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Este artículo contiene 11 páginas, 6 figuras., Background: Interactions between pathogenic oomycetes and microbiota residing on the surface of the host plant root are unknown, despite being critical to inoculum constitution. The nature of these interactions was explored for the polyphagous and telluric species Phytophthora parasitica. Results: Composition of the rhizospheric microbiota of Solanum lycopersicum was characterized using deep re-sequencing of 16S rRNA gene to analyze tomato roots either free of or partly covered with P. parasitica biofilm. Colonization of the host root surface by the oomycete was associated with a shift in microbial community involving a Bacteroidetes/Proteobacteria transition and Flavobacteriaceae as the most abundant family. Identification of members of the P. parasitica-associated microbiota interfering with biology and oomycete infection was carried out by screening for bacteria able to (i) grow on a P. parasitica extract-based medium (ii), exhibit in vitro probiotic or antibiotic activity towards the oomycete (iii), have an impact on the oomycete infection cycle in a tripartite interaction S. lycopersicum-P. parasitica-bacteria. One Pseudomonas phylotype was found to exacerbate disease symptoms in tomato plants. The lack of significant gene expression response of P. parasitica effectors to Pseudomonas suggested that the increase in plant susceptibility was not associated with an increase in virulence. Our results reveal that Pseudomonas spp. establishes commensal interactions with the oomycete. Bacteria preferentially colonize the surface of the biofilm rather than the roots, so that they can infect plant cells without any apparent infection of P. parasitica. Conclusions: The presence of the pathogenic oomycete P. parasitica in the tomato rhizosphere leads to a shift in the rhizospheric microbiota composition. It contributes to the habitat extension of Pseudomonas species mediated through a physical association between the oomycete and the bacteria., This work was supported by a 3-year grant to Marie Larousse funded by INRA and the PACA region (France), and by a 1-year ATER position funded by the University of Nice Sophia Antipolis. Ferran Palero acknowledges a post-doctoral contract funded by the Beatriu de Pinos Programme of the Generalitat de Catalunya.

Outdoor field measurements of bioaerosols are performed within a wide range of basic and applied scientific disciplines, each with its own goals, assumptions, and terminology. This article contains brief reviews of outdoor field bioaerosol research from these diverse interests, with emphasis on perspectives from the atmospheric sciences. The focus is on a high-level discussion of pressing scientific questions, grand challenges, and needs for cross-disciplinary collaboration. The research topics, in which bioaerosol field measurement is important, include (i) atmospheric physics, clouds, climate, and hydrological cycle; (ii) atmospheric chemistry; (iii) airborne allergen-containing particles; (iv) airborne human pathogens and national security; (v) airborne livestock and crop pathogens; and (vi) biogeography and biodiversity. We concisely review bioaerosol impacts and discuss properties that distinguish bioaerosols from abiological aerosols. We give extra focus to regions of specific interest, i.e., forests, polar regions, marine and coastal environments, deserts, urban and rural areas, and summarize key considerations related to bioaerosol measurements, such as of fluxes, of long-range transport, and of sampling from both stationary and vessel-driven platforms. Keeping in mind a series of key scientific questions posed within the diverse communities, we suggest that pressing scientific questions include the following: (i) emission sources and flux estimates; (ii) spatial distribution; (iii) changes in distribution; (iv) atmospheric aging; (v) metabolic activity; (vi) urbanization of allergies; (vii) transport of human pathogens; and (viii) climate-relevant properties.

International audience; In this study, we looked for genetic factors in the pepper (Capsicum annuum) germplasm that control the number of potato virus Y (PVY) particles entering the plant (i.e. effective population size at inoculation) and the PVY accumulation at the systemic level (i.e. census population size). Using genotyping-by-sequencing (GBS) in a core collection of 256 pepper accessions, we obtained 10 307 single nucleotide polymorphisms (SNPs) covering the whole genome. Genome-wide association studies (GWAS) detected seven SNPs significantly associated with the virus population size at inoculation and/or systemic level on chromosomes 4, 6, 9 and 12. Two SNPs on chromosome 4 associated with both PVY population sizes map closely to the major resistance gene pvr2 encoding the eukaryotic initiation factor 4E. No obvious candidates for resistance were identified in the confidence intervals for the other chromosomes. SNPs detected on chromosomes 6 and 12 colocalized with resistance quantitative trait loci (QTLs) previously identified with a biparental population. These results show the efficiency of GBS and GWAS in C. annuum, indicate highly consistent results between GWAS and classical QTL mapping, and suggest that resistance QTLs identified with a biparental population are representative of a much larger collection of pepper accessions. Moreover, the resistance alleles at these different loci were more frequently combined than expected by chance in the core collection, indicating widespread pyramiding of resistance QTLs and widespread combination of resistance QTLs and major effect genes. Such pyramiding may increase resistance efficiency and/or durability.

Évaluation du risque simplifiée du tomato brown rugose fruit virus pour la France métropolitaine. Avis de l'Anses. Rapport d'expertise collective

Translation initiation factors 4E (eIF4E) are the main source of resistance to potyvirus. We systematically assessed tomato single and double knock-out (KO) mutants of members of the eIF4E-coding gene family for resistance to Pepper veinal mottle virus (PVMV), a major constraint to tomato production. We show that the KO mutant of eIF4E2 has partial resistance to PVMV isolate IC, with plants harboring weak symptoms and low virus loads at the systemic level. The causal effect of eIF4E2 loss-of-function on resistance was confirmed on a progeny segregating for the KO mutation. The eIF4E2 KO mutant was resistant to six of the eight PVMV isolates tested and no resistance to other potyviruses was observed. This is the first evidence that mutation of eIF4E2 is in itself conferring resistance to a potyvirus and 3D protein modelling suggests that the eIF4E2 gene could be converted into a functional resistance allele.

Background: Pseudomonas syringae is a very heterogeneous bacterial species, inhabiting various ecological niches, affecting numerous host plants and representing great phylogenetic diversity. In 2013, a leaf spot disease of sugar beet caused by P. syringae was detected for a first time in Serbia.Objectives: We aimed to determine the phylogenetic diversity of isolates from sugar beet and the potential host range in order to define status of isolates within P. syringae species complex and estimate the pathogenic diversity.Methods: Twenty representatives among 104 collected P. syringae isolates from commercial fields of sugar beet were tested. Sequencing of cts gene, sequence analysis by the Neighbor-joining method and comparison with 59 P. syringae strains from 13 phylogenetic groups was performed for all tested isolates. The host range was determined by leaf inoculation of 16 different plant species in controlled greenhouse conditions. The virulence and aggressiveness of tested isolates were measured.Results: Phylogenetic analysis showed that all tested P. syringae isolates from sugar beet belong to the 02b phylogroup within the P. syringae species complex, representing one of the most abundant P. syringae phylogroups in the environment. Host range tests revealed extremely aggressive isolates causing symptoms on every tested plant (70% of tested isolates) as well as weakly aggressive isolates (30% of tested isolates). These findings provide the first insight to status of collected isolates from Serbian sugar beet fields within P. syringae metapopulation and provide information about potential risk to other crops.

Background: Yearly, France produces more than 20000 tons of garlic representing 3500 producersand 3000 ha. Since the mid-2000s and in spite of high demanding production specifications, aphytopathogenic fungus belonging to genus Fusarium, causes damage during storage leading to rootand bulb rots. The annual losses have a major impact on the viability of the French industry.Objectives: Two major objectives were to :• Elucidate the etiology of the disease on garlic• Develop a test to evaluate the aggressiveness of strainsMethods: Strains were isolated from the two major French production areas (South West and SouthEast) during the 2017 and 2018 production campaigns. Eleven garlic varieties on more than 90 plotswere used. All tested cloves were surface-sterilized with NaOCl and fungi were allowed to develop onPDA.To evaluate aggressiveness of each strain, twelve surface-sterilized cloves soaked in 1.0*106spores/mL were used. All cloves were placed separately at 23°C at saturated humidity for 18 days.Symptoms were noted with rating scale from 0 (absence of symptoms) to 5 (clove entirely brown).Every 2 days, Area Under the Disease Progress Curve was calculated for each clove.Results: In total, 1580 strains were successfully isolated, 262 identified (98% F. proliferatum and 2%F. oxysporum) and 48 tested for their aggressiveness. All varieties seemed to be infected equally,some plots more than the others. All tested strains shows aggressiveness on garlic, from 60 to 140%as compared to a reference strain.

Cucumber vein yellowing virus (CVYV) is emerging throughout the Mediterranean Basin, where it causes important damages on cucumber and melon crops. It has been suggested that CVYV originated from the Middle East and has spread only recently to other areas. In this work, an isolate from Sudan was characterized and surveys performed in that country between 1992 and 2012 revealed a long‐term presence of CVYV with a high molecular variability, showing that the virus has long been endemic in Sub‐Saharan Africa. Comparison of the full‐length sequences of 11 CVYV isolates from different geographic origins revealed recombination events in CVYV populations from the Mediterranean Basin and the Middle East, and evidence for different selection pressures along the genome. These results shed a new light on the evolution of CVYV.

Previous studies have shown that rosemary (Rosmarinus officinalis L.) can serve as a companion plant to control Myzus persicae (Sulzer) because of the repellent effect of certain volatile organic compounds (VOCs) that it emits. In the present study, we investigated which of five clones of rosemary may reveal a repellent effect on M. persicae and aimed to determine the possible VOCs involved. Analyses of the mixtures of VOCs released by the different clones revealed the presence of 15 main components. However, each clone was characterized by a specific volatile profile showing the existence of marked chemical variability. By testing the identified VOCs individually, using a dual‐choice olfactometer, we observed that five volatiles had a significant repulsive effect on M. persicae: bornyl acetate, camphor, α‐terpineol, terpinene‐4‐ol and geranyl acetone. In addition, only one clone of rosemary elicited a significant repulsive action. Nevertheless, all of the tested clones released compounds that are repellent to the aphid when tested individually. Therefore, the emission of individual volatiles by a rosemary plant is not sufficient to elicit a repellent effect. The concentration, proportion and even the association/synergy of VOCs in the released olfactory bouquets can probably explain these contrasting results and are worthy of additional exploration in future studies.

Cucurbits are widely grown vegetables in different provinces of Turkey. However their production is restricted by pests and pathogens including different plant viruses, among which Zucchini yellow mosaic virus (ZYMV) is particularly damaging. Infections by this virus during the early stages of plant development causes deformation of fruits and significant yield losses. During 2009-2014, 221 cucurbits samples were collected from fields and greenhouses from different provinces of Turkey. Serological testing was performed by double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) for presence of Watermelon mosaic virus (WMV), ZYMV, Cucumber mosaic virus (CMV), Papaya ring spot virus (PRSV), cucumber green mottle mosaic virus (CGMMV) and Squash mosaic virus (SqMV). For molecular analaysis of ZYMV, full-length CP nucleotide sequences were obtained for 45 ZYMV isolates and compared with sequences from worldwide isolates available in databases. The CP coding regions of Turkish ZYMV were 837 nt long and encoded 279 amino acids (aa). Forty two isolates from different regions were classified in the molecular subgroup Al, the most frequent in the Mediterranean Basin, Europe and Africa. Three isolates collected from Antalya region were classified in subgroup A4 and showed 99 % sequence identity with isolates from the same subgroup that have emerged recently in France.

Chancre de l’abricotier : diversité bactérienne en verger

Strategies to manage plant disease—from use of resistant varieties to crop rotation, elimination of reservoirs, landscape planning, surveillance, quarantine, risk modeling, and anticipation of disease emergences—all rely on knowledge of pathogen host range. However, awareness of the multitude of factors that influence the outcome of plant–microorganism interactions, the spatial and temporal dynamics of these factors, and the diversity of any given pathogen makes it increasingly challenging to define simple, all-purpose rules to circumscribe the host range of a pathogen. For bacteria, fungi, oomycetes, and viruses, we illustrate that host range is often an overlapping continuum—more so than the separation of discrete pathotypes—and that host jumps are common. By setting the mechanisms of plant–pathogen interactions into the scales of contemporary land use and Earth history, we propose a framework to assess the frontiers of host range for practical applications and research on pathogen evolution.

L’utilisation des agents de biocontrôle est plus complexe que l'application de produits chimiques, en raison de leurs caractéristiques (effets partiels et nombreux organismes vivants). Cela entraîne la variabilité de leur efficacité et entrave leur adoption. Pour faciliter les conseils aux agriculteurs, il est nécessaire de développer des outils d’aide à la décision intégrant les caractéristiques (dont les propriétés biologiques) des agents de biocontrôle, celles des agents phytopathogènes et des systèmes de culture. Sur la combinaison Ampelomyces quisqualis / Oidium neolycopersici / tomate, les objectifs de cette étude sont d'identifier, sur la base d'une étude de la littérature scientifique, les principaux facteurs gouvernant l'efficacité de l'agent de biocontrôle et de tester l'effet de facteurs microclimatiques (température, humidité) sur son efficacité., The deployment of biocontrol agents is more complex than applying chemicals due to their characteristics (partial effects and many living organisms). This leads to a variability of their efficacy and hinder their adoption. Thus, to facilitate advice to farmers, it is necessary to develop decision support systems, integrating the characteristics (including biological properties) of biocontrol agents, plant pathogens and cropping systems. On the combination Ampelomyces quisqualis / Oidium neolycopersici /tomato, the objectives of this study are to identify the factors governing the efficacy of the biocontrol agent based on a scientific litterature survey and to test the effect of microclimatic factors (temperature, humidity) on its efficacy

Certains champignons sont très dommageables pour les plantes mais aussi pour la conservation après récolte des produits végétaux. Les restrictions réglementaires concernant l’utilisation des fongicides nécessitent de trouver des solutions alternatives. L'amélioration de la résistance des plantes en utilisant des méthodes physiques, comme les rayonnements UV, peut présenter une alternative prometteuse en association avec d’autres méthodes dans le cadre d’une protection intégrée des cultures. L'objectif de cette thèse a été d’étudier l’effet des rayonnements UV-C sur la sensibilité des plantes aux agents pathogènes. Les rayonnements UV-C ont été appliqués durant la culture, seuls ou en combinaison à des agents de biocontrôle, ou en post-récolte. Les expérimentations ont été menées sur deux espèces végétales : le fraisier et la tomate.Sur fraisier, des traitements UV-C à une dose de 1,70 kJ/m² entraînent une diminution systématique d'environ 20 % de la sensibilité des feuilles à Botrytis cinerea et diminuent jusqu’à 50 % le nombre de feuilles attaquées par Podosphaera aphanis, l’agent causal de l’oïdium. Chez la tomate, la protection des feuilles contre B. cinerea atteint 43 % avec une dose d’UV-C cumulée de 4,0 kJ/m². Ces mêmes traitements UV-C appliqués sur fruits réduisent la sensibilité des fraises vis-à-vis de Rhizopus de 75 % mais aucun effet n’est observé vis-à-vis de B. cinerea. Au contraire, sur fruits de tomate, la sensibilité est diminuée d'environ 63 % contre cet agent pathogène. Parallèlement, des tests biochimiques et gustatifs suggèrent que la qualité des fruits n’est pas significativement améliorée ni altérée par les expositions UV-C. Malgré un effet germicide marqué des rayonnements UV-C sur feuilles de fraisiers, aucun effet bénéfique de l’application de ces rayonnements sur le niveau d’efficacité d’agents de lutte biologique n’a été mis en évidence.Nos observations sont encourageantes pour envisager une utilisation de cette méthode dans un schéma de protection intégrée des cultures. Cependant, une compréhension claire de la façon dont les rayonnements UV-C sont perçus par les plantes et traduits en mécanismes de défense est nécessaire avant que leur utilisation ne soit recommandée sur le terrain., Some fungi are very damaging during plant cultivation and also in post-harvest storage of products. Regulatory restrictions on fungicide use require alternative solutions. Improving plant resistance using physical methods, such as aplication of UV radiation, can be a promising alternative in association with other methods as part of an integrated pest management strategy. The objective of the present thesis was to study the effect of UV-C aplication on the sensitivity of plants to fungal pathogens. UV-C radiation was applied during plant cultivation, alone or in combination with biocontrol agents, or in post-harvest. Experiments were conducted on two plant species: strawberry and tomato.On strawberry plants, UV-C treatments at 1.70 kJ/m² result in a systematic 20 % decrease in leaves sensitivity to Botrytis cinerea and in a reduction by up to 50 % of the number of leaves infected by Podosphaera aphanis, the causal agent of powdery mildew. In tomato, leaves protection against B. cinerea reaches 43 % with a cumulative dose of 4.0 kJ/m². UV-C treatments applied on fruits reduce the strawberry sensitivity to Rhizopus by 75 % but no effect is observed against B. cinerea. On the contrary, sensitivity against B. cinerea is reduced by 63 % on tomato fruit. Biochemical and taste tests suggest that fruit quality is not significantly improved or altered by UV-C treatment. Despite a marked germicidal effect of UV-C radiation on strawberry leaves, it has no significant effect on the protective efficacy of biocontrol agents.Our observations are encouraging to consider the use of this tool in an integrated crop protection scheme. However, a clear understanding of how UV-C radiations are perceived by plants and their translation into defense mechanisms is necessary before their use is recommended in the field.

Protection des cultures contre les maladies à l’aide de microorganismes : état de l’art et perspectives. Med'agri

Les SDP à l'épreuve du terrain: cultures maraîchères. Natural Products & Biocontrol 2018

Des microorganismes contre les agents pathogènes des plantes. Rencontre EMBA (Ecological Management of Bioagressors in Agroecosystems) 2018

Les sucres simples (mono ou disaccharides) sont reconnus comme des molécules de signalisation dans les plantes, capables d'activer les réponses de défense et ainsi d’augmenter leur niveau de résistance face aux bioagresseurs (Bolouri-Moghaddam et Van-den-Ende, 2012. J. Exp. Bot. 63:3989-3998 ; Trouvelot et al. 2014. Front. Plant Sci. 4:1-14 ; Arnault et al. 2016. Pest Manag. Sci. 72, 1901-1909). Appliqués à de faibles doses sur les cultures au champ, leur effet protecteur n'est souvent que partiel et pose souvent des problèmes de répétabilité dans le temps et d'une parcelle à une autre (Arnault et al. 2015. Innov. Agro. 46:1-10). Il convient donc d’identifier les facteurs régissant leur efficacité pour déterminer les conditions optimales de leur utilisation dans le cadre d’une stratégie de protection intégrée des cultures. L’objectif de ce travail, réalisé dans le cadre du projet CASDAR SWEET, est d’étudier certains facteurs de l’efficacité protectrice de sucres contre deux bioagresseurs majeurs de la tomate, Oidium neolycopersici et Botrytis cinerea. Deux pistes d’amélioration de l’efficacité d’un mélange sucrose-fructose ont été explorées au cours de ce projet : le mode de traitement (pulvérisation foliaire vs. traitement racinaire) et le génotype de tomate. Quelles que soient les conditions testées, aucun effet protecteur des sucres n’a été mis en évidence contre B. cinerea. Contre l’oïdium, l’effet protecteur est partiel et il est modulé par chacun des deux facteurs étudiés. Des travaux sont en cours pour explorer l'influence du greffage et de la fertilisation azotée de la tomate sur l’efficacité protectrice des sucres. Des essais dans des conditions proches de la production commerciale de la tomate sous abri seront menés pour valider les résultats obtenus et pour évaluer les effets possibles des sucres sur d'autres bioagresseurs, et sur le rendement de la culture.

Les agents pathogènes fongiques ont un impact majeur sur le fraisier (Fragaria x ananassa) et des traitements fongicides fréquents sont nécessaires pour limiter les pertes économiques. Il est donc important de trouver des solutions alternatives aux produits phytosanitaires. Les rayonnements UV-C (254 nm) ont montré un potentiel intéressant de protection contre des agents pathogènes, suite à des traitements durant la croissance des plantes (Vasquez et al. 2017. Sci. Hort. 222, 32-39), ou en post récoltes (Jin et al. 2017. Sci. Hort. 225:106-111). Au cours de ce travail, nous avons testé l’hypothèse qu’il est possible de diminuer la sensibilité du fraisier et des fraises produites, vis-à-vis de différents agents pathogènes par l’application d’UV-C en cours de culture. Pour cela, trois modalités de traitement des fraisiers ont été réalisées : avant floraison, après floraison, et pendant toute la durée de la culture. Le développement de trois agents pathogènes a été suivi en cours de culture (Botrytis cinerea et Podosphera aphanis) et en post-récolte sur fruits (B. cinerea et Rhizopus sp.). Les traitements UV-C ont un effet significatif sur l’incidence de l’oïdium en cours de culture en diminuant d’environ 50% le nombre de feuilles attaquées par rapport au contrôle non traité. Ils ont également un effet protecteur des fruits en post-récolte contre les attaques de Rhizopus, en réduisant d’environ 75% le nombre de fruits naturellement contaminés. L’effet vis-à-vis de B. cinerea est plus contrasté : une efficacité de protection de 20% est observée sur feuilles détachées après inoculation artificielle, et aucun effet bénéfique n’est observé sur les fruits. Les implications possibles de ces résultats seront discutées.

Apricot, a highly valuable crop is threatened by the growing importance of bacterial canker caused by Pseudomonas syringae. Among the key factors able to control the disease, genetic improvement is a promising measure. The variability of susceptibility on branches and the characterization of genetic determinants through a genome wide association study were thus investigated on a core-collection.73 accessions were annually inoculated in the orchard with an aggressive strain of the bacterium for 4 years. Phenotypic data about the length of both external canker (lgc) and superficial browning (bs) of tissues were collected. The analysis displayed a highly environmental-dependent genetic variation with broad-sense heritabilities of lgc and bs reaching respectively 59% and 78% for the most severe year. Considering the two variance-maximizing years, genetic (G) and genetic x year (GxY) BLUP were predicted for each variable using a linear mixed model. Association analysis were performed with a 63,236 SNP set through both a multi-variate (GEMMA) and a multi-locus genome-wide analysis.By exploiting the between-years (multi-locus model on G and GxY terms) and between-phenotypes (multivariate model on lgc-bs G terms) correlations, 11 significant associations have been detected. Among them, two SNP impacting both lgc and bs expressions over the two studied years and explaining 41% and 31% of the total phenotypic variance were identified on chromosomes 5 and 6. A long-range linkage disequilibrium had been noticed between these two markers suggesting a co-selection effect. The associated SNP reported from this work will open up new opportunities for a Marker-assisted selection strategy.

Apricot, a highly valuable crop is threatened by the growing importance of bacterial canker caused by Pseudomonas syringae. Among the key factors able to control the disease, genetic improvement is a promising measure. The variability of susceptibility on branches and the characterization of genetic determinants through a genome wide association study were thus investigated on a core-collection.73 accessions were annually inoculated in the orchard with an aggressive strain of the bacterium for 4 years. Phenotypic data about the length of both external canker (lgc) and superficial browning (bs) of tissues were collected. The analysis displayed a highly environmental-dependent genetic variation with broad-sense heritabilities of lgc and bs reaching respectively 59% and 78% for the most severe year. Considering the two variance-maximizing years, genetic (G) and genetic x year (GxY) BLUP were predicted for each variable using a linear mixed model. Association analysis were performed with a 63,236 SNP set through both a multi-variate (GEMMA) and a multi-locus genome-wide analysis.By exploiting the between-years (multi-locus model on G and GxY terms) and between-phenotypes (multivariate model on lgc-bs G terms) correlations, 11 significant associations have been detected. Among them, two SNP impacting both lgc and bs expressions over the two studied years and explaining 41% and 31% of the total phenotypic variance were identified on chromosomes 5 and 6. A long-range linkage disequilibrium had been noticed between these two markers suggesting a co-selection effect. The associated SNP reported from this work will open up new opportunities for a Marker-assisted selection strategy.

Apricot, a highly valuable crop is threatened by the growing importance of bacterial canker caused by Pseudomonas syringae. Among the key factors able to control the disease, genetic improvement is a promising measure. The variability of susceptibility on branches and the characterization of genetic determinants through a genome wide association study were thus investigated on a core-collection.73 accessions were annually inoculated in the orchard with an aggressive strain of the bacterium for 4 years. Phenotypic data about the length of both external canker (lgc) and superficial browning (bs) of tissues were collected. The analysis displayed a highly environmental-dependent genetic variation with broad-sense heritabilities of lgc and bs reaching respectively 59% and 78% for the most severe year. Considering the two variance-maximizing years, genetic (G) and genetic x year (GxY) BLUP were predicted for each variable using a linear mixed model. Association analysis were performed with a 63,236 SNP set through both a multi-variate (GEMMA) and a multi-locus genome-wide analysis.By exploiting the between-years (multi-locus model on G and GxY terms) and between-phenotypes (multivariate model on lgc-bs G terms) correlations, 11 significant associations have been detected. Among them, two SNP impacting both lgc and bs expressions over the two studied years and explaining 41% and 31% of the total phenotypic variance were identified on chromosomes 5 and 6. A long-range linkage disequilibrium had been noticed between these two markers suggesting a co-selection effect. The associated SNP reported from this work will open up new opportunities for a Marker-assisted selection strategy.

Apricot, a highly valuable crop is threatened by the growing importance of bacterial canker caused by Pseudomonas syringae. Among the key factors able to control the disease, genetic improvement is a promising measure. The variability of susceptibility on branches and the characterization of genetic determinants through a genome wide association study were thus investigated on a core-collection.73 accessions were annually inoculated in the orchard with an aggressive strain of the bacterium for 4 years. Phenotypic data about the length of both external canker (lgc) and superficial browning (bs) of tissues were collected. The analysis displayed a highly environmental-dependent genetic variation with broad-sense heritabilities of lgc and bs reaching respectively 59% and 78% for the most severe year. Considering the two variance-maximizing years, genetic (G) and genetic x year (GxY) BLUP were predicted for each variable using a linear mixed model. Association analysis were performed with a 63,236 SNP set through both a multi-variate (GEMMA) and a multi-locus genome-wide analysis.By exploiting the between-years (multi-locus model on G and GxY terms) and between-phenotypes (multivariate model on lgc-bs G terms) correlations, 11 significant associations have been detected. Among them, two SNP impacting both lgc and bs expressions over the two studied years and explaining 41% and 31% of the total phenotypic variance were identified on chromosomes 5 and 6. A long-range linkage disequilibrium had been noticed between these two markers suggesting a co-selection effect. The associated SNP reported from this work will open up new opportunities for a Marker-assisted selection strategy.

Risque phytosanitaire (ARP) portant sur [i]Fusarium oxysporum[/i] f. sp.[u] cubense[/u] (agent pathogène responsable de la maladie de Panama) pour les départements d'Outre-mer

Connaissances nécessaires à la gestion du risque "écorces sensibles au nématode du pin"

Intrinsic disorder (ID) in proteins is defined as a lack of stable structure in physiological conditions. Intrinsically disordered regions (IDRs) are highly abundant in some RNA virus proteomes. Low topological constraints exerted on IDRs are expected to buffer the effect of numerous deleterious mutations and could be related to the remarkable adaptive potential of RNA viruses to overcome resistance of their host. To experimentally test this hypothesis in a natural pathosystem, a set of four variants of Potato virus Y (PVY; Potyvirus genus) containing various ID degrees in the Viral genome-linked (VPg) protein, a key determinant of potyvirus adaptation, was designed. To estimate the ID contribution to the VPg-based PVY adaptation, the adaptive ability of the four PVY variants was monitored in the pepper host (Capsicum annuum) carrying a recessive resistance gene. Intriguingly, the two mutants with the highest ID content displayed a significantly higher ability to restore infection in the resistant host, whereas the less intrinsically disordered mutant was unable to restore infection. The role of ID on virus adaptation may be due either to a larger exploration of evolutionary pathways or the minimization of fitness penalty caused by resistance-breaking mutations. This pioneering study strongly suggests the positive impact of ID in an RNA virus adaptive capacity.

Investigations into life history of microorganisms that cause plant diseases have been limited mostly to contexts where they are in interaction with plants, and with cropped or otherwise managed vegetation. Therefore, knowledge about the diversity of plant pathogens, about potential reservoirs of inoculum and about the processes that contribute to their survival and adaptation is limited to these contexts. The agro-centric perspective of plant pathogen life histories is incoherent with respect to the capacity of many of them to persist as saprophytes on various substrates. In this context we have investigated the ubiquity of the broad host range necrotrophic fungus Botrytis cinerea, outside of agricultural settings and have determined if the populations in these natural habitats can be distinguished phenotypically and phylogenetically from populations isolated from diseased crops. Over a period of 5 years, we isolated B. cinerea from 235 samples of various substrates collected in France including rainfall, snowpack, river, and lake water, epilithic biofilms in mountain streams, leaf litter and plant debris, rock surfaces, bird feathers and healthy wild plants from outside of agricultural fields. All substrates except rock surfaces harbored B. cinerea leading us to establish a collection of purified strains that were compared to B. cinerea from diseased tomato, grapes and various other crops in France. Phylogenetic comparisons of 321 strains from crop plants and 100 strains from environmental substrates based on sequences of 9 microsatellite markers revealed that strains from crops and the environment could not be distinguished. Furthermore, the genetic diversity of strains outside of agriculture was just as broad as within agriculture. In tests to determine the aggressiveness of strains on tomato stems, the mean disease severity caused by strains from environmental substrates was statistically identical to the severity of disease caused by strains from tomato, but was significantly greater than the severity caused by strains from grape or other crops. Our results suggest that highly diverse populations of this plant pathogen persist outside of agriculture in association with substrates other than plants and that this part of their life history is compatible with its capacity to maintain its potential as plant pathogen.

International audience; In spite of their widespread occurrence, only few host jumps by plant viruses have been evidenced and the molecular bases of even fewer have been determined. A combination of three independent approaches, (i) experimental evolution followed by reverse genetics analysis, (ii) positive selection analysis and (iii) locus-by-locus analysis of molecular variance (AMOVA) allowed reconstructing the Potato virus Y (PVY; genus Potyvirus, family Potyviridae) jump to pepper (Capsicum annuum), probably from other solanaceous plants. Synthetic chimeras between infectious cDNA clones of two PVY isolates with contrasted levels of adaptation to C. annuum showed that the P3 and, to a lower extent, the CI cistron played important roles in infectivity towards C. annuum. The three analytical approaches pinpointed a single nonsynonymous substitution in the P3 and P3N-PIPO cistrons that evolved several times independently and conferred adaptation to C. annuum. In addition to increasing our knowledge of host jumps in plant viruses, this study illustrates also the efficiency of locus-by-locus AMOVA and combined approaches to reconstruct adaptive mutations in the genome of RNA viruses.

International audience; The management of genes conferring resistance to plant–pathogens should make it possible to control epidemics (epidemiological perspective) and preserve resistance durability (evolutionary perspective). Resistant and susceptible cultivars must be strategically associated according to the principles of cultivar mixture (within a season) and rotation (between seasons). We explored these questions by modeling the evolutionary and epidemiological processes shaping the dynamics of a pathogen population in a landscape composed of a seasonal cultivated compartment and a reservoir compartment hosting pathogen year-round. Optimal deployment strategies depended mostly on the molecular basis of plant–pathogen interactions and on the agro-ecological context before resistance deployment, particularly epidemic intensity and landscape connectivity. Mixtures were much more efficient in landscapes in which between-field infections and infections originating from the reservoir were more prevalent than within-field infections. Resistance genes requiring two mutations of the pathogen avirulence gene to be broken down, rather than one, were particularly useful when infections from the reservoir predominated. Combining mixture and rotation principles were better than the use of the same mixture each season as (i) they controlled epidemics more effectively in situations in which within-field infections or infections from the reservoir were frequent and (ii) they fulfilled the epidemiological and evolutionary perspectives.

International audience; A recommendation – based on reviews by Benoît Moury and ananonymous reviewer – of : Suffert F, Goyeau H, Sache I, Carpentier F, Gelisse S, Morais D, Delestre G. 2017.Epidemiological trade-off between intra- and interannual scales in the evolution ofaggressiveness in a local plant pathogen population. bioRxiv, 151068, ver. 3 of 12thNovember 2017. doi: 10.1101/151068

Assessing the phenotypic and genotypic diversity of [i]Sclerotinia sclerotiorum[/i] in France. 10. Conférence de la Société française de phytopathologie. 12. European foundation for plant pathology conference

International audience; Multiple screening approach for the selection of efficient biological control agents against [i]Botrytis cinerea[/i] on tomato. 10. Conférence de la Société française de phytopathologie. 12. European foundation for plant pathology conference

International audience; Predicting abundance of [i]Botrytis cinerea[/i] airborne inoculum to forecast grey mould epidemics. 10. Conférence de la Société française de phytopathologie. 12. European foundation for plant pathology conference

International audience; Are sown flower strips an efficient tool to limit aphid colonization and viral epidemics in melon crops?. 10. Conférence de la Société française de phytopathologie. 12. European foundation for plant pathology conference

Nouveaux acquis sur la protection des plantes vis-à-vis de [i]Sclerotinia sclerotiorum[/i] à base de l’agent de lutte biologique [i]Coniothyrium minitans[/i]?. Journée Sclerotinia.

Diversité de l’agressivité de [i]Sclerotinia sclerotiorum[/i] sur différentes espèces végétales. Journée Sclerotinia.

Exploring plant tolerance to viruses as a sustainable means of disease control. 16. Rencontres de Virologie Végétale (RVV 2017)

A comparison of methods to preserve RNA viruses. 16. Rencontres de Virologie Végétale (RVV 2017)

paper originating from a presentation made at the 13th International Plant Virus Epidemiology Symposium held at Avignon, France June 6-10, 2016; The “Papaya ringspot virus (PRSV) cluster” of cucurbit-infecting potyviruses contains five acknowledged species that have similar biological, serological and molecular properties. Additional data suggest there are other uncharacterized species from various locations in the world that likely belong to the PRSV cluster including a new PRSV-like virus reported from Sudan in 2003. Molecular and biological data indicated that the virus from Sudan belongs to a new species, tentatively named wild melon vein banding virus (WMVBV). The complete nucleotide sequence of a second virus from Sudan revealed it was a divergent relative of Moroccan watermelon mosaic virus (MWMV). Based on sequence similarity this virus was determined to be a distinct species and tentatively named Sudan watermelon mosaic virus (SuWMV). Molecular analyses indicate that SuWMV is a recombinant between WMVBV- and MWMV-related viruses. Based on surveys performed in Sudan between 1992 and 2012, SuWMV appeared 10 times more frequent than WMVBV in that country (14.6% vs. 1.5% of the samples tested). The geographic structure and molecular diversity patterns of the putative and acknowledged species suggest that the PRSV-like cluster originated in the Old World about 3600 years ago, with an important diversification in Africa.

UMR BFP - Equipe Virologie; Characterization of a complex of necroviruses involved in a necrotic disease of corn salad ([i]Valerianella locusta[/i]). 16. Rencontres de Virologie Végétale (RVV 2017)

UMR BFP - Equipe Virologie UMR BFP - Equipe VirologieUMR BFP - Equipe Virologie; National audience

il s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : DISSERTATION; DEUG; The plant pathogen Sclerotinia sclerotiorum destroys massively diverse crops and produces sclerotia, a conservation structure which is a source of many contaminations. A biocontrol product, Contans WG, containing spores of the mycoparasitic fungus Coniothyrium minitans, can destroy sclerotia in the soil. A previous study has shown differences in sensibility to C. minitans among strains of S. sclerotiorum. Our purpose was to determine if these differences in sensibility could be linked to the morphology of sclerotia. To do so, a first approach consisted in measuring the thickness of sclerotia and their cortex for different strains. Those means were correlated by linear regression with average sensibility indices determined in the previous study. A second approach consisted in carrying out the same linear regression analysis, but this time on data for individual sclerotia. Cross-sections of parasitized sclerotia were measured individually to know their total thickness and the one of their cortex. Then, the same sclerotia were cultivated to determine their level of sensitivity. The regressions obtained with the first approach were not significant and could not explain the differences of sensibility to C. minitans among strains of S. sclerotiorum. However, the study on individual sclerotia showed that up to 33% of sensibility difference among sclerotia could be explained by the sclerotia morphology for some strains. So, there is a link between the sclerotia morphology and the sensibility to C. minitans but one or more factors are clearly more important than this link, such as, possibly, the chemical composition of the cortex.; Le champignon phytopathogène Sclerotinia sclerotiorum détruit massivement les cultures et produit des sclérotes, sources de nombreuses contaminations. Un produit de biocontrôle, Contans WG, contenant les spores d’un mycoparasite, Coniothyrium minitans, permet le nettoyage des champs contaminés par destruction des sclérotes dans le sol. Une précédente étude a montré des différences de sensibilité de souches de S. sclerotinia à C. minitans. Notre objectif était de savoir si cette différence de sensibilité de S. sclerotinia à C. minitans pouvait être liée à la morphologie des sclérotes. Pour cela, une première approche a consisté à mesurer l’épaisseur de sclérotes et de leur cortex pour différentes souches et de relier les valeurs moyennes, par analyse de régression linéaire, aux moyennes d’indices de sensibilité obtenues pour ces souches dans la précédente étude. Une seconde approche a été menée pour réaliser la même régression que précédemment mais en utilisant des données obtenues par sclérote individuel. Des coupes de sclérotes parasités ont été mesurées pour étudier l’épaisseur totale des sclérotes et de leur cortex. Les mêmes sclérotes ont ensuite été mis en culture pour obtenir les indices de sensibilité de façon individuelle. Les régressions obtenues par la première approche n’ont pas montré de lien significatif susceptible d’expliquer les différences de sensibilité à C. minitans par souche de S. sclerotiorum. En revanche, l’étude par sclérote individuel a montré jusqu’à 33% de variabilité de sensibilité expliquée par la morphologie des sclérotes au sein d’une même souche. Par conséquent, il existe un lien entre la morphologie des sclérotes et la sensibilité de S. sclerotiorum à C. minitans mais un ou plusieurs autres facteurs restent prépondérants à ce lien entre souches de S. sclerotiorum, comme peut être la composition du cortex.

During the past decade, knowledge of pathogen life history has greatly benefited from the advent and development of molecular epidemiology. This branch of epidemiology uses information on pathogen variation at the molecular level to gain insights into a pathogen's niche and evolution and to characterize pathogen dispersal within and between host populations. Here, we review molecular epidemiology approaches that have been developed to trace plant virus dispersal in landscapes. In particular, we highlight how virus molecular epidemiology, nourished with powerful sequencing technologies, can provide novel insights at the crossroads between the blooming fields of landscape genetics, phylogeography, and evolutionary epidemiology. We present existing approaches and their limitations and contributions to the understanding of plant virus epidemiology.

Damage caused by pests and diseases on vegetables crops can lead to high economic losses. This is why with current changes to control strategies and a reduction in the use of plant protection products in Europe, knowledge on pests and diseases (host plants, geographic distribution, potential damage level...) has become as an unavoidable topic of work on air- or soil-borne pests and diseases, within the ‘GIS PIClég’ (Scientific Interest Grouping for Integrated Production of Vegetable Crops). In 2014 and 2015, a survey of all the pests anddiseases known in France was carried out, using expert ratings, which were then characterized. In this way, a list of key issues for which further research should be considered was established.; Les légumes sont des cultures pour lesquelles les dégâts engendrés par des bioagresseurs peuvent occasionner d’importantes pertes. C’est pourquoi, dans un contexte européen de modification des stratégies de protection et de réduction de l’utilisation des solutions phytopharmaceutiques, la connaissance des organismes nuisibles (plantes hôtes, répartition géographique, niveau de nuisibilité potentielle…) est apparue, au sein du GIS PIClég, comme un sujet de travail incontournable concernant les bioagresseurs aériens et telluriques. En 2014 et 2015, un recensement et une caractérisation de l’ensemble des bioagresseurs connus en France ont été entrepris, via une notation par des experts. Ainsi, une liste de problèmes clés pour lesquelles des efforts de recherche supplémentaires devront être envisagés.

La modélisation de la dynamique épidémiologique des ascomycètes parasites des arbres fruitiers présente deux aspects très importants : l’évaluation de la quantité d'inoculum et de son évolution, et l’identification des évènements climatiques donnant lieu à une contamination. Le travail présenté aborde ces deux aspects au travers de deux exemples : la tavelure du pommier, et la maladie de l’œil de paon de l’olivier, parasites majeurs pour les filières concernées. L’acquisition des connaissances sur la biologie des deux maladies a été abordée uniquement sur la base de données acquises sur le terrain, ce qui est original car généralement les modèles ont été réalisés sur la base de connaissances établies en conditions contrôlées. Dans le cas de Venturia inaequalis, agent de la tavelure du pommier, la vitesse de développement journalier de l’inoculum a été établie par optimisation numérique, sur la base d’observations réalisées en Provence. Un modèle de dynamique de projection des ascospores incluant la suspension de l’évolution de l’inoculum primaire lors des périodes sèches a été réalisé puis validé sur un jeu de données indépendantes. La transposabilité du modèle a été ensuite étudiée pour une autre région (Aquitaine). Dans le cas de Fusicladium oleagineum, agent de la maladie de l’œil de paon, les conditions de contamination ont été établies en fonction de la température et de l’hygrométrie, d’une part par la réalisation d’un abaque sur la base de points sélectionnés par dires d’expert, et d’autre part de façon automatique à l’aide d’un système par apprentissage (réseau de neurones). Un modèle, liant la température moyenne après la contamination à l’apparition des symptômes a été ensuite réalisé., Apple scab, caused by Venturia inaequalis, and peacoq leaf spot, cause by Fusicladium oleagineum, are key diseases respectively for apple and olive growers. These disease usually require a large number of treatments. Adequate protection need a good evaluation of quantitative disponibility of inoculum, and estimation of infection conditions. In this thesis, these two problems were studied using only field data. This is an original aprroach to obtain knowledge about biology of fungi : most previous works were realised by regression of laboratory data obtained under controled conditions. In the case of Venturia inaequalis, primary inoculum consists of pseudothecia present in leaf litter. Treatments agains ascospore release period is the cornerstone of the strategy against apple scab. However, the existing forecasting models are not reliable, and are all based on degree-day time scale, proposed in 1982. Here, using a corpus of data acquired between 1996 and 2013, including observations of ascospore release and weather data, we assessed the daily rate of development of primary inoculum by fitting generic new time scale functions. Further improvements were then studied to take into account elements reported in litterature about the incidence of rain or wetness.Different methods were tested and adapted for the parameterisation of models by numerical optimisation. Some forcasting models were proposed and adapted to the area where the study was conducted, with parameters including rain and temperature. The validity was tested, and further developements of the forecasting tool was then proposed. In the case of Fusicladium oleagineum, a field-operational model predicting disease outbreaks was established as a function of temperature and relative humidity. First with the help of points selected by experts, Secondly automaticaly using a neural network. A model defining latent period as a function of average temperature after contamination was then realised.

The impact of flower strips on the colonization of crops by the aphid Aphis gossypii and its natural enemies was studied from 2013 et 2015 within the framework of the AGATH project, funded by the Ministère de l’Agriculture, de l’Alimentation et de la Forêt (Casdar) and led by the Ctifl. A mix of flowers, tailored by the INRA (French National Institute for Agricultural Reasearch) to attract natural enemies of aphids in the proximity of melon crops without having a negative impact on the crops, was assessed in a network of plots throughout the three main melon production areas. The attractivity of this mix of flowers to natural enemies was characterized. The density of A. gossypii and of arthropod predator and/or parasitoid populations was compared in melon plots with these flower strips and in identical plots in terms of crop management but with bare soil.; L’effet de bandes fleuries sur la colonisation des cultures par le puceron Aphis gossypii et ses ennemis naturels a été étudié dans le cadre du projet AGATH, soutenu par le ministère de l’Agriculture, de l’Alimentation et de la Forêt (Casdar) et porté par le Ctifl de 2013 à 2015. Un mélange fleuri conçu par l’Inra pour attirer les ennemis naturels de pucerons à proximité des parcelles de melon sans exercer en parallèle d’effet délétère sur les cultures a été évalué dans un réseau de parcelles réparties dans les trois principaux bassins de production de melons. L’attractivité de ce mélange fleuri vis-à-vis des principaux ennemis naturels de pucerons a été caractérisée. Les densités des populations d’A. gossypii et d’arthropodes prédateurs et/ou parasitoïdes de pucerons mesurées dans des parcelles de melon bordées par ce mélange fleuri et dans des parcelles identiques en termes d’itinéraire technique mais bordées par une surface de sol nu ont été comparées.

Plant pathogens can play a role in the competitive interactions between plant species and have been understudied in native prairies, which are declining globally, and in Conservation Reserve Program (CRP) lands in the United States. Barley/Cereal yellow dwarf virus (B/CYDV) are among the most economically important disease-causing agents of small grain cereal crops, such as wheat, and are known to infect over 150 Poaceae species, including many of the grass species present in prairies and CRP lands. Field surveys of Poaceae species were conducted in endangered Palouse Prairie and CRP habitats of southeastern Washington and adjacent northern Idaho, USA from 2010 to 2012 to examine for the presence of B/CYDV among plant hosts and aphid vectors. Viral species were identified via cloning and sequencing. Landscape, soil and climate data were retrieved from USDA-NASS and USDA-NRCS databases. Analyses were conducted to examine effects of diverse agroecological and environmental factors on virus prevalence. A total of 2271 grass samples representing 30 species were collected; 28 of these were infected with BYDV in at least one location. BYDV infection was detected at every CRP and prairie remnant sampled, with an overall infection of 46%. BYDV-SGV and BYDV-PAV were the only two B/CYDV species encountered, with BYDV-SGV being more prevalent. Sampling time (season) and host plant identity were the main variables explaining variation in virus prevalence among sites. BYDV was more prevalent in perennial compared to annual grass species. Aphids were encountered only once suggesting non-colonizing aphids, potentially from neighboring cereal fields, are responsible for disease spread in these habitats. BYDV prevalence increased in sampled habitats as cereal crop cover increased within a 1-km radius of a habitat patch. Results demonstrate moderate to high and persistent prevalence of BYDV in an endangered grassland habitat. Species composition and susceptibility to pathogens should be considered when creating seed mixes for CRP sites, especially in relation to agricultural crops and diseases in a region. Future work exploring host abundance, competence and habitat utilization by vectors is required to fully elucidate BYDV ecology and epidemiology in grassland habitats.

Cacao swollen shoot virus (CSSV) is a major pathogen of cacao (Theobroma cacao) in Africa, and long-standing efforts to limit its spread by the culling of infected trees have had very limited success. CSSV is a particularly difficult virus to study, as it has a very narrow host range, limited to several tropical tree species. Furthermore, the virus is not mechanically transmissible, and its insect vector can only be used with difficulty. Thus, the only efficient means to infect cacao plants that have been experimentally described so far are by particle bombardment or the agroinoculation of cacao plants with an infectious clone. We have genetically transformed three non-host species with an infectious form of the CSSV genome: two experimental hosts widely used in plant virology (Nicotiana tabacum and N. benthamiana) and the model species Arabidopsis thaliana. In transformed plants of all three species, the CSSV genome was able to replicate, and, in tobacco, CSSV particles could be observed by immunosorbent electron microscopy, demonstrating that the complete virus cycle could be completed in a non-host plant. These results will greatly facilitate the preliminary testing of CSSV control strategies using plants that are easy to raise and to transform genetically.

International audience; Several potyviruses affect lettuce (Lactuca sativa) and chicory (Cichorium spp.) crops worldwide and are important constraints for production because of the direct losses that they induce and/or because of their seed transmission. Here, the molecular and biological properties are described of two potyviruses that were recently isolated from lettuce plants showing mosaic or strong necrotic symptoms in an experimental field in southeastern France. The first potyvirus belongs to the species Endive necrotic mosaic virus and is present in a large number of wild plant species, especially Tragopogon pratensis. It is unable to infect lettuce cultivars with a resistance to Turnip mosaic virus that is present in many European cultivars and probably conferred by the Tu gene. The second potyvirus belongs to the tentative species lettuce Italian necrotic virus and was not observed in wild plants. It infected all tested lettuce cultivars. Wild accessions of Lactuca serriola, Lactuca saligna, Lactuca virosa and Lactuca perennis were identified as resistant to one or the other potyvirus and could be used for resistance breeding in lettuce. No resistance against these two potyviruses was observed in the tested Cichorium endivia cultivars. In contrast, all tested Cichorium intybus cultivars or accessions were resistant.

paper originating from a presentation made at the 13th International Plant Virus Epidemiology Symposium held at Avignon, France June 6-10, 2016; Ornamental plants constitute a largely unknown and potentially important source of pathogens affecting not only ornamental plants, but also major crop species. We have carried out studies using high-throughput sequencing of 21-24 nt RNAs from potentially virus-infected ornamental plants, followed by assembly of sequence scaffolds, to identify the virus and viroid genomes present in a panel of 67 plant samples representing 46 species belonging to the main sectors of the ornamental plant industry (cut flowers, pot plants, bulbs). A pilot study demonstrated that samples could be pooled (5 samples per pool), and the overall process simplified without loss of detection of important known pathogens. In a full-scale study, pools of 5 samples were organized in a 5 × 5 matrix to facilitate attribution of a sequence to a precise sample directly from analysis of the matrix. In the total of 67 samples analyzed in the two studies, partial sequences suggesting the presence of 25 previously unknown viruses and viroids were detected, including all types of virus and viroid genomes, and also showed four cases of known viruses infecting previously undescribed hosts. Furthermore, two types of potential mis-assembly were analyzed, and were shown to not affect the conclusions regarding the presence of the pathogens identified, but show that mis-assembly can affect the results when the objective is determining complete bona fide viral genome sequences. These results clearly confirm that ornamental plants constitute a potential source of unknown viruses and viroids that could have a major impact on agriculture, and that sequencing siRNAs of potentially virus- or viroid-infected ornamental plants is an effective means for screening for the presence of potentially important pathogens.