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  1. Crop Ontologies for Agronomic Traits

    Registration now closed! A meeting to discuss the potential application of trait and phenotype ontologies to describe agronomic traits in crop plants.

    tpadmin - 06.05.2014 - 13:37

  2. Training workshop in plant pathogenic genomics

    Registration now closed! A hands-on training workshop in plant pathogenic genomics, focused on the new resource PhytoPath and including coverage of Ensembl Fungi, Ensembl Protists and PHI-base will be held at the EBI in September, aimed at PhD students and post-doctoral researchers who are working on fungal and oomycete-induced disease in plants. Find out more details and register.

    tpadmin - 24.04.2014 - 13:28

  3. Ensembl Plants, Release 13

    This release of Ensembl Plants includes the genome of Brassica rapa [1]. The Brassica include important vegetable and oilseed crops. The B. rapa varieties include Chinese cabbage, pak choi and turnip. The B. oleracea varieties include broccoli, cabbage and cauliflower. Additionally, over 10% of the world's edible vegetable oil comes from B. napus, B. rapa, B. juncea and B. carinata collectively [2]. The Brassica are a classical example of the importance of polyploidy in plant evolution, described by 'U's triangle' [3]. The three diploid species B. rapa (A genome), B. nigra (B genome) and B. oleracea (C genome) having formed the amphidiploid species, B. juncea (A and B genomes), B. napus (A and C genomes) and B. carinata (B and C genomes) by hybridization. Comparative physical mapping studies have confirmed genome triplication in a common ancestor of B. oleracea and B. rapa since its divergence from the A. thaliana lineage at least 13-17 MYA [4-5]. The BrassEnsembl site was initially developed at Rothamsted Research, working in collaboration with the EBI and other partners [6]. From release 13 of Ensembl Genomes, the EBI will be maintaining the genome browser for B. rapa in the context of Ensembl Plants. References [1] The genome of the mesopolyploid crop species Brassica rapa. [2] Importance and origin. in Breeding Oilseed Brassicas. [3] Triangle of U- Wikipedia [4] Rates of nucleotide substitution in angiosperm mitochondrial DNA sequences and dates of divergence between Brassica and other angiosperm lineages. [5] Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. [6] http://www.ensembl.org/info/about/credits.html.

    tpadmin - 08.06.2014 - 15:01

  4. Ensembl Plants, Release 14

    This release of Ensembl Plants includes the newly sequenced Solanum lycopersicum (tomato) genome.

    tpadmin - 08.06.2014 - 15:01

  5. PRI-CAT

    PRI-CAT (Muino et al 2011; http://www.ncbi.nlm.nih.gov/pubmed/21609962) is a user-friendly web-tool for the analysis of plant ChIP-seq experiements. Starting with the raw sequences, the user will obtain the DNA binding maps in a wiggle file format, as well as, the potential target genes of the studied transcription factor. A DAS server was implemented for storage of the resulting DNA binding maps. At the moment, more than 30 binding maps are avaliable. All of them can be visualized with a DAS-compatible genome browser (eg: IGB), or download directly to the GALAXY framwork for futher analysis. PRI-CAT is freely available at http://www.ab.wur.nl/pricat URL:  http://www.ab.wur.nl/pricat/ Organization:  Stichting Dienst Landbouwkundig Onderzoek Resource type:  Database Service

    tpadmin - 04.10.2012 - 10:21

  6. transPLANT Genome Browsers

    We have integrated sequence associated features on the genomes of four species: rice, maize, soybean, and brassica. Features include: genes, transposons and restriction sites, clone information (BACs), genetic markers and maps. These data are notoriously detached from genomic backbones. Overcome this by collecting and associating the diverse datasets with the genomes, making the associations available via visualisation interfaces. This involved close collaboration with the respective national and trans-national sequencing consortia to obtain key data for each species. URL:  http://transplant.keygene.com/ Organization:  Keygene NV Resource type:  Database Service Resource logo: 

    tpadmin - 21.10.2014 - 10:54

  7. Ensembl Plants

    The Ensembl Genomes project produces genome browsers for important species from across the taxonomic range, using the Ensembl software system. Five sites are now available: Ensembl Bacteria, Ensembl Fungi, Ensembl Metazoa, Ensembl Plants, and Ensembl Protists. Ensembl Plants includes reference genome assemblies and gene builds for 15 plant species, including functional, comparative, and variation data for important crop species. URL:  http://plants.ensembl.org Organization:  The European Molecular Biology Laboratory Resource type:  Database Service

    tpadmin - 04.10.2012 - 15:32

  8. transPLANT user training workshop

    Registration now closed! A workshop focused on triticeae (wheat and barley mainly) data resources and tools, and include tutorials on data access and use from INRA, EBI-EMBL, IPK and MIPS. This workshop is targeted at (experimental) biologists, breeders, bio-informaticians and all other data users as no prior (informatics) knowledge or skills are required.

    tpadmin - 24.04.2014 - 13:15

  9. Ensembl Plants, Release 15

    We have added a set of homoeologous SNPs between wheat A, B and D genomes using wheat contigs aligned to Brachypodium distachyon as a reference framework, a structural variation dataset for Sorghum bicolor has been imported from dGVA, and a variety of small improvements to our assembly, annotation and variation datasets have been incorporated. See the Ensembl Plants homepage for details. URL:  http://plants.ensembl.org

    dbolser - 08.06.2014 - 15:01

  10. MIPS PlantsDB

    MIPS PlantsDB is a database framework for integrative and comparative plant genome research and provides data and information resources for individual plant species (including Medicago, Arabidopsis, Brachypodium, Sorghum, maize, rice, barley and wheat). Building up on that, state-of-the-art comparative genomics tools such as CrowsNest are integrated to visualize and investigate syntenic relationships between monocot genomes. Results from novel genome analysis strategies targeting the complex and repetitive genomes of triticeae species (wheat and barley) are provided and cross-linked with model species. The MIPS Repeat Element Database (mips-REdat) and Catalog (mips-REcat) as well as tight connections to other databases, e.g. via web services, are further important components of PlantsDB. URL:  http://mips.helmholtz-muenchen.de/plant/genomes.jsp Organization:  Helmholtz Zentrum Muenchen- Deutsches Forschungszentrum für Gesundheit und Umwelt Resource type:  Database Service

    dbolser - 04.10.2012 - 10:21

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