Bienvenidos a TAIR!

Kate Dreher

curator

TAIR/PMN

TAIR = The Arabidopsis Information Resource

Why Arabidopsis?

What does TAIR do?

What can you do with TAIR?

Introduction to TAIR

Arabidopsis

Introduction to Arabidopsis Basic facts:

“small weed related to mustard” also known as “mouse ear cress” can grow to 20-25 cm tall annual (or occasionally biennial) plant member of the Brassicaceae

broccoli cauliflower radish cabbage

found around the northern hemisphere

Why do so many people study THIS plant?

Arabidopsis has good model organism traits

Fast life cycle (6 weeks) Thousands of plants fit in a small space Fairly easy to grow Thousands of seeds produced by each plant Self-fertile (in-breeding) Many different subspecies/ecotypes Serves as a good model for crop plants

But why Arabidopsis instead of other plants?

Arabidopsis offers some advantages “Good” genome

very small: 125 Mb diploid 5 haploid chromosomes fewer/smaller regions of repetitive DNA than many plants

Quite easily transformable with Agrobacterium NO tissue culture required

Inertia! A group of scientists lobbied for Arabidopsis The genome was sequenced (2000) MANY resources have been developed

Arabidopsis research can be successfully applied to “real plants” Over-expression of the hardy gene from Arabidopsis can improve water use efficiency in

rice (Karaba 2007)

cDNAs from castor bean were over-expressed in Arabidopsis and a high-throughput screen of fatty acid content in Arabidopsis seeds led to the identification of three cDNAs that increase the hydroxy fatty acid levels (Lu 2006)

Endosperm-specific over-expression of the Arabidopsis GTPCHI and ADCS biosynthetic genes can increase folate (vitamin B9) levels by up to 100-fold in rice (Storozhenko 2007)

Studies on a sodium transporter (HKT1) in Arabidopsis helped to identify a durum wheat homolog. It has been introgressed into bread wheat lines and appears to improve their yield on saline soils (Hwang 2006; Byrt 2007, et al)

Both basic and translational experiments using Arabidopsis continue . . .

Arabidopsis data explosion TONS of data are generated about Arabidopsis

Over 2400 “Arabidopsis” articles published each year are indexed in PubMed

Tens of thousands of mutants have been generated

Hundreds of microarray experiments have been performed

Proteomics and metabolomics studies are becoming popular

“1001” Arabidopsis genomes are being sequenced

Large-scale phenotypic studies are scheduled to start soon

TAIR tries to bring data together to benefit scientists and society That includes all of you . . .

What does TAIR do? Curators and computer tech team members work together under great directors

TAIR develops internal data sets and resources

TAIR links to external data sets and resources

TAIR provides free on-line access to everyone: www.arabidopsis.org

Funded by the National Science Foundation of the USA Started in 1999

Dr. Eva HualaDirector

Dr. Sue RheeCo-PI

Curators

Computer tech team members

Internal TAIR data sets

Structural curators try to correctly define gene sequences

Functional curators try to correctly describe gene function

Structural curation at TAIR Structural curators try to answer the question:

What are ALL of the genes in Arabidopsis? Use many types of data

ESTs full-length cDNAs peptides orthology

Determine gene coordinates and features Establish intron, exon, and UTR boundaries Add alternative splice variants Classify genes

protein coding miRNA psuedogene

Keep updating! (even though the genome was sequenced in 2000!) TAIR9 – released June 2009 282 new loci and 739 new gene models

Structural curation at TAIR

Apollo is a program to assist with structural curation

ESTsProtein similarity cDNAs

The seed-bearing structure in angiosperms, formed from the ovary after flowering

Functional curation at TAIR Functional curators try to answer the questions:

What does every gene/protein in Arabidopsis do? When are where does it act?

Functional curation requires controlled vocabularies Allow cross-species comparisons TAIR curators work to develop and agree upon common terms

acheneberry

capsulecaryopsis

circumcissilecapsulecypseladrupefolliclegrainkernel

legumeloculicidal capsule

lomentumnutpod

pomeporicidal capsule

schizocarpsepticidal capsuleseptifragal capsule

silique

FRUIT

Plant Ontology:Structure:PO:0009001

Catalysis of the reaction:auxin + UDP-D-glucose = indole-3-acetyl-beta-1-D-glucose + UDP

Functional curation at TAIR Functional curators try to correctly describe gene function

Functional curators try to help build controlled vocabularies Allow cross-species comparisons Develop and agree upon common terms

indole-3-acetate beta-glucosyltransferase activity

Gene Ontology:Molecular function:GO:0047215

IAA-Glu synthetase activityIAA-glucose synthase activityIAGlu synthase activityindol-3-ylacetylglucose synthase activityUDP-glucose:(indol-3-yl)acetate beta-D-glucosyltransferase activityUDP-glucose:indol-3-ylacetate glucosyl-transferase activityUDP-glucose:indol-3-ylacetate glucosyltransferase activityUDPG-indol-3-ylacetyl glucosyl transferase activityUDPglucose:indole-3-acetate beta-D-glucosyltransferase activityuridine diphosphoglucose-indoleacetate glucosyltransferase activity

Functional curation at TAIR Functional curators use controlled vocabularies to annotate genes

Molecular function Subcellular localization Biological process Expression pattern

Development stage Tissue / organ / cell type

Gene Enter common name, e.g. Nitrate Transporter 2.7, NRT2.7 Prefer to track using AGI (Arabidopsis Genome Initiative) Locus Codes

AT5G14570

Data Sources Published Literature Researchers

Arabidopsis thaliana Chromosome 5

Position along chromosome (between 14560 and 14580)Gene

Functional curation at TAIR Functional curators capture mutant phenotypes

alx8 mutant – mutation in gene At5g63980

External data sets MANY different external data sets are linked to specific genes

EST sequences (Arabidopsis and other species) Transcript expression data Peptide expression data Biochemical pathway data (. . . described in the PMN talk) Epigenetic features Ecotype-specific polymorphisms Publications Seed stocks DNA vectors Interaction partners Promoter elements Post-translational modifications Orthologs

New data types are frequently added

Providing Tools at TAIR Tech (computer) team members and curators

Provide links to external databases from every gene page

Providing Tools at TAIR Tech (computer) team members and curators

Load TAIR and external data sets into existing tools

BLAST

GBrowse

Synteny Viewer (very new)

NBrowse Interaction Viewer (coming soon . . .)

Genbank Green Plant

Providing Tools at TAIR Tech (computer) team members and curators

Develop new tools and modify existing tools

SeqViewer

Patmatch

. . . several others

Providing Tools at TAIR Tech (computer) team members and curators

Create advanced search pages

Other Resources at TAIR Ordering system for the Arabidopsis Biological Resource Center (ABRC)

DNA stocks

Seed stocks

Community member information

Arabidopsis lab protocols

Gene Symbol Registry

Information Portals

Are these data and tools useful?

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Who uses TAIR? (June 4 – July 4, 2009)

Why might you use TAIR? Do you work with plants?

Do you want to take advantage of the tremendous amount of Arabidopsis data?

Do you want to know more about a gene? an enzyme? a protein domain? a DNA regulatory region? an abnormal phenotype? a chromosomal region? a set of orthologous proteins? a biological process? natural variation across populations?

Then please come see if TAIR can help you

Putting TAIR to work for you . . .

You are studying drought tolerance in potato plants

You do a subtractive hybridization study to identify cDNAs that are up-regulated in the roots of drought-stressed plants

You find that a number of the up-regulated cDNAs code for proteins with a new domain: Ser-x-Glu-x-Cys-x-Ala = (SxExCxA)

One of the family members, SECA1, appears to be present at particularly high levels

How can TAIR help?

Putting TAIR to work for you . . .

Are there any proteins with the SxExCxA domain in Arabidopsis?

What do they do in Arabidopsis?

Do they share additional domains?

What is the closest homolog to SECA1?

Are there any phenotypes when SECA1 is mutated?

Can I get a cDNA of this homolog to over-express in my species?

Are there putative SECA1 orthologs in other plant species?

Are there any SxExCxA proteins in Arabidopsis? Find all of the proteins that have the SxExCxA domain

What do the SxExCxA proteins do? Option 1: Get the individual GO annotations for each gene

What do SxExCxA proteins do? Option 2: Get an overview of the information for the set of genes

GO categorization

What do SxExCxA proteins do? Option 3: Get the description of each gene

What other domains do SxExCxA proteins share? Identify all of the other domains found in those proteins

What is the closest homolog to SECA1? Blast SECA1 against the TAIR9 protein data set

Are there any mutant phenotypes associated with At2g04240?

Use the Seed/Germplasm Search page

. . . or look in the Germplasm section of the Locus page

Can I get a cDNA for At2g04240 to overexpress in potato?

Use the DNA Clones Search page

Are there putative SECA1 orthologs in other plant species?

Look for putative orthologs and paralogs using GBrowse Phytozome (orthologs)

InParanoid (paralogs)

We are here to help: www.arabidopsis.org Please use our data

Please use our tools

Please use TAIR to help improve your research on IMPORTANT plants!

Please contact us if we can be of any help! Make an appointment to meet with me during my visit

(Puedo tratar de hablar en español)

curator@arabidopsis.org

www.arabidopsis.org

AcknowledgementsTAIR

Current Curators:

- Tanya Berardini (lead curator – functional annotation)

- David Swarbreck (lead curator – structural annotation)

- Peifen Zhang (Director and lead curator- metabolism)

- A. S. Karthikeyan (curator)

- Philippe Lamesch (curator)

- Donghui Li (curator)

- Rajkumar Sasidharan (curator)

Recent Past Contributors:

- Debbie Alexander (curator)

Eva Huala (Director) Sue Rhee (Co-PI)

Tech Team Members:- Bob Muller (Manager)- Larry Ploetz (Sys. Administrator)- Raymond Chetty- Anjo Chi- Vanessa Kirkup- Cynthia Lee- Tom Meyer- Shanker Singh- Chris Wilks

We are here to help: www.arabidopsis.org Please use our data

Please use our tools

Please use TAIR to help improve your research on IMPORTANT plants!

Please contact us if we can be of any help! Make an appointment to meet with me during my visit

(Puedo tratar de hablar en español)

curator@arabidopsis.org

www.arabidopsis.org

Why Arabidopsis? Plant research can benefit from focusing on a “model” plant

Other model organisms include:

Model organisms are easy to do experiments on Fast life cycle Don’t need much space Easy to take care of Lots of offspring (for genetics) Can be genetically transformed Good model for the really interesting species

humans CROP PLANTS

Communities develop to study model organisms

Many resources become available for model organisms Lab protocols Mutant maps Stock centers Genome sequences . . . and more!

roundworm

yeast

mouse

fruit fly

zebrafish

What should be the model plant?

Have I been able to get useful information at TAIR?

We hope so!

But, if you have any trouble finding the information you want . . .