13 Works

Data from: A mobile laboratory for ancient DNA analysis

Jose Utge, Jean-Marc Elalouf, Noémi Sévêque, Anne-Sophie Lartigot-Campin, Agnès Testu, Anne-Marie Moigne, Régis Vézian, Frédéric Maksud, Robert Begouën, Sylvain Soriano & Chistine Verna
Mobile devices for on-field DNA analysis have been used for medical diagnostics at the point-of-care, forensic investigation and environmental survey, but still have to be validated for ancient DNA studies. We report here on a mobile laboratory that we setup using commercially available devices, including a compact real-time PCR machine, and describe procedures to perform DNA extraction and analysis from a variety of archeological samples within 4 hours. The process is carried out on 50...

Data from: Genome mining reveals the genus Xanthomonas to be a promising reservoir for new bioactive non-ribosomally synthesized peptides

Monique Royer, Ralf Koebnik, Mélanie Marguerettaz, Valérie Barbe, Guillaume P. Robin, Chrystelle Brin, Sébastien Carrere, Camila Gomez, Manuela Hügelland, Ginka H. Völler, Julie Noëll, Isabelle Pieretti, Saskia Rausch, Valérie Verdier, Stéphane Poussier, Philippe Rott, Roderich D. Süssmuth & Stéphane Cociancich
Background: Various bacteria can use non-ribosomal peptide synthesis (NRPS) to produce peptides or other small molecules. Conserved features within the NRPS machinery allow the type, and sometimes even the structure, of the synthesized polypeptide to be predicted. Thus, bacterial genome mining via in silico analyses of NRPS genes offers an attractive opportunity to uncover new bioactive non-ribosomally synthesized peptides. Xanthomonas is a large genus of Gram-negative bacteria that cause disease in hundreds of plant species....

Data from: Genetic footprints of adaptive divergence in the bracovirus of Cotesia sesamiae identified by targeted resequencing

Jeremy Gauthier, Philippe Gayral, Bruno Pierre Le Ru, Séverine Jancek, Stéphane Dupas, Laure Kaiser, Gabor Gyapay & Elisabeth A. Herniou
The African parasitoid wasp Cotesia sesamiae is structured in contrasted populations showing differences in host range and the recent discovery of a specialist related species, C. typhae, provide a good framework to study the mechanisms that link the parasitoid and their host range. To investigate the genomic bases of divergence between these populations, we used a targeted sequencing approach on 24 samples. We targeted a specific genomic region encoding the bracovirus, which is deeply involved...

Microbarom low-frequency data products of the International Monitoring System’s infrasound stations

Patrick Hupe, Lars Ceranna, Alexis Le Pichon, Robin Matoza & Pierrick Mialle
This data series consists of data products derived from broadband signal detection lists that have been processed for the certified infrasound stations of the International Monitoring System. More specifically, this data series covers the dominant frequency range of microbaroms (0.15-0.35 Hz) and is therefore called the ‘mb_lf’ product. The temporal resolution (time step and window length) is 15 min. For processing the infrasound data, the Progressive Multi-Channel Correlation (PMCC) array processing algorithm with a one-third...

Data from: Fifty thousand years of arctic vegetation and megafaunal diet

Eske Willerslev, John Davison, Mari Moora, Martin Zobel, Eric Coissac, Mary E. Edwards, Eline D. Lorenzen, Mette Vestergård, Galina Gussarova, James Haile, Joseph Craine, Gaddy Bergmann, Ludovic Gielly, Sanne Boessenkool, Laura S. Epp, Peter B. Pearman, Rachid Cheddadi, David Murray, Karri Anne Bråthen, Nigel Yoccoz, Heather Binney, Corinne Cruaud, Patrick Wincker, Tomasz Goslar, Inger Greve Alsos … & Pierre Taberlet
Although it is generally agreed that the arctic flora is among the youngest and least diverse on Earth, the processes that shaped it are poorly understood. Here we present 50 thousand years (kyr) of arctic vegetation history, derived from the first large-scale ancient DNA metabarcoding study of circumpolar plant diversity. For this interval we additionally explore nematode diversity as a proxy for modelling vegetation cover and soil quality, and diets of herbivorous megafaunal mammals, many...

Data from: Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges

Jonathan L. Gordon, Pierre Lefeuvre, Aline Escalon, Valérie Barbe, Stéphane Cruveiller, Lionel Gagnevin & Olivier Pruvost
Background: The identification of factors involved in the host range definition and evolution is a pivotal challenge in the goal to predict and prevent the emergence of plant bacterial disease. To trace the evolution and find molecular differences between three pathotypes of Xanthomonas citri pv. citri that may explain their distinctive host ranges, 42 strains of X. citri pv. citri and one outgroup strain, Xanthomonas citri pv. bilvae were sequenced and compared. Results: The strains...

Data from: Phylum-wide comparative genomics unravel the diversity of secondary metabolism in Cyanobacteria

Alexandra Calteau, David P. Fewer, Amel Latifi, Thérèse Coursin, Thierry Laurent, Jouni Jokela, Cheryl A. Kerfeld, Kaarina Sivonen, Jörn Piel & Muriel Gugger
Background: Cyanobacteria are an ancient lineage of photosynthetic bacteria from which hundreds of natural products have been described, including many notorious toxins but also potent natural products of interest to the pharmaceutical and biotechnological industries. Many of these compounds are the products of non-ribosomal peptide synthetase (NRPS) or polyketide synthase (PKS) pathways. However, current understanding of the diversification of these pathways is largely based on the chemical structure of the bioactive compounds, while the evolutionary...

Data from: DNA from soil mirrors plant taxonomic and growth form diversity

Nigel G. Yoccoz, Kari-Anne Brathen, Ludovic Gielly, James Haile, Mary E. Edwards, Tomasz Goslar, H. Von Stedingk, Anne K. Brysting, Eric Coissac, Francois Pompanon, J. H. Sønstebø, Christian Miquel, Alice Valentini, Francesco De Bello, Jérôme Chave, Wilfried Thuiller, Patrick Wincker, Corinne Cruaud, Frederick Gavory, Morten Rasmussen, M. Thomas P. Gilbert, Ludovic Orlando, Christian Brochmann, Eske Willerslev & Pierre Taberlet
Ecosystems across the globe are threatened by climate change and human activities. New rapid survey approaches for monitoring biodiversity would greatly advance assessment and understanding of these threats. Taking advantage of next-generation DNA sequencing, we tested an approach we call metabarcoding: high-throughput and simultaneous taxa identification based on a very short (usually less than 100 base pairs) but informative DNA fragment. Short DNA fragments allow the use of degraded DNA from environmental samples. All analyses...

Higher frequency data products of the International Monitoring System’s infrasound stations

Patrick Hupe, Lars Ceranna, Alexis Le Pichon, Robin Matoza & Pierrick Mialle
This data series consists of data products derived from broadband signal detection lists that have been processed for the certified infrasound stations of the International Monitoring System. More specifically, within the CTBT-relevant infrasound range (around 0.01-4 Hz), this data series covers higher frequencies (1-3 Hz) and is therefore called the ‘hf’ product. The temporal resolution (time step and window length) is 5 min. For processing the infrasound data, the Progressive Multi-Channel Correlation (PMCC) array processing...

Microbarom high-frequency data products of the International Monitoring System’s infrasound stations

Patrick Hupe, Lars Ceranna, Alexis Le Pichon, Robin Matoza & Pierrick Mialle
This data series consists of data products derived from broadband signal detection lists that have been processed for the certified infrasound stations of the International Monitoring System. More specifically, this data series covers, among other phenomena, the upper frequency range of microbaroms (0.45-0.65 Hz) and is therefore called the ‘mb_hf’ product. The temporal resolution (time step and window length) is 15 min. For processing the infrasound data, the Progressive Multi-Channel Correlation (PMCC) array processing algorithm...

French Global Network of Geomagnetic observatories

The Bureau Central de Magnétisme Terrestre (BCMT) is a French organization founded in 1921 and attached to the Institut de Physique du Globe de Paris (IPGP). Two French institutions are involved in BCMT operations: IPGP and École et Observatoire des Sciences de la Terre de Strasbourg (EOST). The primary mission of the BCMT is to provide ground geomagnetic observations of the highest quality to the scientific community, in France and abroad. To achieve its mission,...

French Global Network of Geomagnetic observatories

The Bureau Central de Magnétisme Terrestre (BCMT) is a French organization founded in 1921 and attached to the Institut de Physique du Globe de Paris (IPGP). Two French institutions are involved in BCMT operations: IPGP and École et Observatoire des Sciences de la Terre de Strasbourg (EOST). The primary mission of the BCMT is to provide ground geomagnetic observations of the highest quality to the scientific community, in France and abroad. To achieve its mission,...

Global reference histograms of the IMS infrasound broadband detection lists

Samuel Kristoffersen, Alexis Le Pichon, Patrick Hupe & Robin Matoza
This data set builds upon the broadband detection lists of the International Monitoring System (IMS)’s infrasound stations. The infrasound data of these stations are regularly (re-)processed at the German National Data Centre at BGR (e.g., Ceranna et al., 2019; https://doi.org/10.1007/978-3-319-75140-5_13) using the Progressive Multi-Channel Correlation (PMCC) array processing method (Cansi, 1995; https://doi.org/10.1029/95GL00468). The latest reprocessing with 26 one-third octave spaced frequency bands in the IMS band of interest (0.01 to 4 Hz) included all 53...

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