Bienvenidos a TAIR!

1. Bienvenidos a TAIR! Kate Dreher curator TAIR/PMN

2. TAIR = The Arabidopsis Information Resource Why Arabidopsis? What does TAIR do? What can you do with TAIR? Introduction to TAIR Arabidopsis

3. 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?

4. 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?

5. 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

6. 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 . . .

7. 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 . . .

8. Dr. Eva Huala Director Dr. Sue Rhee Co-PI Curators Computer tech team members What does TAIR do? • Curators and computer tech team members work together under great directors • TAIR developsinternal data sets and resources • TAIR links toexternal 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

9. Internal TAIR data sets • Structural curators try to correctly define gene sequences • Functional curators try to correctly describe gene function

10. 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

11. Structural curation at TAIR • Apollo is a program to assist with structural curation cDNAs Protein similarity ESTs

12. Functional curators try to answer the questions: What does every gene/protein in Arabidopsis do? When are where does it act? Functional curation requirescontrolled vocabularies Allow cross-species comparisons TAIR curators work to develop and agree upon common terms Functional curation at TAIR achene berry capsule caryopsis circumcissile capsule cypsela drupe follicle grain kernel legume loculicidal capsule lomentum nut pod pome poricidal capsule schizocarp septicidal capsule septifragal capsule silique The seed-bearing structure in angiosperms, formed from the ovary after flowering FRUIT Plant Ontology: Structure: PO:0009001

13. 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 Functional curation at TAIR • IAA-Glu synthetase activity • IAA-glucose synthase activity • IAGlu synthase activity • indol-3-ylacetylglucose synthase activity • UDP-glucose:(indol-3-yl)acetate beta-D-glucosyltransferase activity • UDP-glucose:indol-3-ylacetate glucosyl-transferase activity • UDP-glucose:indol-3-ylacetate glucosyltransferase activity • UDPG-indol-3-ylacetyl glucosyl transferase activity • UDPglucose:indole-3-acetate beta-D-glucosyltransferase activity • uridine diphosphoglucose-indoleacetate glucosyltransferase activity Catalysis of the reaction: auxin + UDP-D-glucose = indole-3-acetyl-beta-1-D-glucose + UDP • Gene Ontology: • Molecular function: • GO:0047215 indole-3-acetate beta-glucosyltransferase activity

14. 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 Functional curation at TAIR Position along chromosome (between 14560 and 14580) Gene Arabidopsis thaliana Chromosome 5

15. Functional curators capture mutant phenotypes alx8 mutant – mutation in gene At5g63980 Functional curation at TAIR

16. 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

17. Tech (computer) team members and curators Provide links to external databases from every gene page Providing Tools at TAIR

18. 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 . . .) Providing Tools at TAIR Genbank Green Plant

19. Tech (computer) team members and curators Develop new tools and modify existing tools SeqViewer Patmatch . . . several others Providing Tools at TAIR

20. Tech (computer) team members and curators Create advanced search pages Providing Tools at TAIR

21. Ordering system for the Arabidopsis Biological Resource Center (ABRC) DNA stocks Seed stocks Community member information Arabidopsis lab protocols Gene Symbol Registry Information Portals Other Resources at TAIR

22. Are these data and tools useful? Unique Visitors per Month Visits per Month TAIR I TAIR II TAIR I TAIR II Bytes per Month TAIR I TAIR II

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

24. 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

25. 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?

26. 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?

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

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

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

30. GO categorization

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

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

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

34. Are there any mutant phenotypes associated with At2g04240? • Use the Seed/Germplasm Search page • . . . or look in the Germplasm section of the Locus page

35. Can I get a cDNA for At2g04240 to overexpress in potato? • Use the DNA Clones Search page

36. Are there putative SECA1 orthologs in other plant species? • Look for putative orthologs and paralogs using GBrowse • Phytozome (orthologs) • InParanoid (paralogs)

37. 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

38. Acknowledgements TAIR Eva Huala (Director) Sue Rhee (Co-PI) 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) Tech Team Members: - Bob Muller (Manager) - Larry Ploetz (Sys. Administrator) - Raymond Chetty - Anjo Chi - Vanessa Kirkup - Cynthia Lee - Tom Meyer - Shanker Singh - Chris Wilks

39. 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

40. 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! mouse zebrafish yeast roundworm fruit fly What should be the model plant?

41. Have I been able to get useful information at TAIR? • We hope so! • But, if you have any trouble finding the information you want . . .