ASPB 2013 Booth
Visit a collection of Plant 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 #200
- 1 Genomic Tools Minisymposium
- 2 Plant Genome Resources Outreach Booth
- 2.1 Projects with a Representative On Site
- 2.2 Projects without a Representative On Site (Brochures available!)
- 2.3 Acknowledgements
Genomic Tools Minisymposium
Plan to attend the Genomic Tools Minisymposium on Sunday, July 21, 3:45 - 5:30 PM
Plant biology researchers increasingly rely on databases and other informatics resources to organize, integrate and provide access to the flood of plant biology data now available. We will present the latest developments, data and tools for several important plant informatics resources. Presentations:
- Jason Williams - iPlant
- Doreen Ware - KBase
- Shelby Bidwell - JCVI
- Eva Huala - TAIR/IAIC
- Joshua Stein - Gramene
- Jeremy Edwards - Sol Genomics Network
- Kate Dreher - Plant Metabolic Network
Plant Genome Resources Outreach Booth
Projects with a Representative On Site
File:2013 ASPB plant outreach booth schedule.xls with a representative present at the booth
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 25 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 10 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 121 curated rice pathways. 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.
An overview of the Gramene comparative genomics database as well as latest developments and future plans will be presented by Joshua Stein during the Genomic Tools Minisymposium on Sunday, July 21st at 4:30pm.
P25019 – Gramene: A Resource for Comparative Plant Genomics. Presented by Marcela Karey Monaco
P15030 – Gramene: An Integrated Phylogenomics Resource for the Oryza genus. Presented by Joshua Stein
Gramene representatives will be available to meet with users and answer questions at booth #200 throughout the meeting.
For more information please contact: Gramene Feedback
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".
See TAIR's web page for more information: http://www.arabidopsis.org
The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available from TAIR includes the complete genome sequence along with information concerning gene structures, gene product functions, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, useful tools, and members of the Arabidopsis research community. Gene product function data is updated weekly from the latest published research literature and community data submissions. Gene structures are updated every 2 years using computational and manual methods as well as community submissions of new and updated genes. TAIR also provides extensive links from our data pages to other Arabidopsis resources.
For more information please contact: firstname.lastname@example.org
Plant Metabolic Network
See PMN's web page for more information: Plant Metabolic Network
The Plant Metabolic Network (PMN) provides a broad network of plant metabolic pathway databases that contain curated information from the literature and computational analyses about the genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism in plants.
The PMN has 17 species-specific databases and PlantCyc, a multi-species database with information from over 350 plant species.
Researchers can use these resources to analyze results and form new hypotheses for: Arabidopsis, barley, Brachypodium, cassava, Chinese, cabbage, chlamydomonas, corn / maize, grape, moss (Physcomitrella patens), papaya, poplar, rice, Selaginella, Setaria, sorghum, soybean, switchgrass, and many other species in PlantCyc.
Please come meet with a representative at Poster # P07029, the booth, or at Minisymposium #10 at 5:10 PM on Sunday.
Funding: The PMN is funded by the National Science Foundation (Grants #: 1026003 and 0640769) and the Department of Energy (BER Grant #: ER65472).
Solanaceae Genomics Network
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
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 Genome Release v4.0.
We have continued to curate and improve the M. truncatula genome sequence and annotation. We have combined NexGen sequences with the previous BAC-based assemblies to produce the current Mt 4.0 release. Pseudomolecules were constructed from ALLPATHS scaffolds on the basis of alignments to both the optical and genetic (genotyping-by-sequencing - GBS) maps. Where possible, high quality contiguous BAC sequences were patched into the new v4 pseudomolecules to close sequencing gaps in the ALLPATHS assembly,. Whereas the Mt 3.5 release consisted of ~ 250 Mb in pseudomolecules and ~ 100 Mb of unanchored sequence, the Mt 4 pseudomolecules now encompass approximately 360 Mb of sequences spanning 390 Mb of which ~ 330 Mb aligns accurately with the optical map. Most of the sequences and genes that were previously on unanchored portion of Mt3.5 have now been incorporated into Mt4.0 pseudomolecules, with the exception of only ~20Mb of unplaced sequences. The new pseudomolecules were annotated by an in-house pipeline that combined Mt3.5 gene models, predictions from Augustus and FGENESH with expression data and protein matches primarily using Evidence Modeler (EVM). Medtr identifers have been preserved between Mt 3.5 and Mt 4.0. Many new identifiers have been instantiated to replace the gene identifiers previously found on the unanchored contigs. Look-up tables are provided to allow easy navigation between the two data sets.
An overview of the Medicago truncatula Genome Release v4 and the tools available on the JCVI Website will be given during the Genomic Tools Minisymposium on Sunday, July 21st at 4:10PM.
P15029- Medicago truncatula Genome Resources at the J. Craig Venter Institute
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: MedicMine (Intermine) and WebApollo for gene structure curation by community annotators.
See the JCVI's web page for more information: http://www.jcvi.org/
The Bio-Analytic Resource for Plant Functional Genomics
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 (email@example.com)
The iPlant Collaborative provides a comprehensive cyberinfrastructure (CI) platform for the storage, sharing, and analyses of large datasets – from genomes to image data, and beyond.
iPlant’s vision to enable life science researchers and educators to use cyberinfrastructure to solve problems in biology, and ultimately predict the complexity of biological systems.
Easy-to-use iPlant tools cater to every level of user, from bench-biologists to bioinformaticians. Key components of the include:
· iPlant Discovery Environment- web-based solution for managing data, and running analyses; a scalable and extensible platform featuring hundreds of commonly used bioinformatics tools;
· Atmosphere- customizable on-demand cloud computing;
· DNA Subway – educational platform for genome annotation, DNA barcoding, and RNA-Seq
· Data Store- flexibility and control over your data, fast uploads/downloads, and terabytes of storage.
Please visit our website for more information: www.iplantcollaborative.org
Special Events for Plant Biology 2013
Please visit our Plant Biology 2013 page to take a survey (Win an iPad mini/ASPB conference pass or membership): www.iplantcollaborative.org/aspb2013
Selected Presentations and Posters:
· Plant Biology 2013 Education Booth 312/313: Integrating a Semester-Long Plant Genomics Investigative Research Experience into Introductory and Advanced Courses; Brent Buckner, Truman State University, MO
· Poster P12013: DNA Subway: Genomics, DNA Barcoding, and RNA-Seq - Bringing Cutting-Edge Biology into the Classroom; Jason Williams, Cold Spring Harbor Laboratory, NY
· Poster P15025: DNA Barcode Initiative for the Species of Eastern Nigeria; George Ude, Bowie State University, MD
iPlant is funded by the National Science Foundation: DBI-0735191
See KBase's web page for more information: http://kbase.us
The DOE Systems Biology Knowledgebase (KBase) is a collaborative effort designed to accelerate our understanding of microbes, microbial communities, and plants. It will be a community-driven, extensible and scalable open-source software framework and application system. KBase will offer free and open access to data, models and simulations, enabling scientists and researchers to build new knowledge and share their findings.
Systems Biology Knowledgebase (KBase)
Projects without a Representative On Site (Brochures available!)
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
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
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.
MaizeGDB is currently undergoing a full website redesign (see ) and we would appreciate help and input on making the new site able to meet your research needs!
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 are also coming along at MaizeGDB with access to the eFP Browser images from the Sekhon et al. Maize Gene Expression Atlas via gene model pages (e.g., ) as well as comparisons and views of the same dataset via MapMan where the data can be visualized online directly.
The Outreach Booth was made possible thanks to volunteer organizers:
- Kate Dreher, PMN
- Marcela Karey Monaco, Gramene