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