Analyse de la diversité génétique d'une population restauratrice de fertilité utilisée pour la création de variétés hybrides de riz (Oryza sativa L.)

Afin d'analyser la diversité génétique d'une population restauratrice de fertilité utilisée pour la création de variétés hybrides de riz (Oryza sativa L.), le polymorphisme de 22 loci microsatellites a été examiné sur un échantillon de 150 plantes issues de cette population. L'absence de déficit en hétérozygote (Fis=0,001) a confirmé le comportement panmictique de la population rendue artificiellement allogame par l'utilisation d'un système de stérilité mâle monogénique. La diversité génétique de la population s'est avérée relativement élevée avec un nombre moyen d'allèles détectés par locus égal à 4,32 et un taux d'hétérozygotie de 0,437. Environ la moitié des allèles a été représentée dans la population à une fréquence inférieure à 10%. La population, comparée à la diversité globale des riz cultivés d'origine asiatique, a montré une forte similitude avec les riz indica, mais quelques allèles spécifiques au groupe des japonica ont été trouvés. Les variétés indica IR5, IR8, IR36 et Peta se sont montrées les plus proches génétiquement de la population. Les 7 lignées A avec lesquelles la population est croisée pour l'obtention d'hybrides, se sont avérées appartenir pleinement au groupe des riz indica. Les distances génétiques qui existent entre la population restauratrice et les lignées A, ont été estimées. De tels résultats devraient permettre, d'une part, d'ajuster la richesse allélique de la population pour la rendre plus représentative des riz indica et, d'autre part, de mieux comprendre, aux travers de dispositifs expérimentaux adéquats, la relation qui existe chez le riz entre l'effet d'hétérosis observé chez un hybride et la divergence génétique de ses parents. (Résumé d'auteur

Découverte et analyse de séquences de type Geminiviridae intégrées au génome des Dioscoreaceae : une aide pour la phylogénie ?

Des séquences virales de type Geminiviridae intégrées au génome de quatre espèces d'ignames asiatiques (Dioscorea spp. section Enantiophyllum) ont récemment été découvertes par deux méthodes indépendantes : recherche sans a priori de virus par approche métagénomique, et recherche in silico dans les banques de séquences EST. La caractérisation de ces séquences par Long-PCR et Inverse-PCR, a permis de mettre en évidence des génomes viraux incomplets présentant une forte homologie avec des begomovirus. Des gènes codant pour des protéines de réplication (Rep) et des activateurs de réplication (REn), ainsi que des régions intergéniques (IR) ont été identifiés, mais aucun gène de CP n'a été trouvé. Un fragment de 3086 pb comprenant notamment 2 Rep partielles a été obtenu suggérant la disposition en concaténaire de copies de génomes viraux. Des analyses FISH sur plaques métaphasiques ont confirmé l'intégration de séquences virales chez deux espèces (D. alata et D. nummularia) et révélé un unique locus d'intégration. La recherche de telles séquences chez d'autres espèces d'ignames est envisagée pour clarifier la phylogénie des Enantiophyllum et retracer l'histoire évolutive des begomovirus. (Texte intégral

Evolution of Supermassive Black Holes from Cosmological Simulations

The correlations between the mass of supermassive black holes and properties of their host galaxies are investigated through cosmological simulations. Black holes grow from seeds of 100 solar masses inserted into density peaks present in the redshift range 12-15. Seeds grow essentially by accreting matter from a nuclear disk and also by coalescences resulting from merger episodes. At z=0, our simulations reproduce the black hole mass function and the correlations of the black hole mass both with stellar velocity dispersion and host dark halo mass. Moreover, the evolution of the black hole mass density derived from the present simulations agrees with that derived from the bolometric luminosity function of quasars, indicating that the average accretion history of seeds is adequately reproduced . However, our simulations are unable to form black holes with masses above $10^9 M_{\odot}$ at $z\sim 6$, whose existence is inferred from the bright quasars detected by the Sloan survey in this redshift range.Comment: Talk given at the International Workshop on Astronomy and Relativistic Astrophysics (IWARA 2009), Maresias, Brazil. to be published in the International Journal of Modern Physics

The VgrG Proteins Are "à la Carte" Delivery Systems for Bacterial Type VI Effectors

The bacterial type VI secretion system (T6SS) is a supra-molecular complex akin to bacteriophage tails, with VgrG proteins acting as a puncturing device. The Pseudomonas aeruginosa H1-T6SS has been extensively characterized. It is involved in bacterial killing and in the delivery of three toxins, Tse1–3. Here, we demonstrate the independent contribution of the three H1-T6SS co-regulated vgrG genes, vgrG1abc, to bacterial killing. A putative toxin is encoded in the vicinity of each vgrG gene, supporting the concept of specific VgrG/toxin couples. In this respect, VgrG1c is involved in the delivery of an Rhs protein, RhsP1. The RhsP1 C terminus carries a toxic activity, from which the producing bacterium is protected by a cognate immunity. Similarly, VgrG1a-dependent toxicity is associated with the PA0093 gene encoding a two-domain protein with a putative toxin domain (Toxin_61) at the C terminus. Finally, VgrG1b-dependent killing is detectable upon complementation of a triple vgrG1abc mutant. The VgrG1b-dependent killing is mediated by PA0099, which presents the characteristics of the superfamily nuclease 2 toxin members. Overall, these data develop the concept that VgrGs are indispensable components for the specific delivery of effectors. Several additional vgrG genes are encoded on the P. aeruginosa genome and are not linked genetically to other T6SS genes. A closer inspection of these clusters reveals that they also encode putative toxins. Overall, these associations further support the notion of an original form of secretion system, in which VgrG acts as the carrier

Biofilms and cyclic di-GMP (c-di-GMP) signaling: lessons from Pseudomonas aeruginosa and other bacteria

The cyclic di-GMP (c-di-GMP) second messenger represents a signaling system that regulates many bacterial behaviors and is of key importance for driving the lifestyle switch between motile loner cells and biofilm formers. This review provides an up-to-date compendium of c-di-GMP pathways connected to biofilm formation, biofilm-associated motilities, and other functionalities in the ubiquitous and opportunistic human pathogen Pseudomonas aeruginosa. This bacterium is frequently adopted as a model organism to study bacterial biofilm formation. Importantly, its versatility and adaptation capabilities are linked with a broad range of complex regulatory networks, including a large set of genes involved in c-di-GMP biosynthesis, degradation, and transmission

Diverse circular single-stranded DNA viruses discovered from research greenhouses and agro-ecosystems

This study focuses on the diversity of circular single-stranded DNA (ssDNA) viruses associated with Poaceae growing in the fynbos ecosystem and its neighbouring agroecosystems in the Cape floristic region of Southern Africa. We have developed a sequenceindependent approach that combined two methods, including a first step of rolling circle amplification (RCA) followed by a second step of whole genome amplification (WGA). We have first tested and validated this approach using controls from our laboratory, including 4 Geminiviridae (sugarcane/Sugarcane streak Egypt virus; Datura stramonium/Tomato leaf curl virus, Datura stramonium/Tomato yellow leaf curl virus and Euphorbia caputmedusae/ Euphorbia caput-medusae stunt virus) and 2 double-stranded DNA Caulimoviridae (banana/Banana streak Obino l'Ewai virus and Arabidopsis thaliana/Cauliflower mosaic virus). The RCA/WGA approach was successful for unambiguously detecting the 4 Geminiviridae tested but failed to detect both Caulimoviridae. In addition to the 4 expected Geminiviridae, 2 Mastrevirus (located within the sugarcane plant), two Circovirus (banana and turnip) and three mycoviruses (banana, turnip and Euphorbia caput-medusae) were detected by performing Blast searches. This approach was then used for detecting the presence of circular ssDNA viruses within 23 South African Poaceae. Again, several ssDNA viruses were detected, including Mastrevirus, Begomovirus, Circovirus, mycoviruses and unknown ssDNA viruses. This study confirms the presence of a wealth of ssDNA viral sequences within plants that blur the boundaries between previously well-defined groups and stresses the need to better understand the evolutionary history of circular ssDNA viruses and to revisit current taxonomic classification schemes (Rosario et al., 2012). (Texte intégral

Appui au système national semencier pour la valorisation et l'amélioration variétale des ignames Haïti : rapport de mission du 19 novembre au 4 décembre 2005

Cette mission en république d'Haïti avait essentiellement pour objet d'apporter une analyse critique et un appui au SNS en ce qui concerne les aspects variétaux et l'état sanitaire des différentes ignames cultivées en Haïti. Une tournée dans une des principales zones de culture d'ignames (Grande anse, Sud, Sud-est et Ouest) a permis de se faire une idée de la diversité variétale des ignames et d'y rechercher, notamment, des plantes florifères particulièrement intéressantes pour utilisation en création variétale. Une forte érosion génétique, expliquée en partie par la forte présence des principales maladies (anthracnose sur Dioscorea alata, viroses), a été constatée. Une stratégie visant à accompagner et relancer la production d'igname de qualité est proposée. Elle passe notamment par la sauvegarde et la valorisation des ressources génétiques locales et par l'introduction de ressources exogènes sous forme de clones élites ou de graines non sélectionnées. (Résumé d'auteur

Metagenomic screening of the sugarcane virome in Florida. [P.36]

Viral metagenomics has revolutionized the way pathologists decipher viral diseases. While the impact of this new approach is still debatable in plant virus diagnostics, viral metagenomics has already produced key advances in viral ecology and has the potential to become a central approach for viral surveillance at the ecosystem scale. A viral metagenomics study of the sugarcane virome in Florida was carried out in 2013/2014. One hundred and eighty sugarcane leaf samples were collected from different commercial sugarcane (Saccharum interspecific hybrids) fields in Florida and from other Saccharum and related species taken from two local germplasm collections. Sequence-independent next generation sequencing (NGS) of virion-associated nucleic acids (VANA) was used for detection and identification of viruses present within the collected leaf samples. All four previously reported sugarcane viruses occuring in Florida were detected: Sugarcane yellow leaf virus (149 infected samples out of 180), Sugarcane mosaic virus (2/180), Sugarcane mild mosaic virus (10/180) and Sugarcane bacilliform virus (51/180). Interestingly, this viral metagenomics approach also resulted in the detection of potential new viruses of sugarcane, including Chrysovirus, Mastrevirus, and Umbravirus. This study provided a snapshot vision of the SCYLV genetic diversity in 2013/2014 in Florida where several genotypes of this virus are present. It also allowed us to assemble the whole genome of at least one new mastrevirus species. (Résumé d'auteur

Molecular characterization of Secoviridae and Potexvirus infecting yams (Dioscorea spp)

The prevalence of virus species is generally high among vegetatively?propagated crops, because they cannot be sanitized via seed production and therefore accumulate viruses over long periods of time. In yams (Dioscorea spp), viruses belonging to the families Alphaflexiviridae (genus potexvirus), Betaflexiviridae (genus carlavirus), Caulimoviridae (genus badnavirus), Cucumoviridae (genus cucumovirus) and Potyviridae (genera macluravirus and potyvirus) have been characterized so far. However, it is likely that the diversity of viral species infecting this crop remains underestimated. To test this hypothesis, in silico analyses of ESTs of Dioscorea alata were performed and unveiled the existence of sequences corresponding to several known genera of yam viruses, such as badnavirus and macluravirus, and also to families of unknown yam?associated viruses, including Geminiviridae and Secoviridae. This result has prompted a search for yet uncharacterized viruses infecting yams. RT?PCR performed on crude extracts of symptomatic yams (D. alata, D. trifida) following direct binding of viral particles and using available degenerate primers raised distinct amplification products, which were cloned and sequenced. Some of them displayed significant levels of homologies with potexviruses and with viruses of the family Secoviridae. The 3' end of their genomes was successfully amplified by 3' RACE, cloned and sequenced. Sequence analyses and phylogenetic analyses confirmed the existence in yams of new viral species within the genus potexvirus and the family Secoviridae. These results highlight the need to improve the current taxonomy of yam potexviruses and suggest to further explore the diversity of viruses of the family Secoviridae in yams. (Texte intégral