Chestnut Resources via the Hardwood Genomics Web
Meg StatonUniversity of Tennessee
Department of Entomology and Plant Pathology
Overview
Databases and Websites – the infrastructure to deal with the data deluge and make the resources useful
Hardwood Genomics Content
Hardwood Genomics Tools
Tripal – the database software
Hardwood Genomics Webwww.hardwoodgenomics.org• Website for hardwood tree data
• Transcriptomes
• Whole Genomes
• Genetic and Physical Maps
• Populations
• Phenotypes
• Genotypes
Software tools to find and explore information
Organism Page mRNA Page Genome Page
BLAST Search
Keyword Search
SymapSearch
Pages with information to explore and download
Organism Page
Organism Page
Organism Page
Genes -> mRNAs transcripts
• Genes – the functional units of the genome
• Can produce more than one type of transcript
• (Isn’t biology cool!?!)
• Chinese Chestnut genome has about
• 36,478 genes
• 38,146 transcripts
mRNA Page
mRNA Page
mRNA Page
Chestnut Genome
• Chestnut has an estimated 800,000,000 bases of DNA
• We have sequenced the chestnut genome and placed it into 41,260 pieces covering 724Mb
• Equivalent to a 500,000 page book• Not recommended for
light reading!
• Nathaniel Cannon’s work is putting these pieces in order
41,260
Ways to access the Chestnut genome - Download• Download the raw sequence files:
41,260 of these
Genome Page
Genome Page
Genome Page
TOOLS
Ways to access the Chestnut genome• This 500,000 page file isn’t too useful…
• What does it do? Where are the genes???
I could really use a map!!!
Ways to access the Chestnut genome
Examine a portion of the total genome
Provides navigation tools
Visualizes the location of genes in “tracks”
Visualizes the alignment of genes that originate from other plants such as peach and Arabidopsis
Can select an mRNA to get more information
BLAST
•Bring your own sequence of interest
•Run BLAST
•Compare to
•Chestnut mRNAs
•Chestnut proteins
BLAST
Other ways to find what you need and cool stuff to do
• Searching• Search by gene name• Search by function
• “Cytochrome P450”• “Mitogen-activated
protein kinase”
• Gene annotation• Think we did a bad
job for the “map” of this gene? You can go fix it!
Other ways to find what you need and cool stuff to do
Symap
• Compare the structure of the chestnut genome to other trees
TRIPAL SOFTWARE
A web framework for genetic and genomic data
Goals:
Simplify construction of a community genomics websitesEnable individual labs or research communities Encourage high-quality, standards-based websites for data sharing and collaborationExpand and reuse code
Why use Tripal?
• Open source
• Friendly developers
• Responsive mailing list
• Much of the stuff you need for a website is already there
Modules:• Organisms• Genomes• Transcriptomes• Stocks/Germplasm• Phenotypes• Genotypes
NSF DIBBS Grant• By leveraging the needs across many plant genomic communities,
we can make a strong case for federal support
• Funded development helps everyone!
• DIBBS: Integrate Tripal with Galaxy, an open source, web-based platform for data intensive biomedical research.
Stephen Ficklin
Jack Davitt Nathan Henry Ming Chen
Former Research Associate Research Associate Graduate Student
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