ea (Pisum sativum L., 2n = 14) is the second most important grain legume in the world after common bean and is an important green vegetable with 14.3 t of dry pea and 19.9 t of green pea produced in 2016 (http://www.fao.org/faostat/). Pea belongs to the Leguminosae (or Fabaceae), which includes cool season grain legumes from the Galegoid clade, such as pea, lentil (Lens culinaris Medik.), chickpea (Cicer arietinum L.), faba bean (Vicia faba L.) and tropical grain legumes from the Milletoid clade, such as common bean (Phaseolus vulgaris L.), cowpea (Vigna unguiculata (L.) Walp.) and mungbean (Vigna radiata (L.) R. Wilczek). It provides significant ecosystem services: it is a valuable source of dietary proteins, mineral nutrients, complex starch and fibers with demonstrated health benefits 1-4 and its symbiosis with N-fixing soil bacteria reduces the need for applied N fertilizers so mitigating greenhouse gas emissions 5-7. Pea was domesticated ~10,000 years

A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3

The Wheat@URGI portal has been developed to provide the international community of researchers and breeders with access to the bread wheat reference genome sequence produced by the International Wheat Genome Sequencing Consortium. Genome browsers, BLAST, and InterMine tools have been established for in-depth exploration of the genome sequence together with additional linked datasets including physical maps, sequence variations, gene expression, and genetic and phenomic data from other international collaborative projects already stored in the GnpIS information system. The portal provides enhanced search and browser features that will facilitate the deployment of the latest genomics resources in wheat improvement.Electronic supplementary materialThe online version of this article (10.1186/s13059-018-1491-4) contains supplementary material, which is available to authorized users.

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

26The Wheat@URGI portal (https://wheat-urgi.versailles.inra.fr) has been developed to provide 27 the international community of researchers and breeders with access to the bread wheat 28 reference genome sequence produced by the International Wheat Genome Sequencing 29 Consortium. Genome browsers, BLAST, and InterMine tools have been established for in 30 depth exploration of the genome sequence together with additional linked datasets including 31 physical maps, sequence variations, gene expression, and genetic and phenomic data from 32 other international collaborative projects already stored in the GnpIS information system. The 33 portal provides enhanced search and browser features that will facilitate the deployment of 34 the latest genomics resources in wheat improvement. 35 36 37 Background 38The International Wheat Genome Sequencing Consortium (IWGSC) [1] is an international 39 collaborative group of growers, academic scientists, and public and private breeders that was 40 established to generate a high quality reference genome sequence of the hexaploid bread 41 wheat, and to provide breeders with state-of-the-art tools for wheat improvement. The vision 42 of the consortium is that the high quality, annotated ordered genome sequence integrated 43 with physical maps will serve as a foundation for the accelerated development of improved 44 varieties and will empower all aspects of basic and applied wheat science to address the 45 important challenge of food security. A first analysis of the reference sequence produced by 46 the consortium (IWGSC RefSeq v1.0) was recently published [2]. 47To ensure that wheat breeding and research programs can make the most of this extensive 48 genomic resource, the IWGSC endorsed the establishment of a data repository at URGI (Unité parties in data management as well as analysis and usage of the sequence data. Wheat 54 functional genomics (expression, methylation, etc.), genetic, and phenomic data has increased 55 concurrently, requiring the development of additional tools and resources to integrate 56 different data for biologists and breeders. To manage this escalation of data, URGI have built 57 this data repository for the wheat community with the following specific aims: (i) store 58 resources for which no public archive exists (e.g. physical maps, phenotype information); (ii) 59 enable pre-publication access to specific datasets (e.g. sequence assemblies and annotations, 60 physical maps, markers); and (iii) rapid release of integrated resources upon publication. The 61 repository has been designed in accordance with the "FAIR" principles [3] to ensure that the 62 data are Findable, Accessible, Interoperable and Reusable. To address the challenge of 63 integrating diverse data types from multiple sources, URGI employs solutions that provide 64 enhanced features for data exploration, mining and visualisation using the GnpIS information 65 system [4] combined with a high level of data interoperability. 66Here we describe the data and tools currently available through...

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GnpIS is an information system designed to help scientists working on plants and fungi to decipher the molecular and genetic architecture of trait variations by facilitating the navigation through genetic, genomic, and phenotypic information. The purpose of the present chapter is to illustrate how users can (1) explore datasets from phenotyping experiments in order to build new datasets for studying genotype × environment interactions in traits, (2) browse into the results of other genetic analysis data such as GWAS to generate or check working hypothesis about candidate genes or to identify important alleles and germplasms for breeding programs, and (3) explore the polymorphism in specific area of the genome using InterMine, JBrowse tools embedded in the GnpIS information system.