The 5S rDNA family evolves through concerted and birth-and-death evolution in fish genomes: an example from freshwater stingrays

Background: Ribosomal 5S genes are well known for the critical role they play in ribosome folding and functionality. These genes are thought to evolve in a concerted fashion, with high rates of homogenization of gene copies. However, the majority of previous analyses regarding the evolutionary process of rDNA repeats were conducted in invertebrates and plants. Studies have also been conducted on vertebrates, but these analyses were usually restricted to the 18S, 5.8S and 28S rRNA genes. The recent identification of divergent 5S rRNA gene paralogs in the genomes of elasmobranches and teleost fishes indicate that the eukaryotic 5S rRNA gene family has a more complex genomic organization than previously thought. The availability of new sequence data from lower vertebrates such as teleosts and elasmobranches enables an enhanced evolutionary characterization of 5S rDNA among vertebrates.Results: We identified two variant classes of 5S rDNA sequences in the genomes of Potamotrygonidae stingrays, similar to the genomes of other vertebrates. One class of 5S rRNA genes was shared only by elasmobranches. A broad comparative survey among 100 vertebrate species suggests that the 5S rRNA gene variants in fishes originated from rounds of genome duplication. These variants were then maintained or eliminated by birth-and-death mechanisms, under intense purifying selection. Clustered multiple copies of 5S rDNA variants could have arisen due to unequal crossing over mechanisms. Simultaneously, the distinct genome clusters were independently homogenized, resulting in the maintenance of clusters of highly similar repeats through concerted evolution.Conclusions: We believe that 5S rDNA molecular evolution in fish genomes is driven by a mixed mechanism that integrates birth-and-death and concerted evolution

Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests

High-throughput sequencing (HTS) technologies have the potential to become one of the most significant advances in molecular diagnostics. Their use by researchers to detect and characterize plant pathogens and pests has been growing steadily for more than a decade and they are now envisioned as a routine diagnostic test to be deployed by plant pest diagnostics laboratories. Nevertheless, HTS technologies and downstream bioinformatics analysis of the generated datasets represent a complex process including many steps whose reliability must be ensured. The aim of the present guidelines is to provide recommendations for researchers and diagnosticians aiming to reliably use HTS technologies to detect plant pathogens and pests. These guidelines are generic and do not depend on the sequencing technology or platform. They cover all the adoption processes of HTS technologies from test selection to test validation as well as their routine implementation. A special emphasis is given to key elements to be considered: undertaking a risk analysis, designing sample panels for validation, using proper controls, evaluating performance criteria, confirming and interpreting results. These guidelines cover any HTS test used for the detection and identification of any plant pest (viroid, virus, bacteria, phytoplasma, fungi and fungus-like protists, nematodes, arthropods, plants) from any type of matrix. Overall, their adoption by diagnosticians and researchers should greatly improve the reliability of pathogens and pest diagnostics and foster the use of HTS technologies in plant health

Allelic heterogeneity and trade-off shape natural variation for response to soil micronutrient. PLOS Genetics 8: e1002814. doi

Abstract As sessile organisms, plants have to cope with diverse environmental constraints that may vary through time and space, eventually leading to changes in the phenotype of populations through fixation of adaptive genetic variation. To fully comprehend the mechanisms of evolution and make sense of the extensive genotypic diversity currently revealed by new sequencing technologies, we are challenged with identifying the molecular basis of such adaptive variation. Here, we have identified a new variant of a molybdenum (Mo) transporter, MOT1, which is causal for fitness changes under artificial conditions of both Mo-deficiency and Mo-toxicity and in which allelic variation among West-Asian populations is strictly correlated with the concentration of available Mo in native soils. In addition, this association is accompanied at different scales with patterns of polymorphisms that are not consistent with neutral evolution and show signs of diversifying selection. Resolving such a case of allelic heterogeneity helps explain species-wide phenotypic variation for Mo homeostasis and potentially reveals trade-off effects, a finding still rarely linked to fitness

Innovation technologique, changements organisationnels : quels enjeux pour la prévention ? Conférence scientifique de l'INRS. Nancy, 29-31 mars 2017

International audienceLes nouveaux outils d'aide à la production, les dispositifs informatiques de gestion de la production et des flux d'information obligent à repenser les méthodes de prévention. Dans un contexte d'intensification du travail, d’allongement de la vie active, de vieillissement de la population et de concurrence mondialisée, innovation technologique et changements organisationnels associés peuvent être des facteurs de risque pour la santé, notamment mentale, et la sécurité des travailleurs. Ces journées ont abordé la prévention des risques professionnels en lien avec trois principales familles émergentes d’innovations technologiques : celles de l’information, les nouveaux outils d’aide à la production et enfin les dispositifs informatiques de gestion de la production et des flux d’information. L’ensemble des présentations et le recueil de résumés sont disponibles sur le site : www.inrs-innovorg2017.fr/presentations-powerpoint/

Innovation technologique, changements organisationnels : quels enjeux pour la prévention ? Conférence scientifique de l'INRS. Nancy, 29-31 mars 2017

International audienceLes nouveaux outils d'aide à la production, les dispositifs informatiques de gestion de la production et des flux d'information obligent à repenser les méthodes de prévention. Dans un contexte d'intensification du travail, d’allongement de la vie active, de vieillissement de la population et de concurrence mondialisée, innovation technologique et changements organisationnels associés peuvent être des facteurs de risque pour la santé, notamment mentale, et la sécurité des travailleurs. Ces journées ont abordé la prévention des risques professionnels en lien avec trois principales familles émergentes d’innovations technologiques : celles de l’information, les nouveaux outils d’aide à la production et enfin les dispositifs informatiques de gestion de la production et des flux d’information. L’ensemble des présentations et le recueil de résumés sont disponibles sur le site : www.inrs-innovorg2017.fr/presentations-powerpoint/