Angelique Gautier - Academia.edu (original) (raw)

Papers by Angelique Gautier

La transplantation hépatique ne permet pas, à l’heure actuelle, de prendre en charge tous les pat... more La transplantation hépatique ne permet pas, à l’heure actuelle, de prendre en charge tous les patients atteints d’une hépatite aiguë, voire fulminante ou d’une évolution rapide d’une hépatite chronique. En réanimation, il est nécessaire de disposer de systèmes de suppléance qui permettraient d’assurer la majeure partie des fonctions du foie et ainsi maintenir le patient jusqu’à une transplantation ou une possible régénération. Après une brève revue des fonctions qui seraient à suppléer et de la problématique clinique, nous décrivons les dispositifs actuellement disponibles, en insistant sur les principes physiques et chimiques mis en jeu, puis sur les résultats cliniques obtenus. Enfin, nous présentons l’approche dite « bioartificielle », qui aborde la problématique de la suppléance par la voie de l’utilisation de moyens biologiques (ingénierie tissulaire).Today, hepatic transplantation does not allow to take in charge all patients suffering from acute or fulminant liver failure or from a rapid evolution of chronic liver failure. In critical care units, systems for liver supply are necessary to ensure main liver functions and to bridge patient to transplantation or potential regeneration. After a brief review on the functions needed to be supplied and the clinical problems, the available systems are described, with a focus on the physical and chemical principles involved and the clinical results obtained. Finally, the “bio-artificial” approach is presented showing the potential use of biological components (tissue engineering) to supply patients in the future.

Rev Epidemiol Sante Publ, 2008

Annals of Microbiology, 2009

Abstact -Aspergillus genus is an ubiquitous fungal group that colonizes a wide range of substrate... more Abstact -Aspergillus genus is an ubiquitous fungal group that colonizes a wide range of substrates. A total of 100 Tunisian fungal strains isolated at harvest time from fresh and dried grapes were identified within the section Nigri and tested for their ochratoxin A (OTA) producing abilities. Of the isolates, 45% were identified as Aspergillus tubingensis, 34% as Aspergillus niger, 12% as Aspergillus japonicus and 9% as Aspergillus carbonarius. The OTA production was assessed using Czapeck yeast extract agar which revealed that 25% of the isolates belonging to the Aspergillus niger aggregate were OTA producers, while 97% were identified as belonging to the A. carbonarius species. To distinguish between A. niger and A. tubingensis, PCR was used to amplify the ITS-5.8S rDNA for these two strains. The sequence analysis of the PCR products revealed a full similarity between the two species. Thus, a new molecular strategy has been developed based on the targeting of the gene from nitrate reductase (niiA) and nitrite reductase gene (niaD), as well as the intergenic region of the gene (niiA-niaD). The subsequent screening revealed that two new specific primer pairs can be used to identify specifically A. niger and A. tubingensis.

Tout repeuplement, qu'il s'agisse d'une réintroduction en cas de disparition complète de l'espèce... more Tout repeuplement, qu'il s'agisse d'une réintroduction en cas de disparition complète de l'espèce ou d'un renforcement de population, vise à l'établissement d'une population viable dans le long terme. La réussite d'un repeuplement requiert donc plusieurs étapes : la survie des individus lâchés, leur installation sur la zone de lâcher, leur reproduction et l'émancipation de la nouvelle génération, cette dernière étape signant véritablement la fondation de la « nouvelle » population. La réussite d'un repeuplement se juge d'un point de vue démographique. Elle peut être évaluée directement, par exemple par le biais de dénombrements, ou indirectement en utilisant l'information véhiculée par les gènes car les composantes démographique et génétique sont corrélées. Si l'approche moléculaire peut théoriquement permettre d'estimer la taille d'une population, qu'elle soit ou non réintroduite, elle se révèle particulièrement pertinente lorsqu'il s'agit d'estimer le succès d'un renforcement de population. L'outil génétique peut même s'avérer être l'unique moyen d'appréhender cette problématique lorsque

Bulletin De La Societe Des Sciences Naturelles De L Ouest De La France, 2007

BMC Research Notes, 2011

Background: Puccinia striiformis f.sp. tritici (PST), an obligate fungal pathogen causing wheat y... more Background: Puccinia striiformis f.sp. tritici (PST), an obligate fungal pathogen causing wheat yellow/stripe rust, a serious disease, has been used to understand the evolution of crop pathogen using molecular markers. However, numerous questions regarding its evolutionary history and recent migration routes still remains to be addressed, which need the genotyping of a large number of isolates, a process that is limited by both DNA extraction and genotyping methods. To address the two issues, we developed here a method for direct DNA extraction from infected leaves combined with optimized SSR multiplexing. Findings: We report here an efficient protocol for direct fungal DNA extraction from infected leaves, avoiding the costly and time consuming step of spore multiplication. The genotyping strategy we propose, amplified a total of 20 SSRs in three Multiplex PCR reactions, which were highly polymorphic and were able to differentiate different PST populations with high efficiency and accuracy. Conclusion: These two developments enabled a genotyping strategy that could contribute to the development of molecular epidemiology of yellow rust disease, both at a regional or worldwide scale.

Diabetologia, 2010

Aims/hypothesis Risk factors for incident type 2 diabetes, in particular, hepatic markers, have r... more Aims/hypothesis Risk factors for incident type 2 diabetes, in particular, hepatic markers, have rarely been studied in leaner individuals. We aimed to identify the metabolic and hepatic markers associated with incident diabetes in men and women with a BMI of <27 kg/m 2 and to compare them with those in individuals with a BMI of ≥27 kg/m 2 . Methods Risk factors for 9 year incident diabetes were compared in the French Data from an Epidemiological Study on the Insulin Resistance Syndrome (DESIR) cohort. Comparisons were made between the 2,947 participants with a BMI of <27 kg/m 2 and the 879 with a BMI of ≥27 kg/m 2 . Results There were 92 incident cases of diabetes in individuals with a BMI of <27 kg/m 2 and 111 in those with a BMI of ≥27 kg/m 2 . Among those who were not markedly overweight, classical biological markers were associated with 9 year incident diabetes, glycaemia being the strongest predictor. γ-Glutamyltransferase (GGT), either considered as a continuous variable or at levels ≥20 U/l, was associated with incident diabetes, with a stronger effect in the BMI <27 kg/m 2 group: OR 1.59 (95% CI 1.29-1.97, p<0.001) in comparison with OR 1.07 (95% CI 0.82-1.38, p=0.63) for those with a BMI of ≥27 kg/m 2 (results after adjustment for alcohol intake, alanine aminotransferase, waist circumference and the HOMA insulin resistance index). Conclusions/interpretation In individuals with a BMI of <27 kg/m 2 , GGT was the strongest predictor of diabetes after fasting hyperglycaemia. This association with incident diabetes remained after adjustment for conventional markers of insulin resistance, suggesting potential interactions between GGT, enhanced hepatic neoglucogenesis and/or early alterations of insulin secretion.

Bmc Bioinformatics, Oct 27, 2008

The increasing availability of fungal genome sequences provides large numbers of proteins for evo... more The increasing availability of fungal genome sequences provides large numbers of proteins for evolutionary and phylogenetic analyses. However the heterogeneity of data, including the quality of genome annotation and the difficulty of retrieving true orthologs, makes such investigations challenging. The aim of this study was to provide a reliable and integrated resource of orthologous gene families to perform comparative and phylogenetic analyses in fungi.

Diabetologia, 2010

Aims/hypothesis Risk factors for incident type 2 diabetes, in particular, hepatic markers, have r... more Aims/hypothesis Risk factors for incident type 2 diabetes, in particular, hepatic markers, have rarely been studied in leaner individuals. We aimed to identify the metabolic and hepatic markers associated with incident diabetes in men and women with a BMI of <27 kg/m 2 and to compare them with those in individuals with a BMI of ≥27 kg/m 2 . Methods Risk factors for 9 year incident diabetes were compared in the French Data from an Epidemiological Study on the Insulin Resistance Syndrome (DESIR) cohort. Comparisons were made between the 2,947 participants with a BMI of <27 kg/m 2 and the 879 with a BMI of ≥27 kg/m 2 . Results There were 92 incident cases of diabetes in individuals with a BMI of <27 kg/m 2 and 111 in those with a BMI of ≥27 kg/m 2 . Among those who were not markedly overweight, classical biological markers were associated with 9 year incident diabetes, glycaemia being the strongest predictor. γ-Glutamyltransferase (GGT), either considered as a continuous variable or at levels ≥20 U/l, was associated with incident diabetes, with a stronger effect in the BMI <27 kg/m 2 group: OR 1.59 (95% CI 1.29-1.97, p<0.001) in comparison with OR 1.07 (95% CI 0.82-1.38, p=0.63) for those with a BMI of ≥27 kg/m 2 (results after adjustment for alcohol intake, alanine aminotransferase, waist circumference and the HOMA insulin resistance index). Conclusions/interpretation In individuals with a BMI of <27 kg/m 2 , GGT was the strongest predictor of diabetes after fasting hyperglycaemia. This association with incident diabetes remained after adjustment for conventional markers of insulin resistance, suggesting potential interactions between GGT, enhanced hepatic neoglucogenesis and/or early alterations of insulin secretion.

Mol Breeding, 2004

Negative correlations between quality traits and fruit size may hamper the breeding of fresh mark... more Negative correlations between quality traits and fruit size may hamper the breeding of fresh market tomato varieties for better organoleptic qualities. In a recent QTL analysis, QTLs with large effects on fruit weight, locule number and several quality traits were detected in the distal 50 cM of chromosome 2, but favorable alleles for fruit weight and locule number were unfavorable to quality traits. Substitution mapping was undertaken to determine whether the effects were due to a single QTL or to several tightly linked QTLs. Several chromosomal segments were characterized using near-isogenic lines. Five of them appeared to be involved in one or several traits. Considering the five segments from the top to the bottom of the region, the QTLs detected in each segment controlled the variation of: ͑1͒ fruit weight, ͑2͒ soluble solids content and dry matter weight, ͑3͒ fruit weight, ͑4͒ locule number and ͑5͒ fruit weight, dry matter weight, total sugars, titratable acidity and soluble solids content. This last cluster illustrates an antagonism between fruit weight and four quality traits, as favorable alleles are not conferred by the same parent in both cases. Nevertheless, several antagonistic QTLs were separated from each other in the first four segments, holding the promise for marker-assisted improvement of fruit quality traits without compromising the fruit size.

Data Revues 12623636 V36ss1 S1262363610701579, Mar 1, 2010

Molecular ecology resources, Jan 9, 2016

Inferring reproductive and demographic parameters of populations is crucial to our understanding ... more Inferring reproductive and demographic parameters of populations is crucial to our understanding of species ecology and evolutionary potential but can be challenging, especially in partially clonal organisms. Here, we describe a new and accurate method, CloNcaSe, for estimating both the rate of sexual vs. asexual reproduction and the effective population size, based on the frequency of clonemate resampling across generations. Simulations showed that our method provides reliable estimates of sex frequency and effective population size for a wide range of parameters. The CloNcaSe method was applied to Puccinia striiformis f.sp. tritici, a fungal pathogen causing stripe/yellow rust, an important wheat disease. This fungus is highly clonal in Europe but has been suggested to recombine in Asia. Using two temporally-spaced samples of P. striiformis f.sp. tritici in China, the estimated sex frequency was 75% (i.e., three quarter of individuals being sexually derived during the yearly sexua...

ABSTRACT Plus de 10% du vignoble français est actuellement improductif pour cause de maladies aff... more ABSTRACT Plus de 10% du vignoble français est actuellement improductif pour cause de maladies affectant le bois des ceps. L&#39;ESCA, la principale de ces maladies, est en continuelle progression dans le vignoble français et mondial. Cette maladie est préoccupante car il n&#39;existe aucun traitement efficace depuis l&#39;interdiction de l&#39;arsénite de sodium en 2001. L&#39;ESCA serait provoquée par un complexe de micro-organismes (essentiellement des champignons des genres Phaeomoniella, Chlamydospora, Phaeoacremonium et Botryosphaeria) dont les rôles respectifs restent mal connus. La caractérisation de la microflore colonisant les tissus ligneux des ceps de vigne a été entreprise par une approche de métagénomique consistant en un séquençage haut débit (pyroséquençage 454 Roche) de régions génomiques d&#39;intérêt taxonomique (ITS et ADNr 18S fongique, ADNr 16S bactérien) amplifiés à partir d&#39;ADN extraits de bois de vigne à l&#39;aide d&#39;amorces spécifiques de chaque type d&#39;organisme. Un témoin de pyroséquençage a été constitué avec un mélange d&#39;ADN de champignons connus. Un ensemble de 8 échantillons indépendants issus de zones différentes sur des ceps symptomatiques et asymptomatiques ont été utilisés pour amplifier ces régions génomiques par PCR en vue de leur séquençage. Ainsi, 35 produits de PCR étiquetés par leurs amorces sont mélangés pour la construction des banques de pyroséquençage. Parallèlement à ces expériences, le clonage/séquençage de certains produits de PCR a permis de montrer la spécificité des amorces 18S et ITS choisies. Cependant des problèmes de spécificité des primers de l&#39;ADNr 16S ont été rencontrés et de nouvelles amorces seront utilisées pour le second run. Les expériences de pyroséquençage ont été réalisées sur la plateforme Genotoul de Toulouse. Le nombre de séquences obtenues par échantillon varie de 100 à 100 000 séquences brutes pour un total de 1335000 séquences pour le run. Les analyses bioinformatiques ont été d&#39;abord réalisées sur l&#39;échantillon correspondant à un mélange d&#39;ADN fongiques connus, à l&#39;aide d&#39;un pipeline reposant sur les logiciels QIIME et MEGAN. Cette analyse montre qu&#39;il existe un nombre significatif de variations nucléotidiques provenant de la PCR et du séquençage 454, mais qu&#39;il est néanmoins possible de regrouper les séquences par espèce par ces deux méthodes. Cette analyse montre l&#39;intérêt et les limites du pyroséquencage de produits de PCR de régions génomiques.

ABSTRACT Oral - Session 2 : Taxonomie, Phylogénie Et Ecologie Des Communautés

BMC Research Notes, 2014

Background: Zymoseptoria tritici is a hemibiotrophic ascomycete fungus causing leaf blotch of whe... more Background: Zymoseptoria tritici is a hemibiotrophic ascomycete fungus causing leaf blotch of wheat that often decreases yield severely. Populations of the fungus are known to be highly diverse and poorly differentiated from each other. However, a genotyping tool is needed to address further questions in large collections of isolates, regarding regional population structure, adaptation to anthropogenic selective pressures, and dynamics of the recently discovered accessory chromosomes. This procedure is limited by costly and time-consuming simplex PCR genotyping. Recent development of genomic approaches and of larger sets of SSRs enabled the optimization of microsatellite multiplexing.

La transplantation hépatique ne permet pas, à l’heure actuelle, de prendre en charge tous les pat... more La transplantation hépatique ne permet pas, à l’heure actuelle, de prendre en charge tous les patients atteints d’une hépatite aiguë, voire fulminante ou d’une évolution rapide d’une hépatite chronique. En réanimation, il est nécessaire de disposer de systèmes de suppléance qui permettraient d’assurer la majeure partie des fonctions du foie et ainsi maintenir le patient jusqu’à une transplantation ou une possible régénération. Après une brève revue des fonctions qui seraient à suppléer et de la problématique clinique, nous décrivons les dispositifs actuellement disponibles, en insistant sur les principes physiques et chimiques mis en jeu, puis sur les résultats cliniques obtenus. Enfin, nous présentons l’approche dite « bioartificielle », qui aborde la problématique de la suppléance par la voie de l’utilisation de moyens biologiques (ingénierie tissulaire).Today, hepatic transplantation does not allow to take in charge all patients suffering from acute or fulminant liver failure or from a rapid evolution of chronic liver failure. In critical care units, systems for liver supply are necessary to ensure main liver functions and to bridge patient to transplantation or potential regeneration. After a brief review on the functions needed to be supplied and the clinical problems, the available systems are described, with a focus on the physical and chemical principles involved and the clinical results obtained. Finally, the “bio-artificial” approach is presented showing the potential use of biological components (tissue engineering) to supply patients in the future.

Rev Epidemiol Sante Publ, 2008

Annals of Microbiology, 2009

Abstact -Aspergillus genus is an ubiquitous fungal group that colonizes a wide range of substrate... more Abstact -Aspergillus genus is an ubiquitous fungal group that colonizes a wide range of substrates. A total of 100 Tunisian fungal strains isolated at harvest time from fresh and dried grapes were identified within the section Nigri and tested for their ochratoxin A (OTA) producing abilities. Of the isolates, 45% were identified as Aspergillus tubingensis, 34% as Aspergillus niger, 12% as Aspergillus japonicus and 9% as Aspergillus carbonarius. The OTA production was assessed using Czapeck yeast extract agar which revealed that 25% of the isolates belonging to the Aspergillus niger aggregate were OTA producers, while 97% were identified as belonging to the A. carbonarius species. To distinguish between A. niger and A. tubingensis, PCR was used to amplify the ITS-5.8S rDNA for these two strains. The sequence analysis of the PCR products revealed a full similarity between the two species. Thus, a new molecular strategy has been developed based on the targeting of the gene from nitrate reductase (niiA) and nitrite reductase gene (niaD), as well as the intergenic region of the gene (niiA-niaD). The subsequent screening revealed that two new specific primer pairs can be used to identify specifically A. niger and A. tubingensis.

Tout repeuplement, qu'il s'agisse d'une réintroduction en cas de disparition complète de l'espèce... more Tout repeuplement, qu'il s'agisse d'une réintroduction en cas de disparition complète de l'espèce ou d'un renforcement de population, vise à l'établissement d'une population viable dans le long terme. La réussite d'un repeuplement requiert donc plusieurs étapes : la survie des individus lâchés, leur installation sur la zone de lâcher, leur reproduction et l'émancipation de la nouvelle génération, cette dernière étape signant véritablement la fondation de la « nouvelle » population. La réussite d'un repeuplement se juge d'un point de vue démographique. Elle peut être évaluée directement, par exemple par le biais de dénombrements, ou indirectement en utilisant l'information véhiculée par les gènes car les composantes démographique et génétique sont corrélées. Si l'approche moléculaire peut théoriquement permettre d'estimer la taille d'une population, qu'elle soit ou non réintroduite, elle se révèle particulièrement pertinente lorsqu'il s'agit d'estimer le succès d'un renforcement de population. L'outil génétique peut même s'avérer être l'unique moyen d'appréhender cette problématique lorsque

Bulletin De La Societe Des Sciences Naturelles De L Ouest De La France, 2007

BMC Research Notes, 2011

Background: Puccinia striiformis f.sp. tritici (PST), an obligate fungal pathogen causing wheat y... more Background: Puccinia striiformis f.sp. tritici (PST), an obligate fungal pathogen causing wheat yellow/stripe rust, a serious disease, has been used to understand the evolution of crop pathogen using molecular markers. However, numerous questions regarding its evolutionary history and recent migration routes still remains to be addressed, which need the genotyping of a large number of isolates, a process that is limited by both DNA extraction and genotyping methods. To address the two issues, we developed here a method for direct DNA extraction from infected leaves combined with optimized SSR multiplexing. Findings: We report here an efficient protocol for direct fungal DNA extraction from infected leaves, avoiding the costly and time consuming step of spore multiplication. The genotyping strategy we propose, amplified a total of 20 SSRs in three Multiplex PCR reactions, which were highly polymorphic and were able to differentiate different PST populations with high efficiency and accuracy. Conclusion: These two developments enabled a genotyping strategy that could contribute to the development of molecular epidemiology of yellow rust disease, both at a regional or worldwide scale.

Diabetologia, 2010

Aims/hypothesis Risk factors for incident type 2 diabetes, in particular, hepatic markers, have r... more Aims/hypothesis Risk factors for incident type 2 diabetes, in particular, hepatic markers, have rarely been studied in leaner individuals. We aimed to identify the metabolic and hepatic markers associated with incident diabetes in men and women with a BMI of <27 kg/m 2 and to compare them with those in individuals with a BMI of ≥27 kg/m 2 . Methods Risk factors for 9 year incident diabetes were compared in the French Data from an Epidemiological Study on the Insulin Resistance Syndrome (DESIR) cohort. Comparisons were made between the 2,947 participants with a BMI of <27 kg/m 2 and the 879 with a BMI of ≥27 kg/m 2 . Results There were 92 incident cases of diabetes in individuals with a BMI of <27 kg/m 2 and 111 in those with a BMI of ≥27 kg/m 2 . Among those who were not markedly overweight, classical biological markers were associated with 9 year incident diabetes, glycaemia being the strongest predictor. γ-Glutamyltransferase (GGT), either considered as a continuous variable or at levels ≥20 U/l, was associated with incident diabetes, with a stronger effect in the BMI <27 kg/m 2 group: OR 1.59 (95% CI 1.29-1.97, p<0.001) in comparison with OR 1.07 (95% CI 0.82-1.38, p=0.63) for those with a BMI of ≥27 kg/m 2 (results after adjustment for alcohol intake, alanine aminotransferase, waist circumference and the HOMA insulin resistance index). Conclusions/interpretation In individuals with a BMI of <27 kg/m 2 , GGT was the strongest predictor of diabetes after fasting hyperglycaemia. This association with incident diabetes remained after adjustment for conventional markers of insulin resistance, suggesting potential interactions between GGT, enhanced hepatic neoglucogenesis and/or early alterations of insulin secretion.

Bmc Bioinformatics, Oct 27, 2008

The increasing availability of fungal genome sequences provides large numbers of proteins for evo... more The increasing availability of fungal genome sequences provides large numbers of proteins for evolutionary and phylogenetic analyses. However the heterogeneity of data, including the quality of genome annotation and the difficulty of retrieving true orthologs, makes such investigations challenging. The aim of this study was to provide a reliable and integrated resource of orthologous gene families to perform comparative and phylogenetic analyses in fungi.

Diabetologia, 2010

Aims/hypothesis Risk factors for incident type 2 diabetes, in particular, hepatic markers, have r... more Aims/hypothesis Risk factors for incident type 2 diabetes, in particular, hepatic markers, have rarely been studied in leaner individuals. We aimed to identify the metabolic and hepatic markers associated with incident diabetes in men and women with a BMI of <27 kg/m 2 and to compare them with those in individuals with a BMI of ≥27 kg/m 2 . Methods Risk factors for 9 year incident diabetes were compared in the French Data from an Epidemiological Study on the Insulin Resistance Syndrome (DESIR) cohort. Comparisons were made between the 2,947 participants with a BMI of <27 kg/m 2 and the 879 with a BMI of ≥27 kg/m 2 . Results There were 92 incident cases of diabetes in individuals with a BMI of <27 kg/m 2 and 111 in those with a BMI of ≥27 kg/m 2 . Among those who were not markedly overweight, classical biological markers were associated with 9 year incident diabetes, glycaemia being the strongest predictor. γ-Glutamyltransferase (GGT), either considered as a continuous variable or at levels ≥20 U/l, was associated with incident diabetes, with a stronger effect in the BMI <27 kg/m 2 group: OR 1.59 (95% CI 1.29-1.97, p<0.001) in comparison with OR 1.07 (95% CI 0.82-1.38, p=0.63) for those with a BMI of ≥27 kg/m 2 (results after adjustment for alcohol intake, alanine aminotransferase, waist circumference and the HOMA insulin resistance index). Conclusions/interpretation In individuals with a BMI of <27 kg/m 2 , GGT was the strongest predictor of diabetes after fasting hyperglycaemia. This association with incident diabetes remained after adjustment for conventional markers of insulin resistance, suggesting potential interactions between GGT, enhanced hepatic neoglucogenesis and/or early alterations of insulin secretion.

Mol Breeding, 2004

Negative correlations between quality traits and fruit size may hamper the breeding of fresh mark... more Negative correlations between quality traits and fruit size may hamper the breeding of fresh market tomato varieties for better organoleptic qualities. In a recent QTL analysis, QTLs with large effects on fruit weight, locule number and several quality traits were detected in the distal 50 cM of chromosome 2, but favorable alleles for fruit weight and locule number were unfavorable to quality traits. Substitution mapping was undertaken to determine whether the effects were due to a single QTL or to several tightly linked QTLs. Several chromosomal segments were characterized using near-isogenic lines. Five of them appeared to be involved in one or several traits. Considering the five segments from the top to the bottom of the region, the QTLs detected in each segment controlled the variation of: ͑1͒ fruit weight, ͑2͒ soluble solids content and dry matter weight, ͑3͒ fruit weight, ͑4͒ locule number and ͑5͒ fruit weight, dry matter weight, total sugars, titratable acidity and soluble solids content. This last cluster illustrates an antagonism between fruit weight and four quality traits, as favorable alleles are not conferred by the same parent in both cases. Nevertheless, several antagonistic QTLs were separated from each other in the first four segments, holding the promise for marker-assisted improvement of fruit quality traits without compromising the fruit size.

Data Revues 12623636 V36ss1 S1262363610701579, Mar 1, 2010

Molecular ecology resources, Jan 9, 2016

Inferring reproductive and demographic parameters of populations is crucial to our understanding ... more Inferring reproductive and demographic parameters of populations is crucial to our understanding of species ecology and evolutionary potential but can be challenging, especially in partially clonal organisms. Here, we describe a new and accurate method, CloNcaSe, for estimating both the rate of sexual vs. asexual reproduction and the effective population size, based on the frequency of clonemate resampling across generations. Simulations showed that our method provides reliable estimates of sex frequency and effective population size for a wide range of parameters. The CloNcaSe method was applied to Puccinia striiformis f.sp. tritici, a fungal pathogen causing stripe/yellow rust, an important wheat disease. This fungus is highly clonal in Europe but has been suggested to recombine in Asia. Using two temporally-spaced samples of P. striiformis f.sp. tritici in China, the estimated sex frequency was 75% (i.e., three quarter of individuals being sexually derived during the yearly sexua...

ABSTRACT Plus de 10% du vignoble français est actuellement improductif pour cause de maladies aff... more ABSTRACT Plus de 10% du vignoble français est actuellement improductif pour cause de maladies affectant le bois des ceps. L&#39;ESCA, la principale de ces maladies, est en continuelle progression dans le vignoble français et mondial. Cette maladie est préoccupante car il n&#39;existe aucun traitement efficace depuis l&#39;interdiction de l&#39;arsénite de sodium en 2001. L&#39;ESCA serait provoquée par un complexe de micro-organismes (essentiellement des champignons des genres Phaeomoniella, Chlamydospora, Phaeoacremonium et Botryosphaeria) dont les rôles respectifs restent mal connus. La caractérisation de la microflore colonisant les tissus ligneux des ceps de vigne a été entreprise par une approche de métagénomique consistant en un séquençage haut débit (pyroséquençage 454 Roche) de régions génomiques d&#39;intérêt taxonomique (ITS et ADNr 18S fongique, ADNr 16S bactérien) amplifiés à partir d&#39;ADN extraits de bois de vigne à l&#39;aide d&#39;amorces spécifiques de chaque type d&#39;organisme. Un témoin de pyroséquençage a été constitué avec un mélange d&#39;ADN de champignons connus. Un ensemble de 8 échantillons indépendants issus de zones différentes sur des ceps symptomatiques et asymptomatiques ont été utilisés pour amplifier ces régions génomiques par PCR en vue de leur séquençage. Ainsi, 35 produits de PCR étiquetés par leurs amorces sont mélangés pour la construction des banques de pyroséquençage. Parallèlement à ces expériences, le clonage/séquençage de certains produits de PCR a permis de montrer la spécificité des amorces 18S et ITS choisies. Cependant des problèmes de spécificité des primers de l&#39;ADNr 16S ont été rencontrés et de nouvelles amorces seront utilisées pour le second run. Les expériences de pyroséquençage ont été réalisées sur la plateforme Genotoul de Toulouse. Le nombre de séquences obtenues par échantillon varie de 100 à 100 000 séquences brutes pour un total de 1335000 séquences pour le run. Les analyses bioinformatiques ont été d&#39;abord réalisées sur l&#39;échantillon correspondant à un mélange d&#39;ADN fongiques connus, à l&#39;aide d&#39;un pipeline reposant sur les logiciels QIIME et MEGAN. Cette analyse montre qu&#39;il existe un nombre significatif de variations nucléotidiques provenant de la PCR et du séquençage 454, mais qu&#39;il est néanmoins possible de regrouper les séquences par espèce par ces deux méthodes. Cette analyse montre l&#39;intérêt et les limites du pyroséquencage de produits de PCR de régions génomiques.

ABSTRACT Oral - Session 2 : Taxonomie, Phylogénie Et Ecologie Des Communautés

BMC Research Notes, 2014

Background: Zymoseptoria tritici is a hemibiotrophic ascomycete fungus causing leaf blotch of whe... more Background: Zymoseptoria tritici is a hemibiotrophic ascomycete fungus causing leaf blotch of wheat that often decreases yield severely. Populations of the fungus are known to be highly diverse and poorly differentiated from each other. However, a genotyping tool is needed to address further questions in large collections of isolates, regarding regional population structure, adaptation to anthropogenic selective pressures, and dynamics of the recently discovered accessory chromosomes. This procedure is limited by costly and time-consuming simplex PCR genotyping. Recent development of genomic approaches and of larger sets of SSRs enabled the optimization of microsatellite multiplexing.