Oomycetes, Annu Rev Phytopathol, vol.44, pp.41-60, 2006.

J. Win, K. V. Krasileva, S. Kamoun, K. Shirasu, B. J. Staskawicz et al., Sequence divergent RXLR effectors share a structural fold conserved across plant pathogenic oomycete species, PLoS Pathog, vol.8, pp.8-11, 2012.

L. S. Boutemy, S. King, J. Win, R. K. Hughes, T. A. Clarke et al., Structures of Phytophthora RXLR effector proteins: A conserved but adaptable fold underpins functional diversity, J Biol Chem, vol.286, pp.35834-35842, 2011.

S. C. Whisson, P. C. Boevink, L. Moleleki, A. O. Avrova, J. G. Morales et al., A translocation signal for delivery of oomycete effector proteins into host plant cells, Nature, vol.450, pp.115-118, 2007.

D. Dou, S. D. Kale, X. Wang, R. Jiang, . Bruce-n-a et al., RXLR-Mediated Entry of Phytophthora sojae Effector Avr1b into Soybean Cells Does Not Require Pathogen-Encoded Machinery, Plant Cell, vol.20, pp.1930-1947, 2008.

S. Grouffaud, P. Van-west, A. O. Avrova, P. Birch, and S. C. Whisson, Plasmodium falciparum and Hyaloperonospora parasitica effector translocation motifs are functional in Phytophthora infestans, Microbiology, vol.154, pp.3743-3751, 2008.

S. D. Kale and B. M. Tyler, Entry of oomycete and fungal effectors into plant and animal host cells, Cell Microbiol, vol.13, pp.1839-1848, 2011.

T. Yaeno, H. Li, A. Chaparro-garcia, S. Schornack, S. Koshiba et al., Phosphatidylinositol monophosphate-binding interface in the oomycete RXLR effector AVR3a is required for its stability in host cells to modulate plant immunity, Proc Natl Acad Sci, vol.108, pp.14682-14687, 2011.

B. M. Tyler, S. D. Kale, Q. Wang, K. Tao, H. R. Clark et al., Microbe-independent entry of oomycete RxLR effectors and fungal RxLR-like effectors into plant and animal cells is specific and reproducible, Mol Plant-Microbe Interact, vol.26, pp.611-616, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01001070

W. Morgan and S. Kamoun, RXLR effectors of plant pathogenic oomycetes, Curr Opin Microbiol, vol.10, pp.332-338, 2007.

Q. Wang, C. Han, A. O. Ferreira, X. Yu, W. Ye et al., Transcriptional programming and functional interactions within the Phytophthora sojae RXLR effector repertoire, Plant Cell, vol.23, pp.2064-2086, 2011.

B. S. Kelley, S. J. Lee, C. Damasceno, S. Chakravarthy, B. D. Kim et al., A secreted effector protein (SNE1) from Phytophthora infestans is a broadly acting suppressor of programmed cell death, Plant J, vol.62, pp.357-366, 2010.

M. C. Caillaud, S. Piquerez, G. Fabro, J. Steinbrenner, N. Ishaque et al., Subcellular localization of the Hpa RxLR effector repertoire identifies a tonoplast-associated protein HaRxL17 that confers enhanced plant susceptibility, Plant J, vol.69, pp.252-265, 2012.

J. Sperschneider, A. Catanzariti, K. Deboer, B. Petre, D. M. Gardiner et al., LOCALIZER: subcellular localization prediction of both plant and effector proteins in the plant cell, Sci Rep, vol.7, p.44598, 2017.

H. Mclellan, P. C. Boevink, M. R. Armstrong, L. Pritchard, S. Gomez et al., An RxLR Effector from Phytophthora infestans Prevents Re-localisation of Two Plant NAC Transcription Factors from the Endoplasmic Reticulum to the Nucleus, PLoS Pathog, vol.9, p.1003670, 2013.

Y. Qiao, J. Shi, Y. Zhai, Y. Hou, and W. Ma, Phytophthora effector targets a novel component of small RNA pathway in plants to promote infection, Proc Natl Acad Sci, vol.112, pp.5850-5855, 2015.

P. C. Boevink, H. Mclellan, E. M. Gilroy, S. Naqvi, Q. He et al., Oomycetes Seek Help from the Plant: Phytophthora infestans Effectors Target Host Susceptibility Factors, Mol Plant, vol.9, pp.636-638, 2016.

T. Liu, T. Song, X. Zhang, H. Yuan, L. Su et al., Unconventionally secreted effectors of two filamentous pathogens target plant salicylate biosynthesis, Nat Commun, vol.5, pp.4686-4696, 2014.

E. Evangelisti, B. Govetto, N. Minet-kebdani, M. L. Kuhn, A. Attard et al., The Phytophthora parasitica RXLR effector Penetration-Specific Effector 1 favours Arabidopsis thaliana infection by interfering with auxin physiology, New Phytol, vol.199, pp.476-489, 2013.

X. Zheng, H. Mclellan, M. Fraiture, X. Liu, P. C. Boevink et al., Functionally Redundant RXLR Effectors from Phytophthora infestans Act at Different Steps to Suppress Early flg22-Triggered Immunity, PLoS Pathog, vol.10, pp.1004057-1004074, 2014.

S. Freytag, N. Arabatzis, K. Hahlbrock, and E. Schmelzer, Reversible cytoplasmic rearrangements precede wall apposition, hypersensitive cell death and defense-related gene activation in potato/Phytophthora infestans interactions, Planta, vol.194, pp.123-135, 1994.

D. Takemoto, D. A. Jones, and A. R. Hardham, GFP-tagging of cell components reveals the dynamics of subcellular re-organization in response to infection of Arabidopsis by oomycete pathogens, Plant J, vol.33, pp.775-792, 2003.

I. Hein, E. M. Gilroy, M. R. Armstrong, and P. Birch, The zig-zag-zig in oomycete-plant interactions, Mol Plant Pathol, vol.10, pp.547-562, 2009.

S. Koh and S. Somerville, Show and tell: cell biology of pathogen invasion, Curr Opin Plant Biol, vol.9, pp.406-413, 2006.

Y. J. Lu, S. Schornack, T. Spallek, N. Geldner, J. Chory et al., Patterns of plant subcellular responses to successful oomycete infections reveal differences in host cell reprogramming and endocytic trafficking, Cell Microbiol, vol.14, pp.682-697, 2012.

T. O. Bozkurt, K. Belhaj, Y. F. Dagdas, A. Chaparro-garcia, C. H. Wu et al., Rerouting of Plant Late Endocytic Trafficking Toward a Pathogen Interface, Traffic, vol.16, pp.204-226, 2015.

A. Chaparro-garcia, S. Schwizer, J. Sklenar, K. Yoshida, B. Petre et al., Phytophthora infestans RXLR-WY effector AVR3a associates with dynaminrelated protein 2 required for endocytosis of the plant pattern recognition receptor FLS2, PLoS One, vol.10, p.137071, 2015.

Y. Du, M. H. Mpina, P. Birch, K. Bouwmeester, and F. Govers, Phytophthora infestans RXLR effector AVR1 interacts with exocyst component Sec5 to manipulate plant immunity, Plant Physiol, vol.169, pp.1975-1990, 2015.

Y. F. Dagdas, K. Beihaj, A. Maqbool, A. Chaparro-garcia, P. Pandey et al., An effector of the irish potato famine pathogen antagonizes a host autophagy cargo receptor, Elife, vol.5, pp.1-23, 2016.

P. C. Boevink, X. Wang, H. Mclellan, Q. He, S. Naqvi et al., A Phytophthora infestans RXLR effector targets plant PP1c isoforms that promote late blight disease, Nat Commun, vol.7, pp.10311-10325, 2016.

D. J. Klionsky, Autophagy revisited: A conversation with Christian de Duve, Autophagy, vol.4, pp.740-743, 2008.

Y. Ohsumi, Historical landmarks of autophagy research, Cell Res, vol.24, pp.9-23, 2014.

K. Takeshige, M. Baba, S. Tsuboi, T. Noda, and Y. Ohsumi, Autophagy in yeast demonstrated with proteinase-deficient mutants and conditions for its induction, J Cell Biol, vol.119, pp.301-311, 1992.

M. Baba, K. Takeshige, N. Baba, and Y. Ohsumi, Ultrastructural analysis of the autophagic process in yeast: Detection of autophagosomes and their characterization, J Cell Biol, vol.124, pp.903-913, 1994.

M. Tsukada and Y. Ohsumi, Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae, FEBS Lett, vol.333, pp.169-174, 1993.

M. Thumm, R. Egner, B. Koch, M. Schlumpberger, M. Straub et al., Isolation of autophagocytosis mutants of Saccharomyces cerevisiae, FEBS Lett, vol.349, pp.275-280, 1994.

D. J. Klionsky, Autophagy: from phenomenology to molecular understanding in less than a decade, Nat Rev Mol Cell Biol, vol.8, pp.931-937, 2007.

B. Levine and D. J. Klionsky, Development by self-digestion: Molecular mechanisms and biological functions of autophagy, Dev Cell, vol.6, pp.463-477, 2004.

E. Eskelinen and P. Saftig, Autophagy: a lysosomal degradation pathway with a central role in health and disease, Biochim Biophys Acta, vol.1793, pp.664-673, 2009.

S. Üstün, A. Hafrén, and D. Hofius, Autophagy as a mediator of life and death in plants, Curr Opin Plant Biol, vol.40, pp.122-130, 2017.

A. L. Anding and E. H. Baehrecke, Cleaning House: Selective Autophagy of Organelles, Dev Cell, vol.41, pp.10-22, 2017.

M. Lynch-day and D. J. Klionsky, The Cvt pathway as a model for selective autophagy, FEBS Lett, vol.584, pp.1359-1366, 2011.

G. Zaffagnini and S. Martens, Mechanisms of Selective Autophagy, J Mol Biol, vol.428, pp.1714-1724, 2016.

S. Kwon, . Il, H. J. Cho, J. H. Jung, K. Yoshimoto et al., The Rab GTPase RabG3b functions in autophagy and contributes to tracheary element differentiation in Arabidopsis, Plant J, vol.64, pp.151-164, 2010.

A. Melendez and T. P. Neufeld, The cell biology of autophagy in metazoans: a developing story, Development, vol.135, pp.2347-2360, 2008.

M. C. Maiuri, E. Zalckvar, A. Kimchi, and G. Kroemer, Self-eating and self-killing: crosstalk between autophagy and apoptosis, Nat Rev Mol Cell Biol, vol.8, pp.741-752, 2007.

K. Suzuki and Y. Ohsumi, Molecular machinery of autophagosome formation in yeast, Saccharomyces cerevisiae, FEBS Lett, vol.581, pp.2156-2161, 2007.

J. Marion, L. Bars, R. Besse, L. Batoko, H. Satiat-jeunemaitre et al., Multiscale and Multimodal Approaches to, Study Autophagy in Model Plants. Cells, vol.7, pp.1-17, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02182310

X. F. Zheng, D. Fiorentino, J. Chen, G. R. Crabtree, and S. L. Schreiber, TOR kinase domains are required for two distinct functions, only one of which is inhibited by rapamycin, Cell, vol.82, pp.121-130, 1995.

R. Loewith and M. N. Hall, Target of rapamycin (TOR) in nutrient signaling and growth control, Genetics, vol.189, pp.1177-1201, 2011.

J. S. Stephan, Y. Yeh, V. Ramachandran, S. J. Deminoff, and P. K. Herman, The Tor and PKA signaling pathways independently target the Atg1/Atg13 protein kinase complex to control autophagy, Proc Natl Acad Sci, vol.106, pp.17049-17054, 2009.

R. Torggler, D. Papinski, and C. Kraft, Assays to Monitor Autophagy in Saccharomyces cerevisiae. Cells, vol.6, pp.1-24, 2017.

J. Farré and S. Subramani, Mechanistic insights into selective autophagy pathways: lessons from yeast, Nat Rev Mol Cell Biol, vol.17, pp.537-552, 2016.

T. Yorimitsu and D. J. Klionsky, Atg11 Links Cargo to the Vesicle-forming Machinery in the Cytoplasm to Vacuole Targeting Pathway, Mol Biol Cell, vol.16, pp.1593-1605, 2005.

M. Kijanska and M. Peter, Atg1 kinase regulates early and late steps during autophagy, Autophagy, vol.9, pp.249-251, 2013.

A. Yeasmin, T. M. Waliullah, A. Kondo, A. Kaneko, N. Koike et al., Orchestrated action of PP2A antagonizes atg13 phosphorylation and promotes autophagy after the inactivation of TORC1, PLoS One, vol.11, pp.1-20, 2016.

Y. Kamada, T. Funakoshi, T. Shintani, K. Nagano, M. Ohsumi et al., Tor-mediated induction of autophagy via an Apg1 protein kinase complex, J Cell Biol, vol.150, pp.1507-1513, 2000.

H. Cheong and D. J. Klionsky, Dual role of Atg1 in regulation of autophagy-specific PAS assembly in Saccharomyces cerevisiae, Autophagy, vol.4, pp.724-726, 2008.

K. Suzuki, T. Kirisako, Y. Kamada, N. Mizushima, T. Noda et al., The pre-autophagosomal structure organized by concerted functions of APG genes is essential for autophagosome formation, EMBO J, vol.20, pp.5971-5981, 2001.

R. E. Stanley, M. J. Ragusa, and J. H. Hurley, The beginning of the end: How scaffolds nucleate autophagosome biogenesis, Trends Cell Biol, vol.24, pp.73-81, 2014.

D. C. Rubinsztein, T. Shpilka, and Z. Elazar, Mechanisms of autophagosome biogenesis, Curr Biol, vol.22, pp.29-34, 2012.

K. Obara and Y. Ohsumi, Dynamics and function of PtdIns(3)P in autophagy, Autophagy, vol.4, pp.952-954, 2008.

A. Kihara, T. Noda, N. Ishihara, and Y. Ohsumi, Two distinct Vps34 phosphatidylinositol 3-kinase complexes function in autophagy and carboxypeptidase y sorting in Saccharomyces cerevisiae, J Cell Biol, vol.153, pp.519-530, 2001.

K. Suzuki, Y. Kubota, T. Sekito, and Y. Ohsumi, Hierarchy of Atg proteins in pre-autophagosomal structure organization, Genes to Cells, vol.12, pp.209-218, 2007.

F. Reggiori, K. A. Tucker, P. E. Stromhaug, and D. J. Klionsky, The Atg1-Atg13 Complex Regulates Atg9 and Atg23 Retrieval Transport from the Pre-Autophagosomal Structure, vol.6, pp.79-90, 2004.

D. Papinski and C. Kraft, Atg1 kinase organizes autophagosome formation by phosphorylating Atg9, Autophagy, vol.10, pp.1338-1340, 2014.

K. Sugawara, N. N. Suzuki, Y. Fujioka, N. Mizushima, Y. Ohsumi et al., The crystal structure of microtubule-associated protein light chain 3, a mammalian homologue of Saccharomyces cerevisiae Atg8, Genes to Cells, pp.611-618, 2004.

N. N. Suzuki, K. Yoshimoto, Y. Fujioka, Y. Ohsumi, and F. Inagaki, The Crystal Structure of Plant ATG12 and its Biological Implication in Autophagy, Autophagy, vol.1, pp.119-126, 2005.

N. Mizushima, T. Noda, T. Yoshimori, Y. Tanaka, T. Ishii et al., A protein conjugation system essential for autophagy, Nature, vol.395, pp.395-398, 1998.

T. Hanada, N. N. Noda, Y. Satomi, Y. Ichimura, Y. Fujioka et al., The Atg12-Atg5 Conjugate Has a Novel E3-like Activity for Protein Lipidation in Autophagy, J Biol Chem, vol.282, pp.37298-37302, 2007.

A. Kuma, N. Mizushima, N. Ishihara, and Y. Ohsumi, Formation of the approximately 350-kDa Apg12-Apg5.Apg16 multimeric complex, mediated by Apg16 oligomerization, is essential for autophagy in yeast, J Biol Chem, vol.277, pp.18619-18625, 2002.

Y. Ichimura, T. Kirisako, T. Takao, Y. Satomi, Y. Shimonishi et al., A ubiquitin-like system mediates protein lipidation, Nature, vol.408, pp.488-492, 2000.

Z. Xie, U. Nair, and D. J. Klionsky, Atg8 Controls Phagophore Expansion during Autophagosome Formation, Mol Biol Cell, vol.19, pp.3290-3298, 2008.

R. L. Knorr, H. Nakatogawa, Y. Ohsumi, R. Lipowsky, T. Baumgart et al., Membrane Morphology Is Actively Transformed by Covalent Binding of the Protein Atg8 to PE-Lipids, PLoS One, vol.9, p.115357, 2014.

N. N. Noda, Y. Ohsumi, and F. Inagaki, Atg8-family interacting motif crucial for selective autophagy, FEBS Lett, vol.584, pp.1379-1385, 2010.

Z. Yu, T. Ni, B. Hong, H. Wang, F. Jiang et al., Dual roles of Atg8?PE deconjugation by Atg4 in autophagy, Autophagy, vol.8, pp.883-892, 2012.

J. Sánchez-wandelmer, F. Kriegenburg, S. Rohringer, M. Schuschnig, R. Gómez-sánchez et al., Atg4 proteolytic activity can be inhibited by Atg1 phosphorylation, Nat Commun, vol.8, pp.1-10, 2017.

F. Reggiori and C. Ungermann, Autophagosome Maturation and Fusion, J Mol Biol, vol.429, pp.486-496, 2017.

N. Nakamura, . Matsuura-a, Y. Wada, and Y. Ohsumi, Acidification of vacuoles is required for autophagic degradation in the yeast, Saccharomyces cerevisiae, J Biochem, vol.121, pp.338-344, 1997.

Z. Yang, J. Huang, J. Geng, U. Nair, and D. J. Klionsky, Atg22 Recycles Amino Acids to Link the Degradative and Recycling Functions of Autophagy, Mol Biol Cell, vol.17, pp.5094-5104, 2006.

K. Yoshimoto, Y. Takano, and Y. Sakai, Autophagy in plants and phytopathogens, FEBS Lett, vol.584, pp.1350-1358, 2010.

A. Shemi, S. Ben-dor, and A. Vardi, Elucidating the composition and conservation of the autophagy pathway in photosynthetic eukaryotes, Autophagy, vol.11, pp.701-715, 2015.

T. Avin-wittenberg, A. Honig, and G. Galili, Variations on a theme: Plant autophagy in comparison to yeast and mammals, Protoplasma, vol.249, pp.285-299, 2012.

A. R. Thompson and R. D. Vierstra, Autophagic recycling: Lessons from yeast help define the process in plants, Curr Opin Plant Biol, vol.8, pp.165-173, 2005.

D. C. Bassham, M. Laporte, F. Marty, Y. Moriyasu, Y. Ohsumi et al., Autophagy in development and stress responses of plants, Autophagy, vol.2, pp.2-11, 2006.

R. Kellner, J. C. De-la-concepcion, A. Maqbool, S. Kamoun, and Y. F. Dagdas, ATG8 Expansion: A Driver of Selective Autophagy Diversification, Trends Plant Sci, vol.22, pp.204-214, 2017.

A. Suttangkakul, F. Li, T. Chung, and R. D. Vierstra, The ATG1/ATG13 Protein Kinase Complex Is Both a Regulator and a Target of Autophagic Recycling in Arabidopsis, Plant Cell, vol.23, pp.3761-3779, 2011.

H. Hanaoka, T. Noda, Y. Shirano, T. Kato, H. Hayashi et al., Leaf senescence and starvation-induced chlorosis are accelerated by the disruption of an Arabidopsis autophagy gene, Plant Physiol, vol.129, pp.1181-1193, 2002.

S. Patel and S. P. Dinesh-kumar, Arabidopsis ATG6 is required to limit the pathogen-associated cell death response, Autophagy, vol.4, pp.20-27, 2008.

Y. Xiong, A. L. Contento, and D. C. Bassham, AtATG18a is required for the formation of autophagosomes during nutrient stress and senescence in Arabidopsis thaliana, Plant J, vol.42, pp.535-546, 2005.

J. H. Doelling, J. M. Walker, E. M. Friedman, A. R. Thompson, and R. D. Vierstra, The APG8/12-activating enzyme APG7 is required for proper nutrient recycling and senescence in Arabidopsis thaliana, J Biol Chem, vol.277, pp.33105-33114, 2002.

K. Yoshimoto, H. Hanaoka, S. Sato, T. Kato, S. Tabata et al., Processing of ATG8s, ubiquitin-like proteins, and their deconjugation by ATG4s are essential for plant autophagy, Plant Cell, vol.16, pp.2967-2983, 2004.

A. R. Thompson, J. H. Doelling, A. Suttangkakul, and R. D. Vierstra, Autophagic Nutrient Recycling in Arabidopsis Directed by the ATG8 and ATG12 Conjugation Pathways, Plant Physiol, vol.138, pp.2097-2110, 2005.

A. R. Phillips, A. Suttangkakul, and R. D. Vierstra, The ATG12-Conjugating Enzyme ATG10 Is Essential for Autophagic Vesicle Formation in Arabidopsis thaliana, Genetics, vol.1353, pp.1339-1353, 2008.

M. Surpin, H. Zheng, M. T. Morita, C. Saito, E. Avila et al., The VTI family of SNARE proteins is cecessary for plant viability and mediates different protein transport pathways, Plant Cell, vol.15, pp.2885-2899, 2003.

G. Qin, Z. Ma, L. Zhang, S. Xing, X. Hou et al., Arabidopsis AtBECLIN 1/AtAtg6/AtVps30 is essential for pollen germination and plant development, Cell Res, vol.17, pp.249-263, 2007.

S. H. Kim, C. Kwon, J. H. Lee, and T. Chung, Genes for plant autophagy: Functions and interactions, Mol Cells, vol.34, pp.413-423, 2012.

S. Michaeli, T. Avin-wittenberg, and G. Galili, Involvement of autophagy in the direct ER to vacuole protein trafficking route in plants, Front Plant Sci, vol.5, pp.1-5, 2014.

Y. Wang, B. Yu, J. Zhao, J. Guo, Y. Li et al., Autophagy contributes to leaf starch degradation, Plant Cell, vol.25, pp.1383-1399, 2013.

A. Guiboileau, K. Yoshimoto, F. Soulay, M. P. Bataillé, J. C. Avice et al., Autophagy machinery controls nitrogen remobilization at the whole-plant level under both limiting and ample nitrate conditions in Arabidopsis, New Phytol, vol.194, pp.732-740, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01004199

S. Han, Y. Wang, X. Zheng, Q. Jia, J. Zhao et al., Cytoplastic Glyceraldehyde-3-Phosphate Dehydrogenases Interact with ATG3 to Negatively Regulate Autophagy and Immunity in Nicotiana benthamiana, Plant Cell, vol.27, pp.1-16, 2015.

S. Michaeli, A. Honig, H. Levanony, H. Peled-zehavi, and G. Galili, Arabidopsis ATG8-INTERACTING PROTEIN1 Is Involved in Autophagy-Dependent Vesicular Trafficking of Plastid Proteins to the Vacuole, Plant Cell, vol.26, pp.4084-4101, 2014.

J. Zhou, J. Wang, J. Yu, and Z. Chen, Role and regulation of autophagy in heat stress responses of tomato plants, Front Plant Sci, vol.5, pp.1-12, 2014.

J. Kim, H. Lee, H. N. Lee, S. Kim, K. D. Shin et al., Autophagy-Related Proteins Are Required for Degradation of Peroxisomes in Arabidopsis Hypocotyls during Seedling Growth, Plant Cell, vol.25, pp.4956-4966, 2013.

K. Yoshimoto, M. Shibata, M. Kondo, K. Oikawa, M. Sato et al., Organ-specific quality control of plant peroxisomes is mediated by autophagy, J Cell Sci, vol.127, pp.1161-1168, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01204043

H. Ishida, K. Yoshimoto, M. Izumi, D. Reisen, Y. Yano et al., Mobilization of Rubisco and Stroma-Localized Fluorescent Proteins of Chloroplasts to the Vacuole by an ATG Gene-Dependent Autophagic Process, Plant Physiol, vol.148, pp.142-155, 2008.

M. Izumi, S. Wada, A. Makino, and H. Ishida, The Autophagic Degradation of Chloroplasts via RubiscoContaining Bodies Is Specifically Linked to Leaf Carbon Status But Not Nitrogen Status in Arabidopsis, Plant Physiol, vol.154, pp.1196-1209, 2010.

Y. Liu, J. S. Burgos, Y. Deng, R. Srivastava, S. H. Howell et al., Degradation of the endoplasmic reticulum by autophagy during endoplasmic reticulum stress in Arabidopsis, Plant Cell, vol.24, pp.4635-4651, 2012.

Y. Pu and D. C. Bassham, Links between ER stress and autophagy in plants, Plant Signal Behav, vol.8, p.24297, 2013.

I. Kulich and V. ?árský, Autophagy-related direct membrane import from ER/Cytoplasm into the vacuole or apoplast: A hidden gateway also for secondary metabolites and phytohormones?, Int J Mol Sci, vol.15, pp.7462-7474, 2014.

L. Bars, R. , M. J. , L. Borgne, R. Satiat-jeunemaitre et al., ATG5 defines a phagophore domain connected to the endoplasmic reticulum during autophagosome formation in plants, Nat Commun, vol.5, pp.1-10, 2014.

X. Zhuang, Y. Cui, C. Gao, and L. Jiang, Endocytic and autophagic pathways crosstalk in plants, Curr Opin Plant Biol, vol.28, pp.39-47, 2015.

T. Pe?enková, V. Markovi?, P. Sabol, I. Kulich, V. ?árský et al., Exocyst and autophagyrelated membrane trafficking in plants, J Exp Bot, vol.69, pp.1-11, 2017.

X. Yang and D. C. Bassham, New Insight into the Mechanism and Function of Autophagy in Plant Cells, Int Rev Cell Mol Biol, vol.320, pp.1-40, 2015.

G. Estrada-navarrete, N. Cruz-mireles, R. Lascano, X. Alvarado-affantranger, A. Hernàndez et al., An autophagy-related kinase is essential for the symbiotic relationship between Phaseolus vulgaris and both rhizobia and arbuscular mycorrhizal fungi, Plant Cell, vol.28, pp.2326-2341, 2016.

H. D. Lenz, E. Haller, E. Melzer, K. Kober, K. Wurster et al., Autophagy differentially controls plant basal immunity to biotrophic and necrotrophic pathogens, Plant J, vol.66, pp.818-830, 2011.

Z. Lai, F. Wang, Z. Zheng, B. Fan, and Z. Chen, A critical role of autophagy in plant resistance to necrotrophic fungal pathogens, Plant J, vol.66, pp.953-968, 2011.

Y. Liu, M. Schiff, K. Czymmek, Z. Tallóczy, B. Levine et al., Autophagy regulates programmed cell death during the plant innate immune response, Cell, vol.121, pp.567-577, 2005.

S. Kwon, . Il, H. J. Cho, S. R. Kim, and O. K. Park, The Rab GTPase RabG3b Positively Regulates Autophagy and Immunity-Associated Hypersensitive Cell Death in Arabidopsis, Plant Physiol, vol.161, pp.1722-1736, 2013.

D. Hofius, T. Schultz-larsen, J. Joensen, D. I. Tsitsigiannis, N. Petersen et al., Autophagic Components Contribute to Hypersensitive Cell Death in Arabidopsis, Cell, vol.137, pp.773-783, 2009.

J. Wang, C. Ma, M. Zhang, L. Yang, and W. Chen, ATG5 is required to limit cell death induced by Pseudomonas syringae in Arabidopsis and may be mediated by the salicylic acid pathway, Acta Physiol Plant, vol.37, pp.1-11, 2015.

Y. Wang, M. T. Nishimura, T. Zhao, and D. Tang, ATG2, an autophagy-related protein, negatively affects powdery mildew resistance and mildew-induced cell death in Arabidopsis, Plant J, vol.68, pp.74-87, 2011.

E. Häffner, S. Konietzki, and E. Diederichsen, Keeping Control: The Role of Senescence and Development in Plant Pathogenesis and Defense, Plants, vol.4, pp.449-488, 2015.

K. Yoshimoto, Y. Jikumaru, Y. Kamiya, M. Kusano, C. Consonni et al., Autophagy Negatively Regulates Cell Death by Controlling NPR1-Dependent Salicylic Acid Signaling during Senescence and the Innate Immune Response in Arabidopsis, Plant Cell, vol.21, pp.2914-2927, 2009.

M. Kabbage, B. Williams, and M. B. Dickman, Cell Death Control: The Interplay of Apoptosis and Autophagy in the Pathogenicity of Sclerotinia sclerotiorum, PLoS Pathog, vol.9, p.1003287, 2013.

C. Popa, L. Li, S. Gil, L. Tatjer, K. Hashii et al., The effector AWR5 from the plant pathogen Ralstonia solanacearum is an inhibitor of the TOR signalling pathway, Sci Rep, vol.6, pp.1-14, 2016.

S. Üstün, A. Hafrén, Q. Liu, R. S. Marshall, E. A. Minina et al., Bacteria exploit autophagy for proteasome degradation and enhanced virulence in plants, Plant Cell, vol.30, pp.668-685, 2018.

Y. F. Dagdas, P. Pandey, Y. Tumtas, N. Sanguankiattichai, K. Belhaj et al., Host autophagy machinery is diverted to the pathogen interface to mediate focal defense responses against the Irish potato famine pathogen, p.37476, 2018.

A. Hafrén, J. Macia, A. J. Love, J. J. Milner, M. Drucker et al., Selective autophagy limits cauliflower mosaic virus infection by NBR1-mediated targeting of viral capsid protein and particles, Proc Natl Acad Sci, vol.114, pp.2026-2035, 2017.

J. Jupe, R. Stam, A. Howden, J. A. Morris, R. Zhang et al., Phytophthora capsicitomato interaction features dramatic shifts in gene expression associated with a hemi-biotrophic lifestyle, Genome Biol, vol.14, pp.1-18, 2013.

E. A. Alemu, T. Lamark, K. M. Torgersen, A. B. Birgisdottir, K. B. Larsen et al., ATG8 family proteins act as scaffolds for assembly of the ULK complex: Sequence requirements for LC3-interacting region (LIR) motifs, J Biol Chem, vol.287, pp.39275-39290, 2012.

I. Kalvari, S. Tsompanis, N. C. Mulakkal, R. Osgood, T. Johansen et al., Promponas VJ (2014) iLIR: A web resource for prediction of Atg8-family interacting proteins, Autophagy, vol.10, pp.913-925

A. Jacomin, S. Samavedam, V. Promponas, and I. P. Nezis, iLIR database: A web resource for LIR motifcontaining proteins in eukaryotes, Autophagy, vol.12, pp.1945-1953, 2016.

P. Krenek, O. Samajova, I. Luptovciak, A. Doskocilova, G. Komis et al., Transient plant transformation mediated by Agrobacterium tumefaciens: Principles, methods and applications, Biotechnol Adv, vol.33, pp.1024-1042, 2015.

E. Seo, J. Woo, E. Park, S. J. Bertolani, J. B. Siegel et al., Comparative analyses of ubiquitin-like ATG8 and cysteine protease ATG4 autophagy genes in the plant lineage and crosskingdom processing of ATG8 by ATG4, Autophagy, vol.12, pp.2054-2068, 2016.

T. L. Rose, L. Bonneau, C. Der, D. Marty-mazars, and M. F. , Starvation-induced expression of autophagy-related genes in Arabidopsis, Biol Cell, vol.98, pp.53-67, 2006.

S. Slavikova, S. Ufaz, T. Avin-wittenberg, H. Levanony, and G. Galili, An autophagy-associated Atg8 protein is involved in the responses of Arabidopsis seedlings to hormonal controls and abiotic stresses, J Exp Bot, vol.59, pp.4029-4043, 2008.

C. Grefen, P. Obrdlik, and K. Harter, The determination of protein-protein interactions by the matingbased split-ubiquitin system (mbSUS), Methods Mol Biol, vol.479, pp.217-233, 2009.

E. H. Harris, D. B. Stern, and G. B. Witman, The Genus Chlamydomonas, The Chlamydomonas Sourcebook, 2009.

S. S. Merchant, S. E. Prochnik, O. Vallon, E. H. Harris, S. J. Karpowicz et al., The Chlamydomonas genome reveals the evolution of key animal and plant functions, Science, vol.318, pp.245-250, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00188075

Q. Jiang, L. Zhao, J. Dai, and Q. Wu, Analysis of autophagy genes in microalgae: Chlorella as a potential model to study mechanism of autophagy, PLoS One, vol.7, p.41826, 2012.

M. E. Pérez-pérez and J. L. Crespo, Autophagy in the model alga Chlamydomonas reinhardtii, Autophagy, vol.6, pp.562-563, 2010.

M. E. Pérez-pérez, F. J. Florencio, and J. L. Crespo, Inhibition of target of rapamycin signaling and stress activate autophagy in Chlamydomonas reinhardtii, Plant Physiol, vol.152, pp.1874-1888, 2010.

J. Crespo, S. Díaz-troya, and F. Florencio, Inhibition of target of rapamycin signaling by rapamycin in the unicellular green alga Chlamydomonas reinhardtii, Plant Physiol, vol.139, pp.1736-1749, 2005.

M. E. Pérez-pérez, I. Couso, L. G. Heredia-martínez, and J. L. Crespo, Monitoring Autophagy in the Model Green Microalga Chlamydomonas reinhardtii. Cells, vol.6, pp.1-11, 2017.

J. Neupert, D. Karcher, and R. Bock, Generation of Chlamydomonas strains that efficiently express nuclear transgenes, Plant J, vol.57, pp.1140-1150, 2009.

R. Barahimipour, D. Strenkert, J. Neupert, M. Schroda, S. S. Merchant et al., Dissecting the contributions of GC content and codon usage to gene expression in the model alga Chlamydomonas reinhardtii, Plant J, vol.84, pp.704-717, 2015.

V. Lumbreras, D. R. Stevens, and S. Purton, Efficient foreign gene expression in Chlamydomonas reinhardtii mediated by an endogenous intron, Plant J, vol.14, pp.441-447, 1998.

F. R. Cross and J. G. Umen, The Chlamydomonas cell cycle, Plant J, vol.82, pp.370-392, 2015.

J. M. Zones, I. K. Blaby, S. S. Merchant, and J. G. Umen, High-Resolution Profiling of a Synchronized Diurnal Transcriptome from Chlamydomonas reinhardtii Reveals Continuous Cell and Metabolic Differentiation, Plant Cell, vol.27, pp.2743-2769, 2015.

A. B. Lyons, Analysing cell division in vivo and in vitro using flow cytometric measurement of CFSE dye dilution, J Immunol Methods, vol.243, pp.147-154, 2000.

C. Rioboo, J. E. O'connor, R. Prado, C. Herrero, and A. Cid, Cell proliferation alterations in Chlorella cells under stress conditions, Aquat Toxicol, vol.94, pp.229-237, 2009.

M. Schroda, D. Blöcker, and C. F. Beck, The HSP70A promoter as a tool for the improved expression of transgenes in Chlamydomonas, Plant J, vol.21, pp.121-131, 2000.

I. Couso and J. L. Crespo, The TOR Signaling Network in the Model Unicellular Green Alga Chlamydomonas reinhardtii, Biomolecules, vol.7, pp.1-13, 2017.

J. Jüppner, U. Mubeen, A. Leisse, C. Caldana, A. Wiszniewski et al., The target of rapamycin kinase affects biomass accumulation and cell cycle progression by altering carbon/nitrogen balance in synchronized Chlamydomonas reinhardtii cells, Plant J, vol.93, pp.355-376, 2018.

P. Ylä-anttila, H. Vihinen, E. Jokitalo, and E. Eskelinen, Monitoring Autophagy by Electron Microscopy in Mammalian Cells, Methods in Enzymology, pp.143-164, 2009.

H. Park, L. L. Eggink, R. W. Roberson, and J. K. Hoober, Transfer of proteins from the chloroplast to vacuoles in Chlamydomonas reinhardtii (Chlorophyta): a pathway for degradation, Plant Biol, vol.538, pp.528-538, 1999.

A. Shebanova, T. Ismagulova, A. Solovchenko, O. Baulina, E. Lobakova et al., Versatility of the green microalga cell vacuole function as revealed by analytical transmission electron microscopy, Protoplasma, vol.254, pp.1323-1340, 2017.

I. Couso, M. E. Pérez-pérez, E. Martínez-force, H. Kim, Y. He et al., Autophagic flux is required for the synthesis of triacylglycerols and ribosomal protein turnover in Chlamydomonas, J Exp Bot, vol.69, pp.1-13, 2017.

F. Wattebled, A. Buléon, B. Bouchet, J. Ral, L. Liénard et al., Granule-bound starch synthase I. A major enzyme involved in the biogenesis of B-crystallites in starch granules, Eur J Biochem, vol.269, pp.3810-3820, 2002.
URL : https://hal.archives-ouvertes.fr/hal-00085534

T. Caspar, S. C. Huber, and C. Somerville, Alterations in Growth, Photosynthesis, and Respiration in a Starchless Mutant of Arabidopsis thaliana (L.) Deficient in Chloroplast Phosphoglucomutase Activity, Plant Physiol, vol.79, pp.11-17, 1985.

K. M. Koo, S. Jung, B. S. Lee, J. Kim, Y. D. Jo et al., The Mechanism of Starch Over-Accumulation in Chlamydomonas reinhardtii High-Starch Mutants Identified by, Comparative Transcriptome Analysis. Front Microbiol, vol.8, pp.1-12, 2017.

C. Edner, J. Li, T. Albrecht, S. Mahlow, M. Hejazi et al., Glucan, water dikinase activity stimulates breakdown of starch granules by plastidial betaamylases, Plant Physiol, vol.145, pp.17-28, 2007.

Y. Cao and D. J. Klionsky, Physiological functions of Atg6/Beclin 1: a unique autophagy-related protein, Cell Res, vol.17, pp.839-849, 2007.

N. Ishihara, M. Hamasaki, S. Yokota, K. Suzuki, Y. Kamada et al., Autophagosome requires specific early Sec proteins for its formation and NSF/SNARE for vacuolar fusion, Mol Biol Cell, vol.12, pp.3690-3702, 2001.

D. J. Klionsky, K. Abdelmohsen, A. Abe, M. J. Abedin, H. Abeliovich et al., Guidelines for the use and interpretation of assays for monitoring autophagy, Autophagy, vol.12, pp.1-122, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01396896

H. Z. Yan and R. F. Liou, Selection of internal control genes for real-time quantitative RT-PCR assays in the oomycete plant pathogen Phytophthora parasitica, Fungal Genet Biol, vol.43, pp.430-438, 2006.

B. Thomma, K. Eggermont, I. Penninckx, B. Mauch-mani, R. Vogelsang et al., Separate jasmonate-dependent and salicylate-dependent defense-response pathways in Arabidopsis are essential for resistance to distinct microbial pathogens, Proc Natl Acad Sci, vol.95, pp.15107-15111, 1998.

A. Fong, A. V. Judelson, and H. S. , Cell cycle regulator Cdc14 is expressed during sporulation but not hyphal growth in the fungus-like oomycete Phytophthora infestans, Mol Microbiol, vol.50, pp.487-494, 2003.

N. Mizushima, T. Yoshimori, and B. Levine, Mammalian Autophagy Research. Cell, vol.140, pp.313-326, 2010.

M. Mauthe, I. Orhon, C. Rocchi, X. Zhou, M. Luhr et al., Chloroquine inhibits autophagic flux by decreasing autophagosome-lysosome fusion, Autophagy, vol.14, pp.1435-1455, 2018.

E. Park, A. Nedo, J. L. Caplan, and S. P. Dinesh-kumar, Plant-microbe interactions: Organelles and the cytoskeleton in action, New Phytol, vol.217, pp.1012-1028, 2017.

S. V. Kumar, R. W. Misquitta, V. S. Reddy, B. J. Rao, and M. V. Rajam, Genetic transformation of the green alga--Chlamydomonas reinhardtii by Agrobacterium tumefaciens, Plant Sci, vol.166, pp.731-738, 2004.

B. Menand, T. Desnos, L. Nussaume, F. Berger, D. Bouchez et al., Expression and disruption of the Arabidopsis TOR (target of rapamycin) gene, Proc Natl Acad Sci, vol.99, pp.6422-6427, 2002.
URL : https://hal.archives-ouvertes.fr/hal-02143297

H. Cheong, U. Nair, J. Geng, and D. J. Klionsky, The Atg1 kinase complex is involved in the regulation of protein recruitment to initiate sequestering vesicle formation for nonspecific autophagy in Saccharomyces cerevisiae, Mol Biol Cell, vol.19, pp.668-681, 2008.

D. Ramirez-garcés, L. Camborde, M. Pel, A. Jauneau, Y. Martinez et al., CRN13 candidate effectors from plant and animal eukaryotic pathogens are DNAbinding proteins which trigger host DNA damage response, New Phytol, vol.210, pp.602-617, 2016.

K. C. Yang, P. Sathiyaseelan, C. Ho, and S. M. Gorski, Evolution of tools and methods for monitoring autophagic flux in mammalian cells, Biochem Soc Trans, vol.46, pp.1-14, 2018.

K. C. Kasuba, S. L. Vavilala, D. Souza, and J. S. , Apoptosis-like cell death in unicellular photosynthetic organisms -A review, Algal Res, vol.12, pp.126-133, 2015.

M. Schaaf, T. G. Keulers, M. A. Vooijs, and K. Rouschop, LC3/GABARAP family proteins: autophagy-(un)related functions, FASEB J, vol.30, pp.3961-3978, 2016.

T. N. Nguyen, B. S. Padman, J. Usher, V. Oorschot, G. Ramm et al., Atg8 family LC3 / GAB ARAP proteins are crucial for autophagosome -lysosome fusion but not autophagosome formation during PINK1 / Parkin mitophagy and starvation, J Cell Biol, vol.215, pp.1-18, 2016.

P. N. Dodds and J. P. Rathjen, Plant immunity: towards an integrated view of plant-pathogen interactions, Nat Rev Genet, vol.11, pp.539-548, 2010.

S. Patel, J. Caplan, and S. Dinesh-kumar, Autophagy in the control of programmed cell death, Curr Opin Plant Biol, vol.9, pp.391-396, 2006.

A. S. Zvereva, V. Golyaev, S. Turco, E. G. Gubaeva, R. Rajeswaran et al., Viral protein suppresses oxidative burst and salicylic acid-dependent autophagy and facilitates bacterial growth on virus-infected plants, New Phytol, vol.211, pp.1020-1034, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01378379

S. Svenning, T. Lamark, K. Krause, and T. Johansen, Plant NBR1 is a selective autophagy substrate and a functional hybrid of the mammalian autophagic adapters NBR1 and p62/SQSTM1, Autophagy, vol.7, pp.993-1010, 2011.

M. Duszenko, M. L. Ginger, A. Brennand, M. Gualdrón-lópez, M. I. Colombo et al., Autophagy in protists. Autophagy, vol.7, pp.127-158, 2011.

N. Mizushima, A. Yamamoto, M. Hatano, Y. Kobayashi, Y. Kabey et al., Dissection of autophagosome formation using Apg5-deficient mouse embryonic stem cells, J Cell Biol, vol.152, pp.657-667, 2001.

E. Park, J. Woo, and S. P. Dinesh-kumar, Arabidopsis ATG4 cysteine proteases specificity toward ATG8 substrates, Autophagy, vol.10, pp.926-927, 2014.

J. L. Upson, E. K. Zess, A. Bia?as, C. Wu, . Hang et al., The coming of age of EvoMPMI: evolutionary molecular plant-microbe interactions across multiple timescales, Curr Opin Plant Biol, vol.44, pp.108-116, 2018.

M. Gouy, S. Guindon, and O. Gascuel, SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building, Mol Biol Evol, vol.27, pp.221-224, 2010.
URL : https://hal.archives-ouvertes.fr/lirmm-00511794

S. Kumar, G. Stecher, and K. Tamura, MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets, Mol Biol Evol, vol.33, pp.1870-1874, 2016.

M. Laroche-raynal, L. Aspart, M. Delseny, and P. Penon, Characterization of radish mRNA at three developmental stages, Plant Sci Lett, vol.35, pp.139-146, 1984.

S. J. Clough and A. F. Bent, Floral dip: A simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana, Plant J, vol.16, pp.735-743, 1998.

E. Galiana, M. P. Rivière, S. Pagnotta, E. Baudouin, F. Panabières et al., Plant-induced cell death in the oomycete pathogen Phytophthora parasitica, Cell Microbiol, vol.7, pp.1365-1378, 2005.

F. Kong, Y. Liang, B. Légeret, A. Beyly-adriano, S. Blangy et al., Chlamydomonas carries out fatty acid ?-oxidation in ancestral peroxisomes using a bona fide acyl-CoA oxidase, Plant J, vol.90, pp.358-371, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01692495

K. Futamura, M. Sekino, A. Hata, R. Ikebuchi, Y. Nakanishi et al., Novel full-spectral flow cytometry with multiple spectrally-adjacent fluorescent proteins and fluorochromes and visualization of in vivo cellular movement, Cytom Part A, vol.87, pp.830-842, 2015.

, Supplementary Figure 2: Accumulation of electron-dense, lysosome-like structures in cells from Avh195-expressing Chlamydomonas lines that were not treated with rapamycin

, High resolution TEM micrographs were recorded at different time points after onset of light over a24h-day/night cycle. Appearance of the vesicle likely reflects basal autophagic flux within the cells. Bars represent 1 µm