Bases moléculaires de la variation clonale chez la vigne (Vitis vinifera L.) (approche pangénomique)

L'exploitation de la variation clonale est une des voies d'amélioration utilisée chez un grand nombre de plantes d'intérêts agronomiques telles que la pomme de terre, le café et la vigne. En effet, après plusieurs cycles de reproduction végétative, des caractéristiques agronomiques stables apparaissent donnant naissance à une diversité phénotypique remarquable, appelée diversité clonale . Chez la vigne, cette diversité clonale est d'une importance majeure pour les viticulteurs puisqu'elle permet une amélioration variétale sans changer d'identité de cépage en conformité avec la réglementation fixée par Appellations d'Origine Protégée. L'hypothèse la plus parcimonieuse expliquant cette diversité phénotypique clonale est l'accumulation de mutations somatiques au cours des cycles de reproduction végétative. L'objectif de cette thèse a été de dresser un panorama le plus exhaustif possible des différents polymorphismes moléculaires entre les génomes de plusieurs clones. Dans un premier temps trois clones de Pinot ont été séquencés par la technique 454 GS-FLX puis dans un second temps 11 clones de quatre cépages ont été séquencés la technique Illumina HiSeq 2000. Afin d'analyser la grande quantité de données obtenues, nous avons construit un pipeline d'analyse (Bacchus pipeline) permettant d'identifier tous les types de polymorphismes moléculaires entre les différents génomes.Nos résultats permettent, pour la première fois un inventaire exhaustif des polymorphismes moléculaires dans un contexte multiplication végétatif. L'ensemble des mutations polymorphes entre deux clones a pu être identifié, SNPs, indels (2,5 SNPs et 11,5 indels par Mb en moyenne) ainsi que des variations d'ordre structural (larges insertions ou délétions) représentant la classe la plus fréquente (129 évènements par Mb entre deux clones en moyenne). Afin d'évaluer le polymorphisme d'insertion généré par ces éléments nous en avons étudié quatre par une approche S-SAP sur plusieurs niveaux de diversité (inter-espèces, inter-cépages, inter-clones et entre plusieurs tissus d'un même individu). L'analyse phylogénétique au niveau des espèces est conforme à celle réalisée avec d'autres types de marqueurs moléculaires (SSR, SNP). Cependant, une forte instabilité de ces insertions a été confirmée entre les clones et entre les tissus d'un même d'individu. L'identification des clones par une méthodologie moléculaire serait d'une grande importance pour la filère. Pour cet objectif, nos résultats indiquent que les mutations de types SNP et petits indels qui sont certes moins fréquentes que les variations structurales mais qui sont plus stables semblent plus pertinentes pour la mise en place d'une méthodologie d'identification des clonesClonal variation is considered as an effective contribution to breeding programs of vegetatively propagated species with major agronomical interest such as banana, potato, coffee and grape. Indeed, after several propagation cycles, stable and heritable phenotypic variations appear giving rise to a phenotypic variation termed clonal diversity . This clonal diversity is very important for wine-growers because it allows preserving cultivars identity in the strict respect of Appellation (A.O.P) wines specifications The most parsimonious hypothesis explaining clonal phenotypic diversity is the accumulation of somatic mutations. The objective of my thesis was to provide a broad description of molecular polymorphisms in the context of vegetative propagation. Three clones were first sequenced by 454 GS-FLX technology and eleven clones were then sequenced with Illumina Hiseq2000 technique. To analyse the high quantity of data obtained, we built a pipeline (Bacchus pipeline) allowing the identification of all existing molecular polymorphisms between different genomes.All polymorphism types were observed: indels and SNPs which have a low polymorphism frequency (2.5 SNPs and 11.5 indels per Mb between two clones in average) and structural variations (large insertions or deletions) which have a high polymorphism frequency (129 per Mb between two clones in average) but are unstable. To evaluate stability and polymorphism level of these transposable elements, we have studied 4 elements using S-SAP method at different diversity levels (inter-species, inter-cultivars, inter-clones and between organs/tissues of a single individual). Our interspecific phylogenetic analysis is similar to other phylogenies performed with SSR or SNPs markers. However, we confirm the high instability of these elements between clones and between tissues in single individuals.Clone identification through molecular methods would be of high significance for the wine industry. SNP or small indels mutations are less frequent but more stable than structural variation and could be used for accurate clone identification.MONTPELLIER-SupAgro La Gaillarde (341722306) / SudocSudocFranceF

Transposable Elements Are a Major Cause of Somatic Polymorphism in Vitis vinifera L.

Through multiple vegetative propagation cycles, clones accumulate mutations in somatic cells that are at the origin of clonal phenotypic diversity in grape. Clonal diversity provided clones such as Cabernet-Sauvignon N°470, Chardonnay N° 548 and Pinot noir N° 777 which all produce wines of superior quality. The economic impact of clonal selection is therefore very high: since approx. 95% of the grapevines produced in French nurseries originate from the French clonal selection. In this study we provide the first broad description of polymorphism in different clones of a single grapevine cultivar, Pinot noir, in the context of vegetative propagation. Genome sequencing was performed using 454 GS-FLX methodology without a priori, in order to identify and quantify for the first time molecular polymorphisms responsible for clonal variability in grapevine. New generation sequencing (NGS) was used to compare a large portion of the genome of three Pinot noir clones selected for their phenotypic differences. Reads obtained with NGS and the sequence of Pinot noir ENTAV-INRA® 115 sequenced by Velasco et al., were aligned on the PN40024 reference sequence. We then searched for molecular polymorphism between clones. Three types of polymorphism (SNPs, Indels, mobile elements) were found but insertion polymorphism generated by mobile elements of many families displayed the highest mutational event with respect to clonal variation. Mobile elements inducing insertion polymorphism in the genome of Pinot noir were identified and classified and a list is presented in this study as potential markers for the study of clonal variation. Among these, the dynamic of four mobile elements with a high polymorphism level were analyzed and insertion polymorphism was confirmed in all the Pinot clones registered in France

COVID-19 symptoms at hospital admission vary with age and sex: results from the ISARIC prospective multinational observational study

Background: The ISARIC prospective multinational observational study is the largest cohort of hospitalized patients with COVID-19. We present relationships of age, sex, and nationality to presenting symptoms. Methods: International, prospective observational study of 60 109 hospitalized symptomatic patients with laboratory-confirmed COVID-19 recruited from 43 countries between 30 January and 3 August 2020. Logistic regression was performed to evaluate relationships of age and sex to published COVID-19 case definitions and the most commonly reported symptoms. Results: ‘Typical’ symptoms of fever (69%), cough (68%) and shortness of breath (66%) were the most commonly reported. 92% of patients experienced at least one of these. Prevalence of typical symptoms was greatest in 30- to 60-year-olds (respectively 80, 79, 69%; at least one 95%). They were reported less frequently in children (≤ 18 years: 69, 48, 23; 85%), older adults (≥ 70 years: 61, 62, 65; 90%), and women (66, 66, 64; 90%; vs. men 71, 70, 67; 93%, each P < 0.001). The most common atypical presentations under 60 years of age were nausea and vomiting and abdominal pain, and over 60 years was confusion. Regression models showed significant differences in symptoms with sex, age and country. Interpretation: This international collaboration has allowed us to report reliable symptom data from the largest cohort of patients admitted to hospital with COVID-19. Adults over 60 and children admitted to hospital with COVID-19 are less likely to present with typical symptoms. Nausea and vomiting are common atypical presentations under 30 years. Confusion is a frequent atypical presentation of COVID-19 in adults over 60 years. Women are less likely to experience typical symptoms than men

Molecular bases of clonal variation from grape (Vitis Vinifera L.)

L'exploitation de la variation clonale est une des voies d'amélioration utilisée chez un grand nombre de plantes d'intérêts agronomiques telles que la pomme de terre, le café et la vigne. En effet, après plusieurs cycles de reproduction végétative, des caractéristiques agronomiques stables apparaissent donnant naissance à une diversité phénotypique remarquable, appelée « diversité clonale ». Chez la vigne, cette diversité clonale est d'une importance majeure pour les viticulteurs puisqu'elle permet une amélioration variétale sans changer d'identité de cépage en conformité avec la réglementation fixée par Appellations d'Origine Protégée. L'hypothèse la plus parcimonieuse expliquant cette diversité phénotypique clonale est l'accumulation de mutations somatiques au cours des cycles de reproduction végétative. L'objectif de cette thèse a été de dresser un panorama le plus exhaustif possible des différents polymorphismes moléculaires entre les génomes de plusieurs clones. Dans un premier temps trois clones de Pinot ont été séquencés par la technique 454 GS-FLX puis dans un second temps 11 clones de quatre cépages ont été séquencés la technique Illumina HiSeq 2000. Afin d'analyser la grande quantité de données obtenues, nous avons construit un pipeline d'analyse (Bacchus pipeline) permettant d'identifier tous les types de polymorphismes moléculaires entre les différents génomes.Nos résultats permettent, pour la première fois un inventaire exhaustif des polymorphismes moléculaires dans un contexte multiplication végétatif. L'ensemble des mutations polymorphes entre deux clones a pu être identifié, SNPs, indels (2,5 SNPs et 11,5 indels par Mb en moyenne) ainsi que des variations d'ordre structural (larges insertions ou délétions) représentant la classe la plus fréquente (129 évènements par Mb entre deux clones en moyenne). Afin d'évaluer le polymorphisme d'insertion généré par ces éléments nous en avons étudié quatre par une approche S-SAP sur plusieurs niveaux de diversité (inter-espèces, inter-cépages, inter-clones et entre plusieurs tissus d'un même individu). L'analyse phylogénétique au niveau des espèces est conforme à celle réalisée avec d'autres types de marqueurs moléculaires (SSR, SNP). Cependant, une forte instabilité de ces insertions a été confirmée entre les clones et entre les tissus d'un même d'individu. L'identification des clones par une méthodologie moléculaire serait d'une grande importance pour la filère. Pour cet objectif, nos résultats indiquent que les mutations de types SNP et petits indels qui sont certes moins fréquentes que les variations structurales mais qui sont plus stables semblent plus pertinentes pour la mise en place d'une méthodologie d'identification des clonesClonal variation is considered as an effective contribution to breeding programs of vegetatively propagated species with major agronomical interest such as banana, potato, coffee and grape. Indeed, after several propagation cycles, stable and heritable phenotypic variations appear giving rise to a phenotypic variation termed “clonal diversity”. This clonal diversity is very important for wine-growers because it allows preserving cultivars identity in the strict respect of Appellation (A.O.P) wines specifications The most parsimonious hypothesis explaining clonal phenotypic diversity is the accumulation of somatic mutations. The objective of my thesis was to provide a broad description of molecular polymorphisms in the context of vegetative propagation. Three clones were first sequenced by 454 GS-FLX technology and eleven clones were then sequenced with Illumina Hiseq2000 technique. To analyse the high quantity of data obtained, we built a pipeline (Bacchus pipeline) allowing the identification of all existing molecular polymorphisms between different genomes.All polymorphism types were observed: indels and SNPs which have a low polymorphism frequency (2.5 SNPs and 11.5 indels per Mb between two clones in average) and structural variations (large insertions or deletions) which have a high polymorphism frequency (129 per Mb between two clones in average) but are unstable. To evaluate stability and polymorphism level of these transposable elements, we have studied 4 elements using S-SAP method at different diversity levels (inter-species, inter-cultivars, inter-clones and between organs/tissues of a single individual). Our interspecific phylogenetic analysis is similar to other phylogenies performed with SSR or SNPs markers. However, we confirm the high instability of these elements between clones and between tissues in single individuals.Clone identification through molecular methods would be of high significance for the wine industry. SNP or small indels mutations are less frequent but more stable than structural variation and could be used for accurate clone identification

Dynamic behavior and failure of the base and heat affected materials of a HSS fillet welded joint

Welded joints, due to their manufacturing process, are commonly weakened areas. This study analyses the dynamic behavior of the Base Metal (BM) and the Heat-Affected Zone (HAZ) materials of a HSS (High Strength Steel) fillet welded joint. First, a specific approach is developed to generate the HAZ material using a thermal treatment. Hardness and grain size are used to validate the replicated HAZ. This approach appears efficient and repeatable. Secondly, the true stress-strain quasi-static and dynamic behaviors up to failure of the BM and the HAZ are determined. This characterization is performed thanks to video tracking procedure and Bridgman-LeRoy correction. The comparison between these two materials shows that the thermal field of the welding process increases the HAZ yield stress and hardening while decreasing the strain at failure. It appears that the base metal is not rate sensitive from quasi-static up to 1350 s−1. On the contrary, the heat affected material appears to be rate sensitive but by softening. This unexpected dynamic material softening requires further analyses

Varia

La rubrique Varia regroupe tous les articles qui ne font pas partie d'un dossier thématique. Ces articles peuvent cependant être soit entièrement indépendants, soit réagir à ou compléter un dossier thématique paru précédemment. Pour cette rubrique, les contributions acceptées par le comité de lecture de la revue sont publiées tout au long de l'année, sans périodicité fixe

Additional file 4: of A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea

Sequences alignment of the peptides matching on the predicted TE proteins. This file contains the alignment of the peptides matching on the predicted proteins of the TIR/Mariner Luffy and the TIR/hAT Ace. (PDF 996 kb

Additional file 2: of A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea

Percentage of identity between copies of the expressed TE families. This file lists the percentage of identity between the TE copies of the 17 expressed TE families identified in the genome of Tisochrysis lutea. (XLSX 19 kb

Additional file 5: of A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea

List of non-inventoried sequences added to the databanks used by the pipeline PiRATE. This file lists the non-inventoried sequences added to the databanks used by the pipeline PiRATE, they belong to algae and cyanobacteria. (XLSX 23 kb