Fecal bacterial communities of wild black capuchin monkeys (Sapajus nigritus) from the Atlantic Forest biome in Southern Brazil are divergent from those of other non-human primates

Gut microbiota are influenced by factors such as diet, habitat, and social contact, which directly affect the host's health. Studies related to gut microbiota in non-human primates are increasing worldwide. However, little remains known about the gut bacterial composition in wild Brazilian monkeys. Therefore, we studied the fecal microbiota composition of wild black capuchin monkey (Sapajus nigritus) (n=10) populations from two different Atlantic Forest biome fragments (five individuals per fragment) in south Brazil. The bacterial community was identified via the high-throughput sequencing and partial amplification of the 16S rRNA gene (V4 region) using an Ion Personal Genome Machine (PGMTM) System. In contrast to other studies involving monkey microbiota, which have generally reported the phyla Firmicutes and Bacteroidetes as predominant, black capuchin monkeys showed a high relative abundance of Proteobacteria (X= 80.54%), followed by Firmicutes (X= 12.14%), Actinobacteria (X= 4.60%), and Bacteriodetes (X= 1.31%). This observed particularity may have been influenced by anthropogenic actions related to the wild habitat and/or diet specific to the Brazilian biome's characteristics and/or monkey foraging behavior. Comparisons of species richness (Chao1) and diversity indices (Simpson and InvSimpson) showed no significant differences between the two groups of monkeys. Interestingly, PICRUSt2 analysis revealed that metabolic pathways present in the bacterial communities were associated with xenobiotic biodegradation and the biosynthesis of secondary metabolites, which may suggest positive effects on monkey health and conservation in this anthropogenic habitat. Infectious disease-associated microorganisms were also observed in the samples. The present study provides information about the bacterial population and metabolic functions present in fecal microbiota, which may contribute to a better understanding of the ecology and biology of black capuchin monkeys living in forest fragments within the Atlantic Forest biome in southern Brazil. Additionally, the present study demonstrates that the fecal bacterial communities of wild black capuchin monkeys in this area are divergent from those of other wild non-human primates

Information system for phenotype data: trait, trials and genotypes identification and integration

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GnpIS-Asso : A Generic Database for Managing and Exploiting Plant Genetic Association Studies Results Using High Throughput Genotyping and Phenotyping Data

We will present a new functionality developed in GnpIS information system to manage association studies data (GWAS). A query form is available on http://urgi.versailles.inra.fr/gnpis portal and directly at this URL https://urgi.versailles.inra.fr/association/association/viewer.do#form. The tool allows plant scientists or breeders to get associations values between traits and markers obtained in several association studies. Several filters are available to refine the query, such as the species, trait (s), or marker (s) or panel of germplasms. The tool gives also the possibility in a second round of analysis, to add a new set of filters, i) on statistical values, or ii) on treatment done in the study, or iii) on the location and iv) year of the phenotyping trial or according to the v) statistical model chosen to do the analysis. It allows to view graphically the results with dedicated plots (QQPlot, Manhattan Plot), generated dynamically and to extract data in files to continue the analysis with external tools. After selecting the best markersassociated to trait of interest, the tool allows also to automatically jump on the genome to find where this marker is located on chromosomes and to identify in a very simpler way which genes or other markers or features of interest are near it. This tool is already now used for dealing GWAS studies (association, genotyping and phenotyping data) for 2 species: tomato and maize, data that are already referenced in two 2 publications and will also manage wheat data in 2015

Improving the « FAIRness » of Inra’s data for plant biology and breeding

INRA is involved in several projects (e.g. EU H2020 ELIXIR-Excelerate, n°676559) or global initiatives (e.g. Wheat Initiative, Research Data Alliance) contributing to the development of : (i) community recommandations for data standardisation (e.g. wheatis.org ; doi:10.1038/hortres.2016.56), (ii) data standards for phenotyping data (www.miappe.org), (iii) crop specific ontologies in the frame of the CropOntology (http://www.cropontology.org/) and (iv) standard web services (www.brapi.org). These global resources are used to capture the data produced by INRA and its partners in large scientific projects with a standard and structured vocabulary and to store them into INRA’s central repository for plant genomic, phenomic and genetic data, GnpIS (https://urgi.versailles.inra.fr/gnpis/) under the FAIR principles (https://www.force11.org/group/fairgroup/fairprinciples). For this purpose, standardization good practices are actively promoted in particular in the french community using as levers large french scientific projects centered around crop species (Wheat, Maize, Rapeseed, SunFlower, Pea and Sugar Beet) or infrastructures such as the french node of the European infrastructure for phenotyping (EMPHASIS) or the french infrastructure for biological resources for research in agriculture (AgroBRC). Recently, the standards for phenotyping data have been extended to support forest tree data in collaboration with the french node of the European infrastructure for Analysis and Experimentation on Ecosystems (AnaEE Services). Finally, these progresses in the FAIRness of our data are used to develop or contribute to federations of interoperable information systems (see for instance the Wheat community use case: doi: 10.12688/f1000research.12234.1)

BreedWheat GWAS data in GnpIS information system

Book of abstracts, ISBN: 978-2-9563873-0-5, EAN: 9782956387305Poster PI-05, p. 53BreedWheat project (https://breedwheat.fr/) aims to support the competitiveness of the French wheat breeding sector, answering to societal challenges for a sustainable and quality production. Moreover, the BreedWheat project characterize yet poorly exploited genetic resources to expand the diversity of the elite germplasm. Finally, new breeding methods are developed and evaluated for their socioeconomic impact.The URGI (Research Unit in Genomics Info) is an INRA research unit in genomics and bioinformatics dedicated to plants and their parasites. It develops and maintains an information system in genomics and genetics: GnpIS (Steinbach et al., Database 2013, doi: 10.1093/database/bat058).BreedWheat data available in GnpIS are genetic resources (collection of 5,232 accessions), polymorphisms (724,020 SNPs from 10 sources), genotyping (Affymetrix Axiom TaBW420K array), phenotyping (48,000 micro-plots in 21 locations) and Genome Wide Association Study (775,621 association results calculated from phenotyping and genotyping values): https://wheat-urgi.versailles.inra.fr/Projects/BreedWheat.GnpIS interface allows to display association values (with links to metadata, phenotyping and genotyping related values), these data can be filtered according to several criteria (eg p-val) and visualized graphically (QQplot, boxlplot based on genotyping alleles, Manhattan plot mapped to IWGSC RefSeq v1.0)

Developing grapevine FAIR Data

International audienc

GnpIS: an information system to integrate genetic and genomic data from plants and fungi

Data integration is a key challenge for modern bioinformatics. It aims to provide biologists with tools to explore relevant data produced by different studies. Large-scale international projects can generate lots of heterogeneous and unrelated data. The challenge is to integrate this information with other publicly available data. Nucleotide sequencing throughput has been improved with new technologies; this increases the need for powerful information systems able to store, manage and explore data. GnpIS is a multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. GnpIS is used by both large international projects and plant science departments at the French National Institute for Agricultural Research. Here, we illustrate its use. Database URL: http://urgi.versailles.inra.fr/gnpis

URGI plant and fungi platform: distributed resources through GMOD tools

International audienceNext Generation Sequencing technologies produce very large amount of data. Indeed, genomes are (re-)sequenced at high pace, and new sequences data are produced (eg. RNA-seq, Chip-seq). To face this challenge, the URGI ( http://urgi.versailles.inra.fr ) platform aims at providing tools for genomics, genetics, transcriptomics and polymorphisms comprising: pipelines, databases and user-friendly interfaces to analyze, browse and query the data. We will present plant and fungal genomic resources distributed through GMOD tools integrated in our Information System GnpIS.- Our genome module database (DB) components rely on the well-known schemas from the GMOD consortium. All annotation features and analysis results are primarily stored in the Chado or Bio::SeqFeature schema according to the need. Data can then be searched through GnpIS QuickSearch based on Apache Lucene™. Indexes are generated to query data stored in same or separate GMOD DBs. Query results are returned according to significance with terms, and linked to other GnpIS modules and/or Genome Report System (GRS). Biomart (GMOD) based datamarts were used as an advance search tool. Results of complex search criteria could be exported in different formats or directly send to our Galaxy server for further bioinformatic analysis.- We provide textual or graphical interfaces over the DBs such as GBrowse or Gbrowse_Syn to display sequence annotations or synteny respectively and Apollo for genes structure curation. The GRS provides comprehensive categories of reports through a user-friendly textual interface over structural and functional genomic data stored in Chado databases. - We also present the pipelines we developed for differential gene expression and polymorphism analysis available through our Galaxy server