Genome sequences of plant-associated rhodococcus sp. isolates from Tunisia

The draft genome sequences of plant-associated Rhodococcus spp. from Tunisia are reported here. Two Rhodococcus fascians strains were obtained from almond rootstocks, and one Rhodococcus kroppenstedtii strain was obtained from a pistachio tree. The fourth Rhodococcus sp. strain was isolated from an ornamental plant. 2020 Dhaouadi et al

Interaction Chêne-oïdium : caractérisation moléculaire et adaptation locale du parasite, résistance génétique de l’hôte

L’oïdium est une des maladies les plus communes sur chêne en Europe. Cette maladie a été signalée à partir du début du 20ème siècle. Toutefois, peu de données sont disponibles sur l’identité de l’agent causal et de son interaction avec l’hôte. L’objectif de cette étude est d’améliorer les connaissances sur ce pathosystème : (1) caractériser son agent causal avec un marqueur moléculaire (ADN ribosomal) et étudier la distribution spatiale des différentes lignées ; (2) étudier l’adaptation locale du parasite à son hôte ; (3) explorer le déterminisme génétique de la résistance de l’hôte. L’étude de l’ADN ribosomal (ITS=Internal transcribed region et IGS= Intergenic spacer) a mis en évidence l’existence de quatre haplotypes, dont trois seulement avaient été associés à des agents d’oïdium sur chêne en Europe. Erysiphe alphitoïdes, classiquement considéré comme responsable de l’épidémie du XXème siècle est bien l’espèce prépondérante (environ 80% des détections), E. hypophylla et Phyllactinia sp étant détectés à fréquence beaucoup plus faible. Un résultat inattendu est la détection d’une quatrième séquence, présentant 100% d’homologie avec celle de plusieurs agents d’oïdium d’arbres tropicaux et avec Erysiphe quercicola, très récemment décrit sur chêne en Asie et Australie mais jusqu’alors inconnu en Europe. L’ITS de E. quercicola est détecté dans toutes les régions de France, à une fréquence non négligeable (de l’ordre de 15% en moyenne). On le trouve dans les mêmes parcelles et parfois sur les mêmes arbres, voire dans les mêmes lésions que E. alphitoides. La mise au point d’une méthode d’inoculation artificielle a permis d’étudier de façon quantitative l’interaction chêne-oïdium. Une expérimentation d’inoculations réciproques montre que les souches d’oïdium sont plus performantes sur les descendants des arbres dont elles ont été isolées que sur ceux d’autres arbres, suggèrant une adaptation trans- générationnelle. Des inoculations artificielles, complétées par des observations en conditions naturelles, ont également permis de démontrer un déterminisme génétique de la résistance des chênes, avec l’identification de plusieurs QTL. Certains de ces QTL co-localisent avec des QTL de phénologie, en accord avec l’importance de la résistance ontogénique des chênes à l’oïdium. L’ensemble de l’étude amène à reconsidérer l’oïdium du chêne comme un probable complexe d’espèces cryptiques, dont l’histoire de l’invasion et la co-existence en Europe restent à préciser. Les résultats acquis sur l’héritabilité de la résistance et l’adaptation locale du parasite constituent une première étape dans la compréhension des interactions démo-génétiques entre hôte et parasite dans ce pathosystème.Powdery mildew is the most common disease on oaks in Europe where it was first recorded at the beginning of the 20th century. Yet, little is known about the identity of the causal agent and his interaction with its host. The objective of this study was: (1) to characterize the species responsible of oak powdery mildew with a molecular marker (ribosomal DNA); to study the spatial distribution of these different lineages and (2) to study local adaptation of the parasite to its host (3) to explore the genetic determinism of host resistance. The study of the ITS (internal transcribed region) and IGS (intergenic spacer) diversity revealed the existence of four haplotypes, only three had been already associated with oak powdery mildew in Europe. Erysiphe alphitoïdes, for a long time considered as sole responsible for the epidemic of the XXth century, was the predominant species (~ 80% of detections), E. hypophylla and Phyllactinia sp. were detected at lower frequencies. An unexpected result is the detection of a fourth sequence which show 100% homology with ITS sequences of several powdery mildew agents of tropical trees and Erysiphe quercicola, recently described on oak in Asia and Australia but previously unknown in Europe. E. quercicola ITS was detected in all French regions, at a significant frequency (~ 15%). The study showed that E. alphitoides was often found in association with different ITS types in the same region, the same tree, and even in the same lesion. The development of an artificial inoculation method allowed the quantitative evaluation of the oak-powdery mildew interaction. A reciprocal inoculation experiment showed that powdery mildew strains were more efficient on their mother tress and their descendants than on the other trees, suggesting a trans-generational adaptation. Artificial inoculations, supplemented by observations in natural conditions, have also demonstrated a genetic determination of resistance of oak trees, with the identification of several QTL. Some of these QTL co-localize with QTL controlling phenology, in agreement with the importance of oaks ontogenic resistance to powdery mildew. The entire study leads to reconsider oak powdery mildew as a probable complex of cryptic species; the invasion history and the co-existence in Europe are still to be determined. The results achieved on the heritability of resistance and localization of the parasite are a first step in understanding the demo-genetic interactions between host and parasite in this pathosystem

Isolation and Characterization of Rhodococcus spp. from Pistachio and Almond Rootstocks and Trees in Tunisia

The purpose of this study was to isolate and identify Rhodococcus spp. strains from almond and pistachio rootstocks and trees in Tunisia. Twenty-eight strains were identified through 16S rDNA and vicA genes amplification and sequencing. Pea bioassay was performed to determine the pathogenicity of the strains. Representative 16S rDNA and vicA sequences of eight strains from pistachio and seven strains from almond were closely related (>98% similarity) to Rhodococcus spp. accessions in GenBank. Phylogenetic analysis based on 16S rDNA sequences revealed that the yellow-colored strains clustered with phytopathogenic Rhodococcusfascians. The red and orange-colored strains were separated into a different group with R. kroppenstedtii and R. corynebacteiroides isolates. Eleven strains affected the pea seedlings’ growth and exhibited different levels of virulence. The number of shoots was significantly higher in seedlings inoculated with four Rhodococcus strains, whereas the other three strains caused up to 80% of plant height reduction and reduced root secondary growth compared to non-inoculated pea seedlings. These strains, most of which are epiphytes from asymptomatic hosts, showed strong pathogenicity during pea bioassay and were established endophytically in pea tissues. Ten att and five fas genes were detected in four strains and may represent a novel model of plant pathogenic Rhodococcus virulence. The results of our survey showed that Rhodococcus is present but not prevalent in all visited orchards of almond and pistachio rootstocks and trees. Our surveys complemented the investments being made on ornamental species in Tunisia and unveiled the presence of undocumented plant-associated Rhodococcus spp. on economically important crops

Interaction plante-virus-vecteur. Cas du court-noué de la vigne en Tunisie

Cet article est une synthèse bibliographique portant sur la maladie du court-noué illustrée par des travaux conduits en Tunisie. Cette étude se justifie par le caractère destructif de cette maladie et l’interaction entre les souches virales et les différentes espèces de nématodes vecteurs de cette maladie. Deux népovirus sont associés à cette maladie, le grapevine fan leaf virus (GFLV) et l’arabis mosaic virus (ArMV). Les nématodes Xiphinema index et Xiphinema italiae sont les vecteurs du GFLV. Ils ont une reproduction parthénogénétique. Xiphinema diversicaudatum, avec une reproduction majoritairement sexuée, est considéré comme l’unique vecteur de l’ArMV. Les déterminants de la spécificité de transmission de ces népovirus par leurs vecteurs naturels sont localisés sur la protéine de la capside du virus. L’étude de l’incidence du court-noué au nord de la Tunisie montre que la région du Grombalia présente les taux d’infection par le GFLV et l’ArMV les plus élevés (71 % pour les deux virus), suivie par la région du Rafraf (45 et 38 %). La région de Takelsa quoique proche de Grombalia pour ses caractéristiques écologiques, présente un taux d’infestation similaire à celui de la région de Rafraf. Cette même tendance a été observée en analysant la corrélation entre la symptomatologie et la diversité génétique des souches de GFLV. L’étude de l’interaction virus-nématode montre que dans la quasi-totalité des échantillons de Xiphinema analysés en Tunisie, seul le GFLV est isolé. Cela s’explique par l’absence du vecteur spécifique de l’ArMV sur le territoire

Spatial distribution of lineages of oak powdery mildew fungi in France, using quick molecular detection methods

*L’oïdium est l’une des maladies fongiques les plus importantes sur chênes en Europe. Des études récentes basées sur l’internal transcribed spacer (ITS) ont suggéré l’implication de quatre lignées (espèces putatives) différentes. L’objectif de l’étude était de caractériser la distribution spatiale de ces lignées/espèces et en particulier de tester l’hypothèse d’une différenciation spatiale à plusieurs échelles : régionale (France), altitudinale (transect pyrénéen) et locale (au sein d’une parcelle forestière).*Des méthodes de détection des quatre types d’ITS ont été développées : (1) analyse SCCP ; (2) amplification par PCR de l’ITS par des amorces spécifiques. La SSCP a permis de détecter facilement les ITS correspondant à E. alphitoides et E. quercicola. Par contre, les ITS plus rares correspondant à E. hypophylla et Phyllactinia guttata (sensu lato) n’ont été détectés que par amplification spécifique.*L’étude a confirmé la forte prédominance (avec une fréquence supérieure à 80 %) de la séquence d’ITS associée à E. alphitoides. Les isolats présentant la même séquence d’ITS qu’E quercicola, espèce récemment décrite et encore non mentionnée en Europe, ont également été retrouvés dans toutes les régions françaises à une fréquence importante (15 % en moyenne pour l’échantillonnage national).*Aucune différenciation spatiale entre les espèces putatives n’a pu être mise en évidence : E. alphitoides a souvent été détectée en association avec des isolats de différents types d’ITS dans la même région, le même arbre, voire la même lésion.*Powdery mildew is a major fungal disease of oaks in Europe. Recent studies using internal transcribed spacer (ITS) sequences suggested the presence of four different lineages (putative species). The objective of the study was to investigate the spatial distribution of these lineages/species and, in particular, to test the hypothesis of a spatial differentiation, at various scales: regional (France), altitudinal (a Pyrenean transect) and local (within a forest plot).*Detection methods for the four ITS types were developed: (1) single strand conformation polymorphism analysis (SSCP); (2) PCR amplifications, for which specific primers were designed. SSCP proved to be efficient for the detection of Erysiphe alphitoides and E. quercicola types. In contrast, the rarer ITS types corresponding to E. hypophylla and Phyllactinia guttata (sensu lato) were only detected by specific amplification.*The study confirmed the strong predominance of the ITS sequence associated with E. alphitoides at all spatial scales (with a frequency higher than 80%). Isolates presumably belonging to E. quercicola (i.e. with same ITS type), a recently described species not yet recorded in Europe, were also found in all French regions at a significant frequency (15% at national level).*No pattern of spatial differentiation between the putative species could be demonstrated: E. alphitoides was often found in association with different ITS types in the same region, the same tree, and even in the same lesion

Interspecific and intraspecific diversity in oak powdery mildews in Europe : coevolution history and adaptation to their hosts

Quercus has been reported as the genus with the largest number of attacking powdery mildews. In Europe, oak powdery mildew was rarely reported before 1907, when severe outbreaks were observed. These epidemics were attributed to the newly described species Erysiphe alphitoides, presumed to be of exotic origin. After the burst of interest following the emergence of the disease, research on this topic remained very limited. Interest in research was recently reactivated in response to the availability of molecular tools. This review summarizes current knowledge on the diversity of oak powdery mildews in Europe and their possible evolutionary relationships with European oaks. The most striking results are the evidence of cryptic diversity (detection in France of a lineage closely related to Erysiphe quercicola, previously thought to only have an Asian distribution), large host range (similarity of E. alphitoides and E. quercicola with powdery mildews of tropical plants) but also local adaptation to Quercus robur. These recent findings highlight the complexity of the history of oak powdery mildew in Europe and point to the question of host specialization and host jumps in the evolution of powdery mildew fungi

Preliminary essay on the aggressiveness of Pyrenophora tritici-repentis towards five Tunisian varieties of durum wheat (Triticum durum). Tissaoui, S., Kamel, S., Mougou-Hamdane, A., Chérif, M., and Nasraoui, B. (Tunisia)

This preliminary study aimed to evaluate reaction of fiveTunisian commercial varieties of durum wheat against six populations of Pyrenophora tritici-repentis (Ptr), the causal agent of tan spot, collected from different Tunisian northern regions. Seedlings were sown in growth chamber and inoculated by foliar spray of Ptr suspension. The reactions of durum wheat varieties were evaluated 10 days postinoculation based on necrosis and/or chlorosis severity on leaves. This assessment revealed symptoms of variable intensity on wheat seedlings, with populationsP1 and P6 three times more aggressive than population P5. The variety behavior was quite similar, however Salim followed by Maali were found be the most susceptible ones and Nasr was the most relatively resistant

Quantitative trait loci for resistance to pathogens in pedunculate oak (Quercus robur L.)

International audienc

Barley Net Blotch in Tunisia: Areal Distribution, Forms and Molecular Identification

Net blotch is one of the most important diseases of barley in Tunisia and it frequently causes heavy yield losses. The causal fungal agent is Pyrenophora teres (anamorph: Drechslera teres) with two forms, P. teres f. teres and P. teres f. maculata showing the net type and the spot type symptoms, respectively. In the current study, we characterized the distribution and the severity of the disease in Northern Tunisian areas. It was easy to differentiate the symptoms caused by the two fungal forms (net and spot), but no morphological difference between conidia of these forms was observed. The confirmation of the identity of the fungus was achieved based on molecular techniques, using two specific primers, PTT for the net form and PTM for the spot form

Progression of wheat Tan spot under different bioclimatic stages and agricultural practices

Tan spot, caused by Pyrenophora tritici-repentis, is a severe worldwide wheat foliar disease and has become common in Tunisia. Two hundred wheat field surveys were conducted in northern Tunisia during the 2017-2019 seasons to determine disease intensity and the correlation of the tan spot with agricultural practices and environmental factors. The disease infested 67% of the visited regions. The highest prevalence (87.5%), incidence (> 30%), and severity (> 10%) were observed in sub-humid regions, contrary to the middle semi-arid regions. Logistic regression was used to analyse the correlation of incidence and severity with various factors as independent variables. In a multiple variable model, the bioclimatic stages, variety, previous crop, humidity, and rainfall were significantly associated with tan spot incidence and severity. High incidence and severity were significantly correlated to the sub-humid regions, varieties Maâli, Razzak, Karim, and Carioca, rainfall, high level of humidity, and monoculture. The correlation between the tan spot and several environmental factors must be considered to ensure successful and sustainable disease management strategies