Difference between revisions of "PAG 2016 Booth"

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Revision as of 18:36, 3 December 2015

Plant and Animal Genome 2016

Visit a collection of Plant and Animal Genomics databases and projects with resources for sequenced genomes, ontology development, genetic mapping, functional annotation of genes, mutants and phenotypes, genetic diversity, and bioinformatics tools. Representatives from the projects indicated below will be present to demonstrate tools for cutting-edge genomics and genetics research and to answer questions.

You can find us at Booth #504





Gramene

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See Gramene's web page for more information: http://www.gramene.org

Gramene is a curated resource for comparative functional genomics in crops and model plant species currently hosting 39 complete reference genomes. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data. Gene evolutionary histories are provided in phylogenetic gene trees using a method that infers orthologous relationships and complements whole genome alignments. Variation data is available for 11 species, including Arabidopsis, rice, and maize, and enriched with variant effect prediction. Gramene hosts metabolic pathways databases developed in house or by our collaborators in the BioCyc platform, which facilitates uploading, visualization and analysis. Recently, we began annotating metabolic pathways using the Reactome model, and have released a beta version of the Plant Reactome, a platform for the comparative analysis of plant metabolic and regulatory networks, featuring at present over 200 curated rice pathways and orthologous pathway projections to 58 plant species. We also host many genetic and QTL maps contributed by the broad research community. Gramene is supported by an NSF grant (IOS-1127112), and works closely with EBI-EMBL, OICR, and ASPB.


Gramene workshop: Tuesday, January 12 of 2015 1:30 - 3:40 pm PST in the California Room.


Gramene posters on the following sessions:

  • Bioinformatics
  • Genome Mapping, Tagging & Characterization (Rice)


Gramene representatives will be available to meet with users and answer questions at booth #504 throughout the meeting.


For more information please contact: Gramene Feedback or e-mail feedback@gramene.org


Funding: Our participation at this outreach booth is being made possible thanks to the funding support of NSF award #1127112 to "Gramene - Exploring Function through Comparative Genomics and Network Analysis" and USDA-ARS #1907-21000-030-00D.



MaizeGDB

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See MaizeGDB's web page for more information: http://www.maizegdb.org/

MaizeGDB is a community-oriented, long-term informatics service to researchers focused on the crop plant and model organism Zea mays that is funded by the USDA-ARS.

Of interest to most researchers are the integration of genetics and genomics at MaizeGDB. From the MaizeGDB Genome Browser, cM estimates of genome size are available. Mechanisms to locate loci of interest on the genome are available via the Locus Lookup and Locus Pair Lookup.

Functional genomics tools at MaizeGDB with access to the eFP Browser images from the Sekhon et al. Maize Gene Expression Atlas via gene model pages (e.g., [1]) as well as comparisons and views of the same dataset via MapMan where the data can be visualized online directly.


Crop Ontology

The Crop Ontology is a service of the Integrated Breeding Platform (IBP) developed in collaboration with the CGIAR centers and partners, under the leadership of Bioversity international. The Crop Ontology (www.cropontology.org) provides harmonized and validated breeders’ trait names, measurement methods, scales and standard variables for currently 19 CGIAR crops: banana, barley cassava, cowpea, chickpea, common bean, groundnut, lentil, maize, pearl millet, pigeonpea, potato, sorghum, soybean, sweet potato, rice, wheat, yam. Partners provided their ontologies for oat (Oat Global), solanaceae (SGN) and vitis (INRA).


Crop Ontology is used by the Breeding Management System (BMS) of the IBP and the Next Generation Breeding Databases developed by Boyce Thompson Institute. The Crop Ontology contributes to the content enrichment of the reference ontologies of the Planteome project (http://www.planteome.org/).


To fully understand the implications of varying factors within any cropping system, it is important to combine results of field management practices with crop traits. Therefore, an Agronomy Ontology is being developed to index key agronomic variables that will power an Agronomy Management System and Fieldbook, modeled on a CGIAR Breeding Management System and Fieldbook. The ontology development started with the compilation of existing lists of variables, factors, and methods commonly used by agronomists to described the trial management.



Solanaceae Genomics Network

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See the SGN's web page for more information: http://solgenomics.net


The SOL Genomics Network is a Clade Oriented Database (COD) containing genomic, genetic, phenotypic and taxonomic information for species in the Euasterid clade, including the families Solanaceae (e.g. tomato, potato, eggplant, pepper, petunia) and Rubiaceae (coffee). Genomic information is presented in a comparative format and tied to other important plant model species such as Arabidopsis. SGN is also one of the bioinformatics centers involved in tomato genome sequencing.

One of the major efforts at SGN is linking Solanaceae phenotype information with the underlying genes, and subsequently the genome. As part of this goal, SGN puts the control over the information in the hands of community experts. As a result, SGN annotations are more up-to-date, and richer with detailed descriptions and gene-to-phenotype cross links, than would otherwise be possible without a large curatorial staff.

For more information please contact: SGN Contact



J. Craig Venter Institute

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Plant genomics has been an integral part of the JCVI legacy for many years. Starting with our work on the first sequencing project of a plant, Arabidopsis, we have expanded our activities to genome and EST projects for a wide range of plant species. These include rice, continued work on Arabidopsis, potato, maize, Medicago, soybean, tomato, barley, pine, onion, banana, various pulse crops (legumes) and several microbial pathogens that afflict important crops. Current work is focused primarily on improving the sequence and annotation of Medicago truncatula (barrel medic). We are also involved in consortia sequencing the genomes of Brassica oleracea, Medicago sativa (alfalfa) and Salix purpurea (willow, a potential bioenergy crop). In addition, we provide informatics support for and host the maize cell genomics database.


Medicago truncatula resources at JCVI include:

BLAST Search: Search against Mtv3.5 and Mtv4.0 genome assemblies and annotations. Gene Information Pages: Search for your favorite gene by Idnetifier or Keyword. View all searches completed, functional assignments and gene structure.

JBrowse: View any region of the genome in a Google Maps style interface. Community Annotation: Do you have a favorite gene or gene family? You can manually curate the Medicago truncatula structure and functions. Our EuCAP interface has been improved to include the ability to associate mutant information.

Coming soon:


See the JCVI's web page for more information: http://www.jcvi.org/


The Bio-Analytic Resource for Plant Functional Genomics

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See BAR's web page for more information: http://www.bar.utoronto.ca


The Bio-Analytic Resource at the University of Toronto is a collection of web-based tools for exploring, visualizing and mining large-scale data sets, primarily from Arabidopsis thaliana but also from several other plant species.

These tools include:

eFP Browser (electronic Fluorescent Pictograph Browser) for painting gene expression and other information onto diagrammatic representations of the particular experimental series from which the data were generated. eFP Browsers are available for Arabidopsis, poplar, Medicago truncatula, rice, barley, soybean, maize, potato and cell.

Expression Angler for identifying co-expressed, anti-correlated, or condition/tissue-specific genes using the "custom bait feature" in 5 of the gene expression data sets from the AtGenExpress Consortium, from our in-house database or from NASCArrays, or several other data sets.

Expression Browser for performing electronic northerns.

Arabidopsis Interactions Viewer for querying a database of almost 80,000 predicted and 28,566 documented protein-protein interactions in Arabidopsis.

Promomer for identifying over-represented n-mer words in the promoter of a gene of interest, or in promoters of co-expressed genes.

ePlant: A suite of interactive web-based tools that enables users to explore Arabidopsis data from the kilometre to nanometre scale, including natural variation data, organ and cell-type-specific gene expression patterns, subcellular localization, protein-protein interactions, and protein tertiary structures predicted for ~70% of the proteome.

Next-Gen Mapping: Allows for the rapid localization of recessive EMS induced mutations within an F2 mapping population that has been pooled and sequenced en masse using a next-generation sequencing platform.


Funding: The BAR is funded in part by Centre for the Analysis of Genome Evolution and Function, grants from the Canada Foundation for Innovation to NJP, and from Genome Canada to the Arabidopsis Research Group at the Department of Cell and Systems Biology, University of Toronto.


For more information please contact: Nick Provart (nicholas.provart@utoronto.ca)



SoyKB

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Soybean Knowledge Base (SoyKB) is a comprehensive all-inclusive web resource for soybean translational genomics and breeding. SoyKB handles the management and integration of soybean genomics and multi-omics data (including genomics, transcriptomics, proteomics and metabolomics) along with gene function annotations, biological pathway and trait information. It has many useful tools including Affymetrix probeID search, gene family search, multiple gene/metabolite analysis, motif analysis tool, protein 3D structure viewer and download/upload capacity for experimental data and annotations. It has a user-friendly web interface together with genome browser and pathway viewer, which display data in an intuitive manner to the soybean researchers, breeders and consumers.

SoyKB has new innovative tools for soybean breeding including a graphical chromosome visualizer targeted towards ease of navigation for breeders. It integrates QTLs, traits, germplasm information along with genomic variation data such as single nucleotide polymorphisms (SNPs) and genome-wide association studies (GWAS) data from multiple genotypes, cultivars and G.soja. QTLs for multiple traits can be queried and visualized in the chromosome visualizer simultaneously and overlaid on top of the genes and other molecular markers as well as multi-omics experimental data for meaningful inferences.


SoyKB can be publicly accessed at http://soykb.org



Plant Ontology and Plant Trait Ontology

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See PO's web page for more information: http://www.plantontology.org


The main objective of the Plant Ontology Consortium (POC) is to develop, curate and share controlled vocabularies (ontologies) that describe plant structures and growth and developmental stages and plant traits. The overall goal is to provide a semantic framework for meaningful cross-species queries across databases. The Plant Ontology (PO) and the Plant Trait Ontology (TO) have been developed with the primary goal to facilitate and accommodate functional annotation efforts in plant databases and by the plant research community at large.

As a part of the PO project, participating databases such as TAIR, NASC, Gramene, and MaizeGDB have been using PO to describe expression patterns of genes and phenotypes of mutants and natural variants.

Come see Poster # P28002: The Plant Ontology: A Tool for Linking Plant Anatomy and Development to Genomics Across Plant Taxa.


For more information please contact: PO Feedback



Acknowledgements

The Outreach Booth was made possible thanks to volunteer organizers:

  • Mary Schaeffer, MaizeGDB (University of Missouri)
  • Marcela Karey Tello-Ruiz, Gramene (Cold Spring Harbor Laboratory)
  • Lisa Harper, MaizeGDB
  • Carson Anderson, MaizeGDB (Iowa University)