Metagenómica de lecturas largas: Evaluación sistemática de herramientas de ensamblaje para secuenciación Nanopore

[EN] Microorganisms can produce a wide variety of compounds and are key factors for understanding the behavior of ecological systems. Metagenomics is the tool for achieving this knowledge, studying microorganisms directly from their source through different approaches: focusing on sequencing marker genes (metataxonomics) or puzzling up the whole genetic material into separate genomes (metagenomics). In the recent past, Illumina has been the most sequencing technology used. However, short reads generated by Illumina are hard to assemble, and they produce very fragmented metagenomes. Despite their high intrinsic error, third generation sequencing platforms harbor the potential to overcome this issue thanks to their ability to generate longer reads. In this regard, MinION (Oxford Nanopore Technologies) is very advantageous for metagenomics applications, since it is cheap, portable and provides information in real-time. Many assemblers have been designed for dealing with error-prone data, but there is not a clear consensus about the tools to use to achieve the best results when handling MinION data. It is thus necessary to benchmark these tools and state what, why and when to use them. For that, using the best performing assemblers we know in the present, the aim of the present work is to analyze sequencing data from microbial communities of different complexities and systematically compare the metagenomes retrieved. The final goal of the study is to provide guidance for other scientists to choose the proper software, and to stimulate the rational development of tools and methodologies for this field.[ES] Los microorganismos producen compuestos muy variados y son esenciales para entender el comportamiento de sistemas ambientales. La metagenómica es la vía para obtener este conocimiento, estudiando los microorganismos directamente desde su hábitat usando diferentes enfoques: centrarse en secuenciar genes marcadores (metataxonómica), o montar todo el material genético en genomas separados (metagenómica). En los últimos años, Illumina ha sido la tecnología más usada para secuenciar; sin embargo, las lecturas cortas que genera Illumina son difíciles de ensamblar, y producen metagenomas muy fragmentados. A pesar de su alto error intrínseco, las plataformas de tercera generación tienen potencial para superar este inconveniente gracias a que pueden generar lecturas más largas. En este contexto, MinION (Oxford Nanopore Technologies) es muy conveniente para aplicaciones metagenómicas; ya que es barato, portable y proporciona información en tiempo real. Se han diseñado muchos ensambladores para tratar con datos de mayor error intrínseco, pero no hay un consenso en cuanto a las herramientas que se deben usar para obtener los mejores resultados cuando se usa MinION. Es por tanto necesario evaluar estas herramientas y definir qué, por qué y cuándo usarlas. Para este propósito, y usando los mejores ensambladores que se conocen actualmente, la finalidad de este proyecto es analizar datos secuenciados de comunidades microbianas de varias complejidades y comparar sistemáticamente los metagenomas obtenidos, con el objetivo de orientar a otros científicos para elegir el software adecuado y estimular el desarrollo racional de nuevas herramientas y estrategias para este campo.Blanot, M. (2020). Long-read, error prone metagenomics: Systematic evaluation of assembly tools for nanopore sequencing. http://hdl.handle.net/10251/150739TFG

Entre falaises subverticales et plaines côtières submergées : Réévaluation de l'hostilité des littoraux nord-martiniquais durant le Céramique ancien

International audienceSi l’homogénéité des dynamiques de peuplement des sites du Céramique ancien martiniquais est sans appel, force est de constater que les littoraux actuels du nord-atlantique, alternant falaises subverticales et plages de galets, ne se prêtent pas à l’accostage ni aux activités littorales. Du point de vue culturel et économique, ces populations éminemment maritimes y sont pourtant intrinsèquement liées. Cependant, il n’existe à ce jour aucun indice de la présence saladoïde sur le littoral Nord-Atlantique. S’il existe des théories selon lesquelles la réalité de la côte septentrionale n’aurait que peu évolué durant les deux derniers millénaires, les données à notre disposition nous permettent de contredire ces affirmations ; des mutations paléoenvironnementales importantes se sont opérées sur cet espace depuis le changement d’ère. Cela nous porte à croire que la recherche de vestiges saladoïdes anciens côtiers a potentiellement été biaisée par une conception du paysage que l’on pourrait qualifier de fixiste, sous-évaluant le potentiel archéologique de l’espace infralittoral

Interdisciplinary analysis of partially submerged pre-Columbian sites of Martinique, French West Indies. Research issues, methodology and further perspectives

In the actual alarming context of global warming and environmental change, all eyes are focused on the relative sea level rise and its catastrophic consequences. The impacts of this phenomenon on contemporary societies are extremely diversified. Among them the programmed disappearance in the coming decades of a large part of the coastal cultural heritage requires a specific reflection. The French West Indies are, because of their geographical position and their insularity, dramatically exposed to the coastal regression. This phenomenon of exposure to marine risks is not new. Since the last Pleniglacial period (18,000 BP), marine transgression is estimated to about +120 meters around the Caribbean basin. By developing a diachronic geoarchaeological approach to the material evidence of the submerged history of Martinique, we aim to determine the erosive and relative sea level processes behind the mobility of the shoreline as well as the relationship to the ocean of a corpus of three pre-Columbian deposits distributed on this territory. We will develop an original geoarchaeological methodological approach to the paleoenvironmental, taphonomic and predictive characterization of these sites, witnesses of the holocene land-sea interface in perpetual mutation. Thus, this holistic and unreleased approach in the pre-Columbian context of Martinique raises a plurality of research issues related to the prehistoric occupation modalities of this space. It must therefore fall within a solid methodological framework that must be reproducible on the scale of the entirety of the pre-Columbian submerged Antillean deposits. From sedimentary studies to three-dimensional paleoenvironmental simulations and from archaeologists to the actors of cultural meditation, a plurality of perspectives should emerge from our study which strive to contribute to an interdisciplinary archaeology of West Indies paleolandscapes

Temps et espaces de l’occupation céramique ancienne de la Martinique

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Temps et espaces de l’occupation céramique ancienne de la Martinique

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Temps et espaces de l’occupation céramique ancienne de la Martinique

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Temps et espaces de l’occupation céramique ancienne de la Martinique

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Temps et espaces de l’occupation céramique ancienne de la Martinique

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Micro-Regional Approach to Martinique Early Ceramic Occupation

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Micro-Regional Approach to Martinique Early Ceramic Occupation

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