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Synteny-guided resolution of gene trees clarifies the functional impact of whole genome duplications
No full textWhole genome duplications (WGD) have major impacts on the evolution of species, as they produce new gene copies contributing substantially to adaptation, isolation, phenotypic robustness, and evolvability. They result in large, complex gene families with recurrent gene losses in descendant species that sequence-based phylogenetic methods fail to reconstruct accurately. As a result, orthologs and paralogs are difficult to identify reliably in WGD-descended species, which hinders the exploration of functional consequences of WGDs. Here we present SCORPiOs, a novel method to reconstruct gene phylogenies in the context of a known WGD event. WGDs generate large duplicated syntenic regions, which SCORPiOs systematically leverages as a complement to sequence evolution to infer the evolutionary history of genes. We applied SCORPiOs to the 320-million-year-old WGD at the origin of teleost fish. We find that almost one in four teleost gene phylogenies in the Ensembl database (3,391) are inconsistent with their syntenic contexts. For 70% of these gene families (2,387), we were able to propose an improved phylogenetic tree consistent with both the molecular substitution distances and the local syntenic information. We show that these synteny-guided phylogenies are more congruent with the species tree, with sequence evolution and with expected expression conservation patterns than those produced by state-of-the-art methods. Finally, we show that synteny-guided gene trees emphasize contributions of WGD paralogs to evolutionary innovations in the teleost clade
Adiposité et génétique chez le porc : état des lieux et nouveaux enjeux pour la qualité des produits
No full textCarcass adiposity of pigs slaughtered in France has decreased by 45% on average between 1977 and 2016. The production of increasingly lean animals has been initiated in the 1950-1960’s by setting up commercial grading scales for carcasses and differentiated payment according to their lean content, to the detriment of fatty tissues. This evolution led to a standardization of production, leading to difficulties in meeting the quality demand of certain market segments. However, a renewed interest for fat has occurred recently within the French pork industry. Indeed, fatty tissues have many advantages, both for ability for processing into cured products and delicatessen, as for sensory and nutritional qualities of products. This review provides an update on pig genetics’ improvement in France in relation to adiposity and product quality. After a reminder of the characteristics of fat tissues and their importance for the quality of meat and pork products, the factors influencing adiposity and the traits related to fat quantity taken into account in breeding programs are presented. An inventory of the genetic variability of fatness that remains within French pig populations (selected and local breeds) is drawn up. This will allow defining future selection strategies, to better meet the various expectations of pork industry and consumer
La biodiversité des sols : un fantastique patrimoine à préserver et valoriser par les services écosystémiques
No full textNetworking Agro-Ecology - reconciling the different needs for ecological functions provided by biodiversity
No full textAssociation and linkage mapping to unravel genetic architecture of phenological traits and lateral bearing in Persian walnut (Juglans regia L.)
No full textPlace des agricultures européennes dans le monde à l’horizon 2050 : Entre enjeux climatiques et défis de la sécurité alimentaire mondiale
No full textLignocellulosic biomass mild alkaline fractionation and resulting extract purification processes: Conditions, yields, and purities
No full textFractionation of lignocellulose is a fundamental step in the valorization of cellulose, hemicelluloses, and lignin to produce various sustainable fuels, materials and chemicals. Strong alkaline fractionation is one of the most applied processes since the paper industry has been using it for more than a century, and the mineral acid fractionation process is currently the most applied for the production of cellulosic ethanol. However, in the last decade, mild alkaline fractionation has been becoming increasingly widespread in the frame of cellulosic ethanol biorefineries. It leads to the solubilization of hemicelluloses and lignin at various extent depending on the conditions of the extraction, whereas the cellulose remains insoluble. Some studies showed that the cellulose saccharification and fermentation into ethanol gave higher yields than the mineral acid fractionation process. Besides, contrary to the acid fractionation process, the mild alkaline fractionation process does not hydrolyze the sugar polymers, which can be of interest for different applications. Lignocellulosic mild alkaline extracts contain hemicelluloses, lignin oligomers, phenolic monomers, acetic acid, and inorganic salts. In order to optimize the economic efficiency of the biorefineries using a mild alkaline fractionation process, the purification of the alkaline extract to valorize its different components is of major importance. This review details the conditions used for the mild alkaline fractionation process and the purification techniques that have been carried out on the obtained hydrolysates, with a focus on the yields and purities of the different compounds
Un siècle de recherche sur les bactériophages
No full textLes bactériophages tiennent une place prépondérante dans le monde vivant. Du point de vue épistémologique, ils participent à la compréhension du vivant via trois aspects fondamentaux : (i) les mécanismes moléculaires les plus intimes du fonctionnement des infections virales et de celui des cellules elles-mêmes (biologie moléculaire) ; (ii) le fonctionnement des écosystèmes (écologie) ; et (iii) la dynamique adaptative des populations virales et bactériennes (évolution). À travers une présentation historique de la découverte des bactériophages et de leurs fascinantes propriétés, cette revue relate la genèse des découvertes fondamentales associées à l’étude des bactériophages et présente une vision synthétique des champs de recherche actuels.Bacteriophages have a prominent place in the living world. They participate to our understanding of the living world through three main aspects : (i) the dissection of the most intimist aspects of viral infection molecular mechanisms (molecular biology), (ii) the description and functioning mechanisms of ecosystems (ecology), and (iii) the adaptive dynamics of integrated viral and host-cell populations (evolution). This review looks back at the genesis of these fundamental findings and draws a picture of the most active fields of current research