cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15454/ilmsyg
title: Characterization of lactic acid bacteria by FTIR and other analytical approaches to identify markers of cryoresistance

description: This data set concerns the biochemical and biophysical characterization of three lactic acid bacteria exhibiting different resistance to freezing to identify markers of cryoresistance. Carnobacterium maltaromaticum CNCM I-3298 (most freeze-resistant), Lactobacillus delbrueckii ssp bulgaricus ATCC 11842 and Lactobacillus delbrueckii ssp bulgaricus CFL1 (most freeze-sensitive) were investigated. The dataset includes for each of the three strains: i) biological activity (culturability and acidifying activity) and ii) biochemical composition by Fourier transform infrared microscopy of cells in an aqueous environment before and after freeze-thawing; iii) membrane characterization: fatty acid composition, membrane fluidity following cooling, lipid phase transition following freezing and iv)intracellular glass transition temperature
DOI: 10.15454/jeot4o
title: A richer community of Botryosphaeriaceae within a less diverse community of fungal endophytes in grapevines than in adjacent forest trees revealed by a mixed metabarcoding strategy.

description: Botryosphaeriaceae are a diverse group of endophytic fungi colonizing the inner tissue of many woody species. As opportunist pathogens, they have been increasingly involved in diebacks worldwide. Nonetheless, the diversity of Botryosphaeriaceae, especially in asymptomatic plants, remains largely unknown. Using an innovative and mixed strategy of metabarcoding, this study aims to investigate the diversity of the fungal endophyte community, with a focus on Botryosphaeriaceae which colonize grapevine and adjacent oak and pine trees in a French landscape. These data were used to test if the differentiation between hosts is more important than geographical effects for shaping the Botryosphaeriaceae communities and that similarity is higher between communities of grapevine and oak - both Angiosperms - than between oak and pine trees. Finally, we revealed a high level of diversity in Botryosphaeriaceae fungi, in both grapevines and forest trees, with a greater richness for grapevines. Contrasting results were obtained for the endophytic community, which was more diverse in forest trees. Our results support the hypothesis that host factors prevail on geographic effects to explain the diversity of Botryosphaeriaceae at the studied spatial scale. However, the features of the agro-eco-system, such as management practices, were suggested to be more important than phylogeny to structure the fungal community. This highlights the importance of management practices for the microbiome of plant trees.
DOI: 10.15454/elcszi
title: simulator METAGENE Fortran code

description: Fortran code of simulator used to generate norms of reaction
DOI: 10.15454/gsjsww
title: Intensive study site: INRAE chestnut germplasm collection (Domaine de la Grande Ferrade, Villenave d'Ornon)

description: This intensive study plot is located in Villenave d’Ornon, near Bordeaux in southwestern France (44.788319 N, -0.577062 E). It includes the INRAE chestnut germplasm collection and all isolated trees located in the immediate surroundings (1 km from the INRAE research site). The germplasm collection is distributed in two nearby orchards. The first orchard was planted in 1970 and comprises 29 widely spaced trees on 2.3 ha while the second orchard was planted in 1990 and includes 211 trees on 3.5 ha. In contrast to the Asiatic chestnut species, the European chestnut is very vulnerable to blight and ink diseases originating from Asia (Gonthier and Robin 2019). Cross-breeding between Asiatic species and European chestnut has been carried out to select new tolerant hybrid cultivars (Barreneche et al. 2019), some of which have been massively planted for fruit production. Hence, the two orchards include different taxa: 117 C. sativa (European chestnut), 22 C. crenata (Japanese chestnut), 20 C. mollissima (Chinese chestnut) and 81 interspecific hybrids, including 56 C. sativa x C. crenata. In some cases, both parental trees and their offspring are found in the orchards. Most trees are grafted on both rootstocks: Marsol (CA07) or Maraval (CA74). Pollination and hence pollen limitation are still poorly understood in chestnuts (Larue et al. 2021a). To investigate these topics, the site described above, which is fairly isolated from other chestnut pollen sources, seemed appropriate. Our ultimate goal is to develop a spatially explicit individual-based mating model to investigate intra- and interspecific mating events with pollen coming from inside and outside of the INRAE germplasm collection. This model will allow a simultaneous estimation of all parameters influencing not only male but also female fecundity and pollen dispersal using a Bayesian approach for random effect mating model (Klein et al. 2008, 2011; Chybicki et al. 2021). Many efforts were made to gather a comprehensive data set as input for this model and for other studies. All trees of the intensive study plot were genotyped and their phenotypes were precisely described, including floral characters. We scored their phenology with a newly developed BBCH scale adapted for chestnut (Larue et al. 2021b), and we estimated seed-set during two consecutive years.
DOI: 10.15454/hkiqfj
title: Consumer perception data about food packaging functionalities for fresh strawberries - Consumers’ answers to poll for Plastic rigid lid
DOI: 10.15454/htrlxe
title: Hourly weather data from 2020 recorded in a French orchard in Hauts d'Anjou (Loire Valley)

description: This dataset contains daily meteorological data from September 2020 recorded in a French orchard in the Hauts d'Anjou (Loire Valley), and more precisely on the estate "La Rétuzière" belonging to the Horticultural Experimental Unit. For more details, see the "read-me meteo Hauts Anjou" file.
DOI: 10.15454/kew474
title: Assembly and annotation of 'Regina' sweet cherry genome

description: This dataset includes the preliminary assembly and structural annotation of the version 1 (V1) of 'Regina' sweet cherry genome, following genome sequencing using PacBio long reads and optical mapping. We have reconstructed the pseudomolecules at near chromosome level using high density genetic linkage maps with GBS data.
DOI: 10.15454/eclygt
title: Land Use Land Cover High Resolution Map (5-m) for Côte-d’Or (21)

description: The LULC HRL Map is produced from a combination of multi-sources data: the French national topographic database; the Land Parcel Identification System (LPIS) database; and Corine Land Cover. The LULC HRL classification contains 11 land cover categories: 11 Industrial or Commercial buildings and other Facilities 12 Agricultural buildings 13 Low-rise Residential or Mixed buildings 14 High-rise Residential or Mixed buildings 2 Fields 3 Meadows/Grassy plots 4 Bushes/Shrubs 5 Trees/Forest 6 Vineyards 7 Water bodies 8 Others artificial surfaces
DOI: 10.15454/fz9nn6
title: Spatio-temporal diversity of thermal responses in populations of the wheat pathogen Zymoseptoria tritici

description: Characterisation of the physiological thermal responses linking environmental temperatures to fitness of 350 Z. tritici strains. Thermal parameters retrieved from thermal performance curves obtained in vitro under laboratory-standardised conditions (monitoring of growth kinetics within aliquots of different spore suspensions exposed to 12 temperatures).
DOI: 10.15454/ihyjcx
title: Cross-reference table for Botrytis cinerea B0510 and T4 gene ids

description: Botrytis cinerea, the grey mould fungus, is a plant pathogen with a necrotrophic lifestyle causing serious pre- and post-harvest diseases on a variety of plant species worldwide. Several genome annotations have been released in the past years : T4-URGI, B0510-BROAD (Amselem et al., 2011) ; T4vanKan - B0510vanKan (Staats and van Kan, 2012) ; BcinB0510 (van Kan et al., 2016) ; GenBank (individual submissions). We established a cross-reference table between Botrytis cinerea BcinB010 gene ids and the gene ids in the other annotations. Individual gene informations can also be retrieved at : https://bioinfo.bioger.inrae.fr/portal/genome-portal/1/
DOI: 10.15454/j9ko72
title: LC-MS metabolomic analyses of maize young leaf cultivated in a growth chamber

description: Analyses performed on 18 genetically-diverse hybrids using leaf methanolic extracts.
DOI: 10.15454/kb0nl3
title: Data and Jags code for Folio et al. : Genotype by environment interaction drives the maintenance of genetic variation in a brown trout hybrid zone.

description: This dataset contains data and code regarding a manuscript submitted to Evolutionary Applications: "Genotype by environment interaction drives the maintenance of genetic variation in a brown trout hybrid zone. ". These data describe the parental traits of brown trout used in a fertilization protocol and the experimental design for the obtained clutches. The code describes a statistical model for mixed-effects GLM under JAGS software, to estimate the different factors influencing the survival between fertilization to hatching in natural rivers.
DOI: 10.15454/kld0gh
title: A dataset for analysing the genetic progress in maize: yield in multi site field experiments and traits in phenotyping platforms

description: Breeding and improved agronomic practices increased maize yields with the genetic component evaluated in panels of varieties released over decades. We performed a comprehensive analysis that links, in common genetic material, yield progress to underlying physiological traits and corresponding genomic regions. We analyzed a maize panel including the 66 most successful European hybrids released from 1950 to 2015. The dataset consists of (i) measured yield and its components in 30 environments across Europe, together with environmental variables collected every day in each experiment, (ii) phenological, architectural, physiological and reproductive traits measured in ten high-precision experiments in three phenotyping platforms in controlled conditions and two phenotyping platforms in the field
DOI: 10.15454/ffkgup
title: Histoire évolutive et impact des différents processus évolutifs sur la diversité génétique de l’abricotier (Prunus armeniaca L.)

description: Supplemental data files from Shuo LIU's PhD
DOI: 10.15454/frof42
title: Taxonomic distribution of M. incognita Diamond hits against the NCBI's nr library

description: Taxonomic distribution of M. incognita Diamond hits against the NCBI's nr library. The taxonomy has been determined by Diamond LCA algorithm via outformat 102. Two reports are available: 1- all the M. incognita proteins as queries 2- PPN-specific M. incognita proteins as queries The first column represent the number of hist returning hits of the taxonomic entity under consideration. All the other columns represent the hierarchy of the taxonomic lineage. Krona graphs providing a visual and interactive taxonomic distribution of the Diamond hits are also available for each report. (all proteins and PPN-specific only).
DOI: 10.15454/fzhie0
title: Effect of fermentation pH, temperature, and harvest on cell growth and functional properties of frozen and freeze-dried Lactobacillus delbrueckii subsp. bulgaricus CFL1

description: This dataset concerns the study of the effect of three fermentation parameters (pH, temperature, and harvest time) on the functional properties of Lactobacillus delbrueckii subsp. bulgaricus CFL1 at different production process steps: fermentation (initial), freezing, freeze-drying, and freeze-dried storage. The two dataset files include: (i) the fermentation parameters (temperature, pH, and base addition) and the bacterial growth properties (optical density at 880 and 600 nm, dry cell weight, glucose consumption, and lactic acid production in g∙L-1) monitored throughout bacterial growth; (ii) the functional properties: acidifying activity (Cinac system) and culturability (plate count method) after fermentation and protection (initial), after freezing, after freeze-drying, and after freeze-dried storage (25°C, 15 days). Finally, the water content of samples after freeze-drying is also included.
DOI: 10.15454/gjgiah
title: Phytoplankton morpho-functional trait dataset from French water-bodies

description: The recent development of functional approaches may allow evaluating other aspects of ecosystem quality, functions and interactions with abiotic parameters or other communities. Here, our aim was to create a phytoplankton trait database at the national scale for France. This database will be relevant to analyze phytoplankton communities for a better understanding of phytoplankton functional ecology in lakes of France and other European countries with similar biological communities. For this purpose, we used a French national database of phytoplankton occurrences sampled from lakes over the entire French metropolitan territory. The observed taxa list was used to compile 53 morpho-functional traits associated with phylogeny information. The morpho-functional traits encompassed variables such as shape, biovolume, motility, toxin production and Reynolds groups.
DOI: 10.15454/h0uqz9
title: Gold standard alignments between Ciqual and IFIP food product terms and FoodOn food concepts

description: This dataset contains two Gold standard alignments between Ciqual food product terms and FoodOn food concepts. The first one, called GS100, includes a representative selection of 100 food meat products from Ciqual meat families. Each food product has been manually aligned with the closest concept in the SIREN subpart of FoodOn and associated FoodOn family. Sometimes, it was not possible to find a closest food product in FoodOn, but it was always possible to find a closest family. The second one, called GS300, which is extended by food products belonging to other families of product. GS300 also includes 23 food products from an additional data source provided by a technical institute (IFIP) specialized in meat food products. The dataset also includes scores computed using the alignment method using Langual as background knowledge in CSV format and alignment API RDF format for GS100 and GS300.
DOI: 10.15454/h9jj7j
title: Atlas des stations de sports d'hiver des Alpes françaises

description: Au cœur de l’économie des territoires de montagne, les stations de sports d’hiver doivent relever de nombreux défis. Changement climatique, renouvellement des équipements et maturité du marché sont autant d’impératifs d’une adaptation permanente. Pour mieux cerner ces enjeux et y répondre, un système d’information s’imposait : Irstea dispose aujourd’hui d’une base de données dédiée, la BD Stations réalisée sous la coordination scientifique d'E. George-Marcelpoil avec la collaboration de G. Fablet, notamment pour les questions foncière et immobilière, F. Bray, responsable du pôle SI, C. Achin, A. Torre et J.-B. Barré.
DOI: 10.15454/hkgmas
title: MUNQ - Malus UNiQue genotype code for grouping apple accessions corresponding to a unique genotypic profile

description: This dataset corresponds to the assignment of MUNQ (Malus UNiQue genotype) codes to a large set of apple accessions genotyped with common SSR (microsatellite) markers. The MUNQ assignment was performed as described in Muranty-Denancé et al. (2020; https://doi.org/10.1186/s12870-019-2171-6) as a development from the FBUNQ code (for FruitBreedomics UNiQue genotype code) assigned by Urrestarazu-Denancé et al. (2016; https://doi.org/10.1186/s12870-016-0818-0) to more than 2,400 accessions from 14 mostly European apple germplasm collections after their genotyping with up to 16 SSR. When SSR marker data were obtained at other sites than IRHS (INRAE, Angers, France), SSR allele sizes were carefully adjusted between the alternative collections and the IRHS collection, both by use of reference accessions known to be in common between collections and by re-genotyping a subset of each collection with the full set of 16 SSR markers to confirm the allele adjustment. The MUNQ assignment was extended to the whole National Fruit Collection (NFC, Brogdale, UK) by using the genotyping data produced for 12 common SSR markers by Fernandez-Fernandez (2010; Fingerprinting the National Apple and Pear Collections - Final Report N° GC0140; http://sciencesearch.defra.gov.uk) with updates according to Ordidge-Venison (2018; https://researchdata.reading.ac.uk/163/). This file will be progressively completed with MUNQ assigned to accessions from other apple germplasm collections in Europe, USA and elsewhere.
DOI: 10.15454/ivbodd
title: Expression of muscle genes related to magnesium transport and homeostasis in response to Mg status in mice

description: Chronic Mg2+ deficiency is at the origin of a broad range of health dysfunctions. Because 25% of body Mg2+ is located in the skeletal muscle, Mg2+ transport and homeostasis systems (MgTHs) in muscle are critical for whole body Mg2+ homeostasis. In the present study, we assessed whether Mg2+ deficiency alters muscle fiber characteristics and major pathways regulating muscle physiology. C57BL/6J mice were fed for 14 days either a control, mildly or severely Mg2+-deficient diet (0.1%; 0.01%; and 0.003% Mg2+ wt/wt, respectively). Mg2+ deficiency slightly decreased body weight gain, muscle Mg2+ concentrations, but was not associated with detectable variations in gastrocnemius muscle weight, fiber morphometry and capillarization. Nonetheless, to maintain Mg2+ homeostasis muscles exhibited decreased expression of several MgTHs (Magt1, Cnnm2, Cnnm4 and Trpm6). MgTHs mRNA levels were positively correlated with body weight gain. Moreover, TaqMan Low Density Array (TLDA) analyses further revealed that, before the emergence of major muscle dysfunctions, even a mild Mg2+ deficiency was sufficient to alter expression of genes critical for muscle physiology, including energy metabolism, muscle regeneration, proteostasis, mitochondrial dynamics and excitation-contraction coupling.
DOI: 10.15454/jhdcqm
title: R language Dynamic game theory code for Chevalier et al. manuscript in American Naturalist.

description: The present dataset includes three main items. The first item is the code of the model used in Chevalier et al. 2020, published in American Naturalist. It can be run in R software as it is. It simulates the dynamics of optimal choosiness in a game where both sexes can select their partner(s) in a finite time window, with respect to partner quality. The second item is R code for Shiny Application, that can be run directly in R software. It allows exploring the results of the model in terms of partner availability, under different simulation scenarios. The third item is also R code for Shiny Application, that can be run directly in R software. It allows exploring the results of the model in terms of optimal choosiness, under different simulation scenarios. These two last items are provided as compressed .tar files.
DOI: 10.15454/foifcn
title: Developement of sequence-based microsatellite genotyping methods at the Bordeaux Genome Transcriptome Facility PGTB

description: Characteristics of the developed sequence-based microsatellite genotyping methods at the Bordeaux Genome Transcriptome Facility (PGTB ; https://pgtb.cgfb.u-bordeaux.fr/ ; https://pgtb.fr/)
DOI: 10.15454/ixshf7
title: Individual liveweight of Mérinos d'Arles ewe lambs, measured with a Walk-over-Weighing (WoW) system under Mediterranean grazing conditions

description: The dataset compiles the total of individual liveweight (LW, kg) measures collected during four months of an experiment carried out with 100 recently weaned Mérinos d'Arles ewelambs reared under the Mediterranean grazing conditions of Domaine du Merle Experimental farm (Salon de Provence, France). The files included are as follows: - Raw database - Database1: Corresponding to the database obtained after the first filtering step, process considering the removal of outliers provoked by animal misbehaviour (data abnormally too low e.g. 0, or toow high with regard to the average individual value to be expected e.g. 100, 200 kg (meaning that more than one animal was in the platform) - Database2: Corresponding to the database obtained after the second filtering step, process considering the removal of outliers at the experimental group level (i.e. abnormal values with regard to the minimum and maximum liveweight value to be considered on each experimental group) - Database3(Final): Corresponding to last database obtained after the third filtering step, process considering the removal of outliers at the individual level (i.e. abnormal values with regard to the minimum and maximum liveweight value to be cexpected for each individual at a give date) - DatabaseStatic_GoldStandard: Corresponding to the liveweight data measured with the static scale, as a reference, once a week, for comparing with the automatic records registered by the WoW - R-Codes: the codes used for database filtering steps are provided as are those for the Lin’s Concordance Correlation Coefficient and for the statistical analysis Several columns are provided on each Excel Dataset including the individual electronic identification of each animal (ID), the date of each LW measurement (or passage through the WoW platform), the experimental week (Week), the liveweight measured and registered by the WoW (WoW_LW, kg) and the individual LW estimated for that individual animal at that date (LW_estimated), based on the calculated average daily gain between the results of two successive weeks of LW measurements, with the static (Gold Standard) scale. The standard deviation (minimum and maximum) as well as the LW sub-group of each animal are also provided. For the GS dataset, the ID, the date of measurement (once a week) and the registered static LW value for each individual at that date are included. For the databases 1, 2 and 3(final) (i.e. resulting from successive data filtering processes) the columns are similar to those previously described for WoW datasets.
DOI: 10.15454/jb2wce
title: Woody Plant Ontology

description: The Woody Plant Ontology lists reference variables used for experimentations and observations on woody plants (forest trees and shrubs, and possibly fruit trees). It is an international initiative based on various communities (French, Portuguese and European). Terms are collected from various sources and organized following the Crop Ontology standard which provides harmonized variables composed composed by a triplet: (i) a trait, the studied character, (ii) a method, the measurement protocol and (iii) a scale, the unit of measurement or scoring scale. The Woody Plant Ontology is available in various formats used by the community: CropOntology Excel, Adonis Variable Library, JSON, OWL and RDF La Woody Plant Ontology répertorie les variables de référence utilisées pour les expérimentations et les observations sur les plantes ligneuses (arbres et arbustes forestiers, et éventuellement arbres fruitiers). Il s'agit d'une initiative internationale basée sur différentes communautés (française, portugaise et européenne). Les termes sont collectés à partir de diverses sources et organisés selon le standard de la Crop Ontology qui défini des variables harmonisées composées d'un triplet : (i) un trait, le caractère étudié, (ii) une méthode, le protocole de mesure et (iii) une échelle, l'unité de mesure ou l'échelle de notation. La Woody Plant Ontology est disponible sous différents formats utilisés par la communauté : Excel CropOntology, Bibliothèque de variables Adonis, JSON, OWL and RDF