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The OMAP Project: Advancing Understanding of Oryza Genus

Explore Oryza genomes through evolutionary, biochemical, and physiological analyses, construct BAC libraries, physical maps, and perform comparative genomics. Public data release via Genbank and Gramene.

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The OMAP Project: Advancing Understanding of Oryza Genus

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  1. The Oryza Map Alignment Project (OMAP) • Overview of the OMAP project • OMAP data in Gramene • Future directions Bonnie Hurwitz, Gramene SAB meeting, January 13th 2006

  2. Overview of the OMAP Project • Develop a deeper understanding of the genus Oryza through evolutionary, biochemical, and physiological analysis of wild rice genomes • Construct 12 wild rice deep coverage BAC libraries • Construct physical maps for the 12 species • Create BAC end sequences for each library • Perform comparative genome analysis with the sequenced genomes for O. sativa and O. indica • Release data to the public domain through Genbank and Gramene

  3. OMAP Data Timeline in Gramene The Genome Browser October 2004: Added O. nivara, O.rufipogon and O. brachyantha alignments March 2005: Added O. alta, O. glaberrima and O. punctata alignments October 2005: Added O. coarctata and O. minuta Updated O. brachyantha and O. alta alignments

  4. OMAP Data Timeline in Gramene Cmap: The Comparative Map Viewer March 2005: Added O. nivara and O.rufipogon FPC maps July 2005: Added O. alta, O. glaberrima, O. brachyantha, O. punctata, and O. australiensis FPC maps

  5. BAC End Sequence Alignment Statistics Total BES: TIGR 614,332 IRGSP 657,711 Total Clones: TIGR 442,091 IRGSP 422,339

  6. Future Directions for OMAP Gramene: 2006 • Add alignment data to the TIGR and IRGSP assemblies as new BAC end sequences are deposited to Genbank • Update FPC maps with hand-edited maps • Incorporate variation data in the Gramene SNP view • Add comparative genome analysis data for rearrangements • Provide Gramene data for the wild rice genomes to the Rice Annotation Project (RAP)

  7. Transcript SNP View in Gramene

  8. Thanks to the OMAP team AGI: Dave Kudrna Yeisoo Yu HyeRan Kim William Nelson Kiran Rao Andrea Zuccolo AZ Genomics Lab: William Nelson Kiran Rao Purdue: Rick Westerman Phillip San Miguel Barbara Hass-Jacobus Brain Abernathy Principal Investigators: Rod Wing (AGI) Scott Jackson (Purdue) Cari Soderlund (AGI) Lincoln Stein (CSHL) Doreen Ware (CSHL) CSHL: Gramene team

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