Supplementary information for \"The rice ILI2 locus is a bidirectional target of the African Xanthomonas oryzae pv. oryzae major Transcription Activator-Like Effector TalC but does not contribute to disease susceptibility\"Hinda Doucouré, Florence Auguy, Servane Blanvillain-Baufumé, Sandrine Fabre, Marc Gabriel, Emilie Thomas, Fleur Dambreville, Coline Sciallano, Boris Szurek, Ousmane Koita, Valérie Verdier & Sebastien Cunnac
This dataset contains additional supporting information related to the discovery of an alternative transcriptional target locus of the Xanthomonas oryzae pv. oryzae (Xoo) TalC effector in the rice genome as described in a manuscript submitted for publication. Xoo strains that cause Bacterial Leaf Blight (BLB), limit rice (Oryza sativa) production and require breeding more resistant varieties. Transcription Activator-Like Effectors (TALE) activate transcription to promote leaf colonization by binding to specific plant host DNA sequences termed...
ECOMED Database structure schema
Source code of CulebrONT: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomesJulie Orjuela, Aurore Comte, Sébastien Ravel, Florian Charriat, Tram Vi, François Sabot & Sébastien Cunnac
CulebrONT is an open-source, scalable, modulable and traceable snakemake pipeline, able to launch multiple assembly tools in parallel and providing help for choosing the best possible assembly. Documentation: https://culebront-pipeline.readthedocs.io/en/2.1.1/ Code development: https://github.com/SouthGreenPlatform/culebrONT The authors acknowledge the IRD i-Trop HPC (South Green Platform) from IRD Montpellier for providing resources that contributed to this work.
HYDROTHIEM observatory (eastern tropical coast of New Caledonia, South West Pacific): water resource observation data, 2018-2021Pierre Genthon, Caroline Tramier, Quentin Delvienne, Pascal Dumas, Nathalie Rouché, Kavya Wijesurya, Jean-Jérôme Cassan & Angeline Goue
HydroThiem observatory, located in the humid eastern coast of New Caledonia is devoted the study of impact of invasive ungulate species and bushfires on the amount of water resource, erosion and water quality in a catchment used for drinking water. Data from this observatory can be used as a comparison with other catchments submitted to different or similar disturbances
Wind erosion, meteorological and wind profile monitoring in a groundnut field in Bambey, Senegal, 2020-2021 (ENCAS project)Caroline Pierre
In order to measure horizontal flux of aeolian sediment and the main dynamic parameters (wind erosion threshold, aerodynamic roughness length), a set of instruments was set up in February 2020 in the framework of the ENCAS research project. In a groundnut field of about 100 m x 100 m, we installed 5 anemometers (2 dimensional (2D) sonic anemometers WindSonicTM Gill Instruments Ltd) at 0.25m, 0.66m, 1m, 1.5m, and 1.9m agl, a rain gauge (ARG100 Tipping...
Test data, reports and documentation for CulebrONT software: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomesJulie Orjuela, Aurore Comte, Sébastien Ravel, Florian Charriat, Tram Vi, Francois Sabot & Sébastien Cunnac
Related to CulebrONT software, this dataset includes: - data used to test the software - 2 reports generated by the software : from the test data and from other data - supplementary technical information about CulebrONT pipeline
The dataset includes a sample of fishery data on reef fish catches (catch per fishing trip, fish length, and catch composition at family level), minimal length at maturity for reef fishes, and fisher census in the Bay of Toliara, southwest Madagascar. These data were collected as part of a participatory survey from May 2018 to April 2019 at 8 villages in the Bay of Toliara. Specifically, 4 data files are provided: (1) suivi_part_toliara.xlsx ; (2)...
This dataset includes 1,407 pairs of threatened native–invasive alien plants extracted from the IUCN Red List of Threatened Species (https://www.iucnredlist.org/). For each pair, the threat category of the threatened native species (NT, VU, EN, CR, EW, EX), its population trend (increasing, stable, decreasing, unknown), whether the native species is restricted to islands (yes, no, partially) and whether the native species has been classified as threatened based exclusively on IUCN-red-list criterion B (restricted geographic range size)...
Data were collected in southern Madagascar between 2018 and 2019 from a cohort of 600 households. They were collected as part of a project to evaluate a multi-sectoral program set up by the World Food Program (WFP) with the objective of improving the resilience of households in Madagascar. The Committee of Ethics of Biomedical Research of Madagascar approved the survey protocol. A Data Plan Management was prepared, as provided. Data were collected in tree times,...
Description of the model The model is described in Bonnin et al, Predicting the effects of climate change on dengue vectors densities in Southeast Asia through process-based modeling, submitted The original model was developped by Tran et al 2020 Tran, A. et al. Complementarity of empirical and process-based approaches to modelling mosquito population dynamics with Aedes albopictus as an example—Application to the development of an operational mapping tool of vector populations. PLOS ONE 15, e0227407...
Erasmus + european ECOMED project final report Facebook Page
Location and morphological status of spring mounds in the Nefzaoua Province in western Tunisia in 2020.A. Raddadi & P. Podwojewski
This dataset holds the location and the morphological characteristics of spring mounds in the Nefzaoua Province (governorate of Kebili) in western Tunisia. Overall, in an area of 3 000 km2, 126 spring mounds of 7 types were identified, of which 112 (89%) were degraded. Due to the low salt content in spring mound sediments, they are excavated and used as a soil amendment to expand new palm plantations. Only 14 mounds (11%) are presently preserved....
This dataset holds the sedimentary analysis of two spring mounds comprised of four sections. The two spring mounds Aïn Ouled Aïssa and Aïn Chardiouss are located in the Nefzaoua Province (governorate of Kebili) in western Tunisia. Each section is illustrated by analytical data, some photos and a geological section. The dataset also holds some situation maps
This dataset holds the boundary of the nature reserve Lamto in Côte d'Ivoire. We digitized the boundary from the map “Carte du recouvrement ligneux de la réserve de Lamto" published by Gautier in 1990. Bandama river delimits the nature reserve naturally in the southwest. The source map does not indicate if the boundary of the nature reserve follows the bank or the mid-channel of the stream. The dataset contains two shapefiles for both situations.
This dataset has been collected thanks to the long-term partnership with Department of Agricultural Land Management (DALaM), Lao PDR, which granted the permission for field access, and to the financial, scientific, technical, and/or logistical support of the Multiscale TROPIcal CatchmentS (SNO M-TROPICS; https://mtropics.obs-mip.fr/) critical zone observatory (previously MSEC). This .csv dataset includes Burkholderia pseudomallei concentrations (CFU g-1) within a 300-cm soil profile, along with physico-chemical parameters: soil texture, i.e. clay < 2 μm, silt 2–50...
Projet STABILITY : interrogation de la base de données d'observations sur l’utilisation de la végétation pour prévenir et lutter contre les glissements de terrain et l’érosionJerome Perez
Requêtes PostgreSQL développées dans le cadre du projet STABILITY pour créer la base de données , extraire les types d'habitat, l'ensemble des localisations, aires, villes, continents, pays, districts, risques, sols, typologies racinaires, bibliographies, éco-ingéniérie, écologies, types d'habitat, morphologies, modes de reproduction, systèmes racinaires, familles, genres, espèces, espèces infra-spécifiques des végétaux, types biologiques, climats, contraintes, observations et les fichiers textes tabulaires contenant les données associées. PostgreSQL queries developed as part of the STABILITY project to create...
Whole-genome genotyping data of 323 Beninese individuals followed for malaria infections and malaria-related phenotypesBenoit Henry, Geoffrey Volle, E. Hilaire Akpovi, Laure Gineau, Camille Roussel, Papa Alioune Ndour, Félicien Tossou, Felipe Suarez, Friso Palstra, Aurélie Fricot, Charlotte Chambrion, Julien Solinc, Julie Nguyen, Mathilde Garé, Florentin Aussenac, Charles-Henry Cottart, Christine Keyser, Rafiou Adamou, Magalie Tichit, David Hardy, Nadine Fievet, Jérôme Clain, André Garcia, David Courtin, Olivier Hermine … & Pierre Buffet
This dataset consists of whole-genome genotyping data for 323 Beninese individuals followed for malaria infections and malaria-related phenotypes in north Benin. Study participants belong to the Fulani, Gando, Bariba, and Otamari ethnic groups and live in sympatry in four rural villages (Goufanrou, Gorgoba, Tamande, Kouboro) located 3-15 km apart, in the Birni district of the Atacora department, a region of northwestern Benin. Genotyping was performed on Illumina HumanOmni5-4v1 chips, in accordance with the standard protocol...
Hydroclimatic vulnerability of peat carbon in the central Congo Basin: codes for age-depth models, geospatial data processing and analysisYannick Garcin, Enno Schefuß, Greta C. Dargie, Donna Hawthorne, Ian T. Lawson, David Sebag, George E. Biddulph, Bart Crezee, Yannick E. Bocko, Suspense A. Ifo, Y. Emmanuel Mampouya Wenina, Mackline Mbemba, Corneille E.N. Ewango, Ovide Emba, Pierre Bola, Joseph Kanyama Tabu, Genevieve Tyrrell, Dylan M. Young, Ghislain Gassier, Nicholas T. Girkin, Christopher H. Vane, Thierry Adatte, Andy J. Baird, Arnoud Boom, Pauline Gulliver … & Simon L. Lewis
This dataset includes two packages: Age_depth_models and Tropical_Peats for the creation of the age-depth models and the processing and analysis of the geospatial data, which are presented in the article Hydroclimatic vulnerability of peat carbon in the central Congo Basin. The package Age_depth_models includes the data and R codes to run the age/depth models of cores CEN-17.4, LOK5-5 and BDM1-7. The package Tropical_Peats (JupyterHub notebooks https://jupyter.org) includes all the codes for the processing and analysis...
Monthly input of Escherichia coli within the Houay Pano headwater catchment, Northern Lao PDR (2001-2021) calculated from from human, goat, swine, and poultry frequentationBounsamay Soulileuth, Laurie Boithias, Keooudone Latsachack, Chanthamousone Thammahacksa, Emma Rochelle-Newall & Olivier Ribolzi
This dataset has been collected thanks to the long-term partnership with Department of Agricultural Land Management (DALaM), Lao PDR, which granted the permission for field access, and to the financial, scientific, technical, and/or logistical support of the Multiscale TROPIcal CatchmentS (SNO M-TROPICS; https://mtropics.obs-mip.fr/) critical zone observatory (previously MSEC). This .csv dataset includes monthly human, goat, swine, and poultry frequentation and respective numbers of Escherichia coli cells estimated with Causse et al. (2015; https://doi.org/10.1016/j.jher.2015.03.003) as sources...
Microbiology and soil characteristics in different situations, below different types of plants in Lamto savanna, Côte d’Ivoire, 2014S. Barot, J.-C. Lata & K.F. Koffi
The goal of the sampling was to describe the impact of the vegetation and different plant species on soil microbiology with a focus on nitrogen cycling. This sampling was achieved in Lamto savanna, Côte d’Ivoire, in April 2014 during the long rainy season. Samples were collected from the top soil layer (0-15 cm). We sampled four types of situations: below the canopy of tree clumps, next to the trunks of isolated trees (four species, Bridelia...
Institut de Recherche pour le Développement7
Marine Biodiversity Exploitation and Conservation2
Ministry of Marine Affairs and Fisheries1
Institut Pasteur de Dakar1
Indonesian Institute of Sciences1
Institut Sénégalais de Recherches Agricoles1
Laboratoire des Sciences de l'Environnement Marin1