From metagenome to gene : Identification of the first Synchytrium endobioticum effector through comparative genomics
Notice bibliographique
Résumé
Plant pathogens can have great social and economic impact, and are a continuous threat to food security. This is clearly the case for Synchytrium endobioticum, the species causing potato wart disease. S. endobioticum is an obligate biotrophic fungus of the phylum Chytridiomycota (chytrids), which is a basal lineage in the fungal kingdom. The lack of chemical control agents, the impact of the pathogen (complete loss of tuber yields from infected field have been reported), and the production of resting spores that remain viable and infectious in infested soils for decades, led to a quarantine status for S. endobioticum in most countries world-wide. Potato wart disease has been reported from all continents where potato is cultivated, and strict phytosanitary control measures are enforced to prevent the introduction and spread of the pathogen. The use of resistant potato varieties has proven successful in achieving these goals. In chapter 1, over a century of potato wart research is reviewed to place our current knowledge in historic perspective. Observations from light microscopy and electron microscopy studies of S. endobioticum performed in the twentieth century are combined with recent molecular studies. Based on our current knowledge on molecular plant-pathogen interactions, a model is presented to describe the interaction between S. endobioticum and its host in particular with respect to plant resistance. Chapter 2 describes the independent sequencing, assembly and functionally annotation of two S. endobioticum genomes. A comparative genomics approach, in which knowledge acquired from other fungal taxa is exploited, is used to gain insights into genomic features underlying the obligate biotrophic and pathogenic lifestyle of the pathogen. Our study underlines the high diversity in chytrids compared to the well-studied Ascomycota and Basidiomycota, and reflects biological differences between the phyla. Moreover, it highlights the surprising commonalities between plant pathogenic fungi that are so evolutionary distinct. In chapter 3, the within-species diversity is determined using mitochondrial genomes, and four major mitochondrial lineages are identified. Furthermore, mitochondrial genomic variation shows that S. endobioticum has likely been introduced into Europe multiple times, and that several pathotypes emerged multiple times. We also demonstrate that isolates represent communities of different genotypes, and that the use of semi-resistant potato cultivars triggers a rapid shift in the mitochondrial haplotype. This shift is associated with 266 increased virulence and is likely the result of disruptive selection in the community. Our analysis reveals diversity of S. endobioticum isolates, which is undetected with the currently used bioassays. In chapter 4, by means of an alternative “aboveground” bioassay, it is demonstrated that potato resistance genes are expressed in green aboveground plant organs similar to etiolated “belowground” sprouts. As potato wart resistance is active in both belowground and aboveground organs, the alternative bioassay can potentially speed up screening for S. endobioticum resistance in potato breeding programs as it omits the requirement for tuber formation. In addition, possibilities arise to express S. endobioticum effectors in potato leaves through agroinfiltration, thereby providing additional phenotyping tools for research and breeding. Chapter 5 describes the identification of the S. endobioticum effector AvrSen1, which represents the first effector gene identified in Chytridiomycota. A single dominant gene (Sen1) governs pathotype 1(D1) resistance and we hypothesized that the underlying molecular model would involve a pathogen effector (AvrSen1) that is recognized by the host. Expression of AvrSen1 in Sen1 plants showed a hypersensitive response which co-segregated with Sen1 in potato populations. In non-pathotypes 1(D1) isolates, five different variants resulting in the loss of recognition by the plant were observed suggesting that AvrSen1 is under strong selective pressure. Chapter 6 is a summarizing discussion in which the chapters are integrated, and several aspects linked to pathogenicity and pathotype diversity are further discussed. The impact of the research described in chapters 2 to 5 is specified. Finally, opportunities and challenges for future research on S. endobioticum are presented with a central role for an improved Avr-R gene based pathotyping system, which will contribute to the improvement of durable potato wart resistance breeding and phytosanitary control.
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Comment cette classification a été obtenuedéplier
Prédiction distillée sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Apprise à partir de 10 348 étiquettes directes de Codex et de 10 348 étiquettes directes de Gemma. Le mode candidate est l'union des têtes enseignantes seuillées; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont ni des étiquettes humaines ni des étiquettes directes de modèles de pointe.
Scores Codex et Gemma par catégorie
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,000 | 0,000 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,000 |
| Bibliométrie | 0,000 | 0,000 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,000 | 0,000 |
| Science ouverte | 0,001 | 0,000 |
| Intégrité de la recherche | 0,000 | 0,000 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,000 | 0,000 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule tête enseignante, pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».