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The Oryza Map Alignment Project (OMAP)

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. Overview of the OMAP Project.

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The Oryza Map Alignment Project (OMAP)

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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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