VectorBase BRC Overview

1. VectorBase BRC Overview Scott Emrich BRC 2011 – Annual Meeting UT Southwestern Medical Center Dallas, TX 26-27 September 2011

2. VectorBase http://www.vectorbase.org Scott Emrich (on behalf of VectorBase consortium) University of Notre Dame

6. Upcoming vector genomes NHGRI White papers Others Sandflies Lutzomyia longipalpis Phlebotomus papatasi Anopheles (AGCC) Anopheles arabiensis Anopheles quadriannulatus Anopheles merus Anopheles melas Anopheles christyl Anopheles epiroticus Anopheles stephensi Anopheles maculatus Anopheles funestus Anopheles minimus Anopheles culicifacies Anopheles farauti Anopheles dirus Anopheles atroparvus Anopheles albimanus Simulium Simulium vittatum Simulium sirbanum Simulium damnosum Simulium ochraceum Simulium squamosum Simulium thyolense Simulium santipauli Simulium woodi Simulium exiguum Simulium yahense Anopheles Anopheles darlingi* Anopheles stephensi Aedes Aedes albopictus Glossina Glossina palpalis Glossina fuscipes Glossina pallidipes Glossina brevipalpis Glossina austeni Stomoxys calcitrans Musca domestica Culex cluster? ... Aedes cluster? Tick & Mites Leptotrombidium deliense Ixodes scapularis* Dermacentor variabilis Ornithodorus turicata VectorBase http://www.vectorbase.org BRC MeetingSeptember 2011

7. Summary of current contents VectorBase http://www.vectorbase.org BRC MeetingSeptember 2011

8. Upcoming challenges • We expect to receive over 30 vector genomes in the next 1-2 years • Further, our community is generating “-omics” transcriptome data for emerging genomes that need to be integrated • To address these issues, we introduced “prerelease” sites VectorBase http://www.vectorbase.org BRC MeetingSeptember 2011

9. Pre-sites for upcoming genomes VectorBase http://www.vectorbase.org BRC MeetingSeptember 2011

10. Pre-sites for upcoming genomes Genome browser BLAST search VectorBase http://www.vectorbase.org BRC MeetingSeptember 2011

11. Supporting species without genomic resources VectorBase http://www.vectorbase.org BRC MeetingSeptember 2011

12. VectorBase RNAseq data Leslie Vosshall, Rockefeller University

13. Integrating experimental data RNA-Seq VectorBase http://www.vectorbase.org BRC MeetingSeptember 2011

14. Projection build Integrating legacy (BRC#1) annotation data EBI Projection from reference • Aim: • Gene prediction using ‘high’ quality reference set from a related species. • Overview • When annotating a species for which we have a closely related reference species we can align the genomes and project from the ‘high’ quality set onto the new assembly. • This is more effective than a similarity build as it allows for building genes across contigs regardless of the assembly. • Whole-genome alignment (WGA) between reference and target using BLASTz. • Custom filter to ensure that each bp in the target genome is aligned to no more than one position in the reference genome. • Project predictions through transformation of coordinates between reference and target assemblies. • Summary • Effective for low coverage and poor quality assemblies. • Limited to reflect only orthologous loci between reference and target, i.e. no novel gene prediction. VectorBase http://www.vectorbase.org BRC MeetingSeptember 2011

15. Examples of integrating data http://funcgen.vectorbase.org/PopulationBETA/ • Still under active development • Currently > 15k samples from 1600 field collections UC-Davis data IR-base data Neafsey et al. SNP-chip data

18. GMOD natdiv consortium:

19. GMOD Natural Diversity module • Lightweight schema • All objects defined by ontologies • General • SO / GO / PATO • Spp. specific • IDOMAL / MIRO • Flexible • can handle all data from consortium • Vector spp. & butterflies • Rice & peaches

20. Ontologies hosted by VB • TGMA – Mosquito Anatomy Ontology; CARO/BFO • TADS – Tick Anatomy Ontology; CARO/BFO • MIRO – Ontology of Insecticide Resistance • IDOMAL – Malaria Ontology; extension: transmission • “VBCV” – Ontology/CV for “completion” of PopGen • OPL (Parasite Lifecycle) with Priti Parykh, Chris Stoeckertet al. • New IDO extensions: “IDODEN” (with S. Lonzano & R. Scheuerman) and “IDOCHA”

21. Goal: Anopheles gambiae reference • Many issues with the PEST assembly as a reference • S molecular form is proposed as the next reference Metrics of success Sanger* Hybrid assembly strategy • Project existing gene predictions • de novo prediction in novel regions • Re-map important datasets Illumina† 454 VectorBase http://www.vectorbase.org BRC MeetingSeptember 2011

22. Anopheles gambiae reference sequence Validation of the assembly by normal metrics Emphasis on the concordance with large scale restriction map (optical map) VectorBase http://www.vectorbase.org Kolymbari MeetingJuly 2011

23. Acknowledgements • V • EMBL-EBI Daniel Lawson Derek Wilson Gautier Koscielny Karyn Megy Martin Hammond Daniel Hughes Ewan Birney Paul Kersey Imperial College Fotis Kafatos Bob MacCallum George Christophides Seth Redmond Frank Collins Nora Besansky Greg Madey Rob Bruggner Nate Konopinski EO Stinson Scott Emrich Andrew Sheehan Rory Carmichael Dave Cieslak Dave Campbell Ryan Butler Katie Cybulski Neil Lobo NoTre Dame New MexicO Maggie Werner-Washburne Phil Baker HaRvard Bill Gelbart Susan Russo Dave Emmert Pinlei Zhou Lynn Crosby Kathy Campbell IMBB Kitsos Louis Pantelis Topalis Emmanuel Dialynas A Sequencers TIGR/JCVI WashU Broad Institute Baylor EnsEmbl VectorBase http://www.vectorbase.org BRC MeetingSeptember 2011