Dynamics of Molecular Evolution and Phylogeography of Barley yellow dwarf virus-PAV

Barley yellow dwarf virus (BYDV) species PAV occurs frequently in irrigated wheat fields worldwide and can be efficiently transmitted by aphids. Isolates of BYDV-PAV from different countries show great divergence both in genomic sequences and pathogenicity. Despite its economical importance, the genetic structure of natural BYDV-PAV populations, as well as of the mechanisms maintaining its high diversity, remain poorly explored. In this study, we investigate the dynamics of BYDV-PAV genome evolution utilizing time-structured data sets of complete genomic sequences from 58 isolates from different hosts obtained worldwide. First, we observed that BYDV-PAV exhibits a high frequency of homologous recombination. Second, our analysis revealed that BYDV-PAV genome evolves under purifying selection and at a substitution rate similar to other RNA viruses (3.158×10−4 nucleotide substitutions/site/year). Phylogeography analyses show that the diversification of BYDV-PAV can be explained by local geographic adaptation as well as by host-driven adaptation. These results increase our understanding of the diversity, molecular evolutionary characteristics and epidemiological properties of an economically important plant RNA virus

Populations naturelles du BYDV-PAV en jachère fixe de Raygrass et en grande culture de céréales

absentLa jaunisse nanisante de l'orge est une maladie qui entraine des pertes de rendement considérables chez les céréales à paille. Elle est associée à plusieurs virus de la famille des lutéoviridae (pav, mav, rpv, rmv, sgv, gpv). Des prélèvements effectues dans plusieurs parcelles de raygrass cultives en jachère, dans le val d’Oise, ont montré que les virus pav, mav et rpv sont présents a des fréquences variables, mais non négligeables. L'impact du flux viral des plantes réservoirs (graminées pérennes, repousses, mais), vers les céréales est, jusque-là, difficilement quantifiable, en absence de marqueurs hote-spécifique, aussi bien aphidien que viraux. Néanmoins l'analyse des propriétés biologiques et sérologiques d'isolats de pav (le virus le plus répandue), a révélé que le raygrass héberge des isolats létaux pour l'orge. Certains de ces isolats déterminent des symptômes particuliers chez le maïs. L'analyse de la variabilité moléculaire du gène capside de pav provenant de différentes plantes hôtes (orge, blé, mais, raygrass), a montré que les populations du pav se subdivisent en deux groupes cpa et cpb. Le groupe cpb est quasi absent dans le raygrass et majoritaire dans les céréales et le maïs (>70%). A partir d'un panel d'anticorps anti-protéines de structure de ce virus cette dichotomie a été mise en évidence et d'autres variants sérologiques rares ont été détectés. Certains monoclonaux, bien que dirigés contre des épitopes conformationels ont confirmé l'existence de contraintes structurales communes aux deux genres de la famille des lutéoviridae (lutéovirus, polérovirus). L'analyse de séquences partielles de la moitie 3 de 23 isolats du groupe cpa (dont certains entrainent la mort d'un cultivar d'orge sensible), a montré que ce groupe est génétiquement hétérogène. Les différents domaines génomiques évoluent a des vitesses variables illustrant l'existence de contraintes différentes. La comparaison des séquences des isolats létaux et modérés, a révélé l'existence de substitutions et d'insertions, dont le lien avec l'agressivité n'a pu être montre. Ces données biologiques moléculaires et immunologiques peuvent être exploitées dans le cadre de l'étude des flux de ce virus

Sequence of the 3' halves of the genomes of barley yellow dwarf virus-PAV cpA isolates that vary in symptom severity

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Nano-Heteroepitaxy An Investigation of SiGe Pillars Coalescence

International audienceIn this paper, SiGe nano-pillars coalescence was investigated using a 300 mm industrial Reduced Pressure-Chemical Vapor Deposition tool. An integration scheme based on diblock copolymer patterning provided nanometer size templates for the selective epitaxy of SiGe 25% nano-pillars. In order to study coalescence, thicknesses ranging from 20 to 35 nm were grown and samples characterized by Atomic Force Microscopy, X-Ray Diffraction, Scanning Spreading Resistance Microscopy and Transmission Electron Microscopy. The evolution in terms of grain shape, size and number was examined, with individual pillars merging into larger grains above 30 nm thickness. High degrees of macroscopic strain relaxation were obtained at the different stages of nano-pillars merging. Defects such as stacking faults and twins were identified as occurring at the early stages of nano-pillar coalescence

Book 7 of Ibn al-Nafīs’s commentary on the Hippocratic Aphorisms

The interest in plant virus evolution can be dated to the late 1920s, when it was shown that plant virus populations were genetically heterogeneous, and that Ihcir composition changed according to the experimental conditions. Many important ideas were generated prior to the era of molecular virology, such as the role of hostand vector-associated selection in virus evolution, and also that small populations, gene coadaptation and evolutionary trade-offs could limit the efficiency of selection. The analysis of viral genomes in the 1980s and 1990s established the quasispecieslike structure of their populations and allowed extensive analyses of the relationships among vims strains and species. The concept that vims populations had huge sizes and high rates of adaptive mutations became prevalent in this period, with selection mostly invoked as explaining observed patterns of population structure and evolution. In recent times vims evolution has been coming into line with evolutionary biology, and a more complex scenario has emerged. Population bottlenecks during host colonization, during host-to-host transmission or during host population fluctuations may result in smaller population sizes, and genetic drift has been recognized as an important evolutionary factor. Also, particularities of viral genomes such as low levels of neutrality, multifunctionality of coding and encoded sequences or strong epistasis could constrain the plasticity of viral genomes and hinder their response to selection. Exploring the complexities of plant vims evolution will continue to be a challenge for the future, particularly as it affects host, vector and ecosystem dynamics