cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15454/ojmrdd
title: Ancestral reconstruction of the origin of M. incognita effectors in the Meloidogyne genus

description: Based on the mapping of non-redundant known M. incognita subventral (SvG) and dorsal (DG) gland effectors on the genomes of five Meloidogyne species ancestral numbers were deduced across their phylogeny using parsimony inference with Mesquite (Maddison Maddison, 2014). In the genomes of M. incognita, M. arenaria, M. javanica and M. entetolobii, only genes mapping with &gt;90% identity on &gt;66% of their length were considered unambiguously present (character state ‘1’ in Mesquite). Genes with a significant spaln mapping but that did not meet the % identity and % coverage thresholds were considered as unsure to be present (character state ‘?’ in Mesquite). Because M. hapla is phylogenetically much more distant, only a length coverage threshold was used to infer unambiguous presence following a significant spaln mapping from the ATG position. Genes that returned no significant spaln mapping were considered absent from the genomes under consideration (character state ‘0’ in Mesquite). The tree topology of the five Meloidogyne species used for ancestral states reconstruction was taken from (Álvarez-Ortega, Brito, Subbotin, 2019). We used the analysis ‘Trace all Characters’ to reconstruct characters (presence / absence of each effector) at each ancestral branch. To infer the minimal unambiguous number of effectors at each ancestral branch the sum of 1’s at this branch was calculated while equi-parsimonious 0/1’s ancestral state were considered an absence in a conservative scenario.
DOI: 10.15454/pdlq1x
title: Projet SHORELINE - Capbreton (Landes, France) - Questionnaire de l'enquête "Quel regard portez-vous sur votre commune ?"

description: Le projet | SHORELINE (Stratégies adaptatives, cHOix résidentiels et RElocalisation face au risque LIttoral en Nouvelle-AquitainE), projet de recherche soutenu par la région Nouvelle Aquitaine, propose de produire de la connaissance sur les préférences des habitants de zones littorales exposées au risque érosion en matière de gestion du risque, et en particulier au regard d’une éventuelle stratégie de relocalisation. La démarche repose en partie sur des enquêtes par questionnaire auprès de résidents de deux communes du littoral Atlantique, Lacanau en Gironde et Capbreton dans les Landes. Le questionnaire | Il s'agit du questionnaire d'enquête en français proposé en ligne, pour Capbreton, au cours de 2 vagues, la première à l'été 2020 et la seconde à l'été 2021. Il avait pour objectif de recueillir des informations sur le rapport au lieu des populations résidentes de Capbreton, à travers différents critères dont le rapport à la mer (localisation et distance à la mer, nature des pratiques liées à la mer, etc.) ou encore l'attachement au lieu (parcours et projet résidentiels, valeurs accordées à la résidence littorale dans l'espace de vie, modalités et rythmes de fréquentation, etc.). Ces informations permettent de comprendre les préférences résidentielles face au risque d'érosion du littoral. Le questionnaire visait les résidents principaux et secondaires de cette commune. Il est structuré de la façon suivante : Pour faire connaissance : questions sociodémographiques pour connaître l'individu et son ménage (Q1 à Q9) ; Vous et le risque : questions pour évaluer l'aversion au risque des répondants (Q10 à Q12) ; Vous et Capbreton : questions permettant de connaître le rapport qu'entretiennent les répondants avec la commune de Capbreton (rapport au lieu) et les activités qui y sont pratiquées (Q13 à Q21) ; Vous et votre logement à Capbreton : questions relatives au logement que les répondants possèdent à Capbreton (Q22 à Q30) ; Vous et le risque d'érosion du littoral : questions pour évaluer le degré de perception des risques environnementaux qui menacent le littoral et la commune de Capbreton, avec une partie spécifiquement dédiée aux risques d'érosion du littoral (Q31 à Q36) ; Pour finir : une question sur les projets résidentiels à 5 ans, ainsi qu'une question ouverte permettant aux enquêtés de s'exprimer librement. Il a été créé sous Sphinx iQ2 et administré avec SphinxOnline.
DOI: 10.15454/pins1h
title: A novel histologic approach to quantify the intra-annual dynamics of carbon sequestration in spruce forming wood

description: The dataset is compoused of two main variables (xylem radial increment measured along three radial files M1-M2-M3, and cell wall proportion CWP measured in the forming xylem) needed in a novel histologic approach to estimate the intra-annual dynamics of stem radial growth and aboveground woody biomass production. Data were acquired from seven dominant spruce trees, on which we weekly sampled microcores containing the cambium, the forming phloem and xylem from March to December 2015 in Hesse forest (North-East, France).
DOI: 10.15454/pjkd06
title: Soil Water Potential 2018-2019

description: Soil water potential along an elevational gradient at Massif de Belledonne, France
DOI: 10.15454/nbfe4f
title: Data from : Fir expansion not controlled by moderate densities of large herbivores: a grassland conservation issue

description: Raw data of fir trees’ age structure that was analysed by dendrochronology, individual growth patterns and injury recorded in their tree-ring series. Data were collected in the northern Mediterranean mountain in a context of increase of grazing disturbance.
DOI: 10.15454/ova9so
title: Fine resolution map of top- and subsoil carbon sequestration potential in France

description: Although soils have a high potential to offset CO2 emissions through its conversion into soil organic carbon (SOC) with long turnover time, it is widely accepted that there is an upper limit of soil stable C storage, which is referred to SOC saturation. In this study we estimate SOC saturation in French topsoil (0–30 cm) and subsoil (30–50 cm), using the Hassink equation and calculate the additional SOC sequestration potential (SOCsp) by the difference between SOC saturation and fine fraction C on an unbiased sampling set of sites covering whole mainland France. We then map with fine resolution the geographical distribution of SOCsp over the French territory using a regression Kriging approach with environmental covariates. Results show that the controlling factors of SOCsp differ from topsoil and subsoil. The main controlling factor of SOCsp in topsoils is land use. Nearly half of forest topsoils are over-saturated with a SOCsp close to 0 (mean and standard error at 0.19 ± 0.12) whereas cropland, vineyard and orchard soils are largely unsaturated with degrees of C saturation deficit at 36.45 ± 0.68% and 57.10 ± 1.64%, respectively. The determinant of C sequestration potential in subsoils is related to parent material. There is a large additional SOCsp in subsoil for all land uses with degrees of C saturation deficit between 48.52 ± 4.83% and 68.68 ± 0.42%. Overall the SOCsp for French soils appears to be very large (1008 Mt C for topsoil and 1360 Mt C for subsoil) when compared to previous total SOC stocks estimates of about 3.5 Gt in French topsoil. Our results also show that overall, 176 Mt C exceed C saturation in French topsoil and might thus be very sensitive to land use change.
DOI: 10.15454/pooz2h
title: Données agronomiques du projet SAFARI (Santé, Fertilité, Adaptation, Résilience)

description: Jeu de données agronomiques sur la culture de blés et légumineuses sur 3 ans (2018-2021) et 5 lieux (région Bretagne / Pays de la Loire) du projet SAFARI.
DOI: 10.15454/ppe5td
title: RPG complété 2018 département 45

description: RPG complété 2018. Complète le RPG campagne 2018 pour le département 45. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2020.
DOI: 10.15454/pq3ukw
title: Size-density data from pure even-aged stands of sycamore maple (Acer pseudoplatanus L.) growing at maximum density

description: For sycamore, data from unthinned long-term permanent plots were not available (Le Goff et al, 2011). The establishment of the maximum size–density relationship for sycamore relied only on temporary plots installed in spring 2006 in fully stocked stands with no sign of recent cleaning or thinning treatment and presenting natural mortality, in Lorraine and Alsace regions (NE France). In these plots live trees were generally inventoried at two dates for the purpose of this study, in years 2006 and 2007. Dead trees at plot installation were also inventoried by sorting them by “age” class (see Le Goff et al. 2011). In the sample plots, sycamore trees appeared often mixed with other tree species (most often ash and beech) and may be also over-topped by an upper layer of older trees reducing significantly the transmitted radiation. Selection criteria were then defined to ensure homogeneous growing conditions among selected plots: 1) stands relatively pure, sycamore trees representing more than 80% of the stand, in terms of number of trees and total basal area 2) minimum annual mortality rate of 1%, so that stands were close to maximum density 3) trees not completely covered by an upper layer. Moreover, the data from plot 5 of “Matstall” in 2007 were discarded, an over-topping tree being removed at the end of 2006. The selection criteria are notified for each plot in Table 2 of the related publication, but they also appear in the dataset. Inventories were extended for one or more years beyond the year 2007, depending on the plot (variable “Sel-data” = “extra” in the data set), allowing representing a part of the size-density trajectory of sycamore at maximum density, with an insight into the possible impacts of species mixture and upper layer cover on the trajectory. The following data appear for each inventoried plot in the sycamore dataset: “Plot” (name of plot location), “Dep” (department number), NoPlot (plot number), “Cover“ (upper layer cover: “none”, “half-covered gap”, “whole covered gap”), “Mixed” (other species present: “no”, “yes”), “Mixed-species” (species in mixture, if any), “Sel-data” (“yes”, if inventory year data were selected for maximum size-density line fitting in the related publication, “no” or “extra data” if not), “Year“ (year of inventory), “Age“ (stand age, in years), “Ntot” (total number of live trees per ha), “Nsyc%” (relative number of sycamore live trees, in %), “Gtot” (total basal area of live trees, m2 ha-1), “Gsyc%” (sycamore basal area, in %), “Cg” (quadratic mean girth at breast height of all live trees, cm), “Hg” (mean height of sycamore trees at the date of plot installation, m).
DOI: 10.15454/pwkbfb
title: Data associated to the paper "A genomic map of climate adaptation in Mediterranean cattle breeds" (Flori et al., Molecular Ecology, Epub 2018 Dec 29. doi: 10.1111/mec.15004)

description: This dataset consists of genotypes of 640 animals for 39921 variants (SNPs). Animals belong to 21 Mediterranean cattle populations. The compressed archive contains two files (in plink format): i) a genotyping data file named "MED_set.ped" (640 rows, 79848 columns) that contains, for each individual, six information columns (breed ID, animal ID and four columns with data coded 0 or U) and the genotypes (alleles 1 and 2) for the 39921 SNPs (ACGT, Illumina TOP format) ; and ii) a map file named "MED_set.map" (39921 rows, 4 columns) that contains for each SNP, the autosome number, the SNP name, a column with data coded 0 and the SNP position on autosome.
DOI: 10.15454/qle7ea
title: Données article Fourrages "Novak et al. 2020"

description: Ce jeu de données est constitué des valeurs de compositions chimiques des feuilles de 31 espèces d’arbre, 14 espèces d’arbuste et 7 espèces de liane, ainsi que de 8 espèces herbacées prélevées au mois d’août des années 2014 à 2017 dans différentes régions de France. Ces données ont été acquises dans le cadre des projets Casdar Arbele, ADEME REACTIF Parasol, FP 7 AgForward et Fondation Liséa Biodiversité Ruminarbre, conduits par Jean-Claude Emile et Sandra Novak à l’Unité Expérimentale Fourrages, Ruminants et Environnement d’INRAE à Lusignan (UE FERLUS). Il comporte, pour chaque espèce, le nombre d’individus analysés (n), ainsi que les valeurs médianes (MED), moyennes (MOY), minimales (mini), maximales (maxi) et l’écart-type (ET) des teneurs en matière sèche (TMS), matières minérales (MM), matières azotées totales (MAT), fibres NDF-ADF-ADL, tanins condensés (TANc), P, Ca, Mg, Na, K, Cu, Fe, Mn, Zn et digestibilité in vitro de la matière sèche (DIGz). This dataset contains the contents on dry matter (TMS), ash (MM), crude protein (MAT), fibres NDF-ADF-ADL, condensed tannins (TANc), minerals (P, Ca, Mg, Na, K, Cu, Fe, Mn, Zn) and in vitro dry matter digestibility (DIGz) of leaves collected on 31 tree-, 14 shrub-, 7 liana- and 8 herbaceous species collected in August 2014 to 2017 in France. These data were collected in the frame of 4 projects (Casdar Arbele, ADEME REACTIF Parasol, FP 7 AgForward, Fondation Liséa Biodiversité Ruminarbre) led by Jean-Claude Emile and Sandra Novak at the Forage, Ruminants and Environment Experimental Unit of INRAE in Lusignan (UE FERLUS). For each species, the files give the number of individuals analysed, the median (MED), mean (MOY), minimum (mini), maximum (max) and standard deviation (ET).
DOI: 10.15454/r2e0xd
title: Annotation data about Multi Criteria Assessment Methods used in Science for Food and Bioproduct Engineering : the French National Institute for Agricultural Research (INRA-CEPIA) experience

description: This data article contains annotation data characterizing Multi Criteria Assessment Methods proposed in the scientific literature by INRA researchers belonging to the Science for Food and Bioproduct Engineering department. Those researchs concern the sectors of food, biotechnologies (pharmacy, cosmetology) and green chemistry (biofuels, materials, biomolecules).
DOI: 10.15454/rueioa
title: Replication Data for the article: Effects of climate warming on the pine processionary moth at the southern edge of its range: a retrospective analysis on egg survival in Tunisia

description: This dataset includes raw data and R code to reproduce the charts presented in the following article deposited on bioRxiv (10.1101/2021.08.17.456665) and PCI Ecology: Effects of climate warming on the pine processionary moth at the southern edge of its range: a retrospective analysis on egg survival in Tunisia by Bourougaaoui A., Robinet C., Ben Jamâa M. L. and Laparie M. Not all analyses and figures produced in the R scripts are presented or used in the final manuscript. Statistical analyses performed in SPSS by AB are not included due to SPSS analyses not being scripted, but raw data are available and tests are detailed in the Methods for replication. The same files and any later updates are available with version history as a public git repository at https://sourcesup.renater.fr/projects/ppm-eggs.
DOI: 10.15454/p5yigx
title: Mapping of known effector genes on five Meloidogyne genomes

description: Based on the literature, we established a manually curated list of M. incognita genes specifically expressed in sub-ventral or dorsal secretory gland cells. We started from the list published in (Truong, Nguyen, Abad, Quentin, Favery, 2015) and manually checked the figures associated with the cited references to only keep genes with evidence for specific expression via in-situ hybridization. We completed this list with the Mi-PNF3 gene published more recently (Leelarasamee, Zhang, Gleason, 2018) and eliminated redundancy between the sequences at the protein level. We retrieved the corresponding CDS sequences and aligned them to the M. incognita, M. arenaria, M. javanica, M. enterolobii and M. hapla genome sequences (Blanc-Mathieu et al., 2017; Koutsovoulos et al., 2020, Opperman et al. 2008) using the splice aware aligner SPALN (Iwata Gotoh, 2012) with the following parameters. 'spaln -Q7 -O4 -M -d Mi.mfa CDS &gt; input.gff -M = report multiple hits and only the best -Q4= DP mode, 5-7 = maximum number of reported hsp -O4= megablast-like format We performed this operation for the subventral (SvG) and (DG) subsets, separtely and provide a summary of the results in MS Word and PDF Format.
DOI: 10.15454/pa6uhy
title: Wild bees of wooded and herbaceous semi-natural habitats

description: The aim was to assess the difference in bee communities in three types of wooded and herbaceous habitats (permanent grassland,hedgerow and forest edge). The bees were netted in each of these habitats,in 30 landscapes selected according to a gradient of % of woodland. Wild bees were collected in May and June 2016 using an insect net along transects in each sampling point. Bees were hunted for 10 minutes,excluding time of capture and preparation of each individual insect. The transects were 100 m long and 5 m wide and were located in the middle of grasslands and along forest edges and hedgerows.
DOI: 10.15454/rlddks
title: Parameters model

description: This document describes all the input parameters used for the models in connection with the deliverable 3.2.
DOI: 10.15454/pdxrym
title: Acceptability and Grain-Legumes WoS DataSet 1980-2018

description: The text file corresponds to the search query capturing the main research theme on consumer acceptance of grain-legumes (both soya and pulses, see Species Grain-Legumes WoS dataset) to be applied on the WoS (Web of Knowledge). This search query is restricted to the main types of scientific literature documents, namely the types: article, book, book chapter, and review. This translated into the query DT = ("Article" OR "Book" OR "Book Chapter" OR "Review"); the time range selected is 1980-2018 (PY = "1980-2018"). Acceptability theme refers here only to sensorial and organoleptic analysis for consumer acceptance. UT file corresponds to the results of this search query (UT refers to a WoS unique identifier for each record retrieved) after a post-processing step which eliminated the records captured by the Wos KeyWord Plus : ie, the UT file correspond to records containing terms of the search query only in title, abstract, and (regular) keywords. See the related publication for more information.
DOI: 10.15454/pexzce
title: RPG complété 2018 département 30

description: RPG complété 2018. Complète le RPG campagne 2018 pour le département 30. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2020.
DOI: 10.15454/pl3hwq
title: Statistical analysis scripts to analyze metabarcoding data of fungal communities associated with two grapevine varieties (Vitis vinifera ‘Regent’ and ‘Cabernet-Sauvignon’)

description: This archive provides the statistical analysis scripts used to analyze a metabarcoding dataset (available at https://www.ncbi.nlm.nih.gov/bioproject/678415) representing foliar fungal communities associated with two grapevine varieties (Vitis vinifera ‘Regent’ and ‘Cabernet-Sauvignon’) inoculated with powdery mildew (Erysiphe necator) under various drought conditions. Bioinformatic scripts and raw and filtered ASV tables in QIIME2 format and R phyloseq format have been deposited in Dataverse (https://doi.org/10.15454/KMAU1G). This archive provides the statistical analysis scripts and the rarefied ASV tables used for the analyses.
DOI: 10.15454/qbnhad
title: Daily feed intake, growth, and feed efficiency in chicken

description: This data file reports daily data of body weight (BW), feed intake (DFI), cumulative feed conversion ratio (DCFCR), breast meat yield (BMY) and breast meat pH (pHu) in two broiler lines divergently selected on breast meat pHu. Genotypes Animals were issued from two fast-growing broiler lines divergently selected on breast meat pH, 24h after slaughter. Daily data are coming from generation 14. Breast yield and pH data are coming from all generations of selection. Line 1 is selected for high pHu, line 2 for low pHu. Collection of data and rearing conditions Data have been collected thanks to eletronic feed stations BIRD-e (https://hal.inrae.fr/hal-02627687). Birds were reared in pens of 300 animals, on floor. Two groups were reared, the first from 2019-11-27 to 2020-01-09, the second from 2019-12-03 to 2020-01-15. The two groups were reared in adjacent and similar rooms. Both males and females were used in the experiment. Measures : BWX: body weight at X days (from 3 to 42 d). Expressed in g. DFIX : daily feed intake at day X (from 5 to 42 d). Expressed in g. ADGX : average daily gain at day X (from 3 to 42 d). Expressed in g. DCFCRX : cumulative feed conversion ratio from 5 to X days. Calculated as the total feed intake from 5 to X days to the weight gain during the same period. Expressed in g.g-1. BMY : breast meat yield. Equal to the ratio of Pectoralis major+Pectoralis minor (without skin and bone) on body weight at slaughter * 100. Expressed in percentage. pHu : pH of Pectoralis major Other information: Sex of animals (1 for males, 2 for females) Batch (31 batches over 14 generations, batches 30 and 31 are those with full data collection) Maternal permanent environment effect (2076 levels, among which 101 for batches 30 and 31)
DOI: 10.15454/qy4uvn
title: Biodivers OSCAR project - data for the France Stream macroinvertebrates biodiversity analysis

description: This dataset contains the data that were used in the Biodiversa OSCAR project (Optimising the configuration of woody riparian buffer strips along rivers to enhance biodiversity and ecosystem services) to study the effect of riparian woody buffers percentages on stream macroinvertebrates communities in French streams. It contains: - stream macroinvertebrates metrics and indices (at the genus level), extracted from Naiades database - physico-chemistry data, extracted from Naïades database - woody riparian buffers percentages at different spatial extents, derived from IGN databases - Land cover percentages at the basin scale and at a local buffer scale, derived from Corine Land Cover database - Hydromorphological pressures metrics, extracted from the Syrah_CE project.
DOI: 10.15454/r5vv8z
title: Conifer exome capture data

description: Variant calling files (vcf) and associated sample descriptions (metadata) for five conifer species
DOI: 10.15454/rfj5ty
title: Turn-on power measurements on B2-EM003-S4 RAIN transponder

description: Turn-on power measurements on B2-EM003-S4 RAIN transponder and associated environmental data
DOI: 10.15454/rm6tyy
title: Data to inform the modelling of direct nitrogen field emissions from global agriculture

description: To inform the parameterisation of the Indigo-N v.3 nitrogen direct field emissions estimation model, published as “Indigo-N v.3, a semi-mechanistic operational model for direct field N emissions in LCA of cropping systems under contrasting agricultural situations” [1], we compiled data pertaining to crop characteristics, mineral and organic fertiliser characteristics, soil characteristics and climate; at the global scale. Most of the data were obtained from published sources, such as scientific literature and data repositories. Pedoclimatic data were recomputed to cells defined as the combination of a country and a Global Ecological Zone [2]. The described data can be useful for other N emission estimation approaches.
DOI: 10.15454/rwollq
title: Supplementary tables to manuscript: “Metagenomic analysis of virome cross-talk between cultivated Solanum lycopersicum and wild Solanum nigrum”

description: Supplementary tables to manuscript in Chapter 4.
DOI: 10.15454/rzxmmh
title: RPG complété 2018 département 60

description: RPG complété 2018. Complète le RPG campagne 2018 pour le département 60. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2020
DOI: 10.15454/pd5rdb
title: Instructions for use SS4I Software

description: Instructions for use SS4I Software