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Medicago genome sequencing initiative

Medicago genome sequencing initiative. Medicago as a model legume. Photo: R. Guerts, Wageningen. Choi HK, et al (2004) PNAS 101:15289-15294. Limpens & Bisseling (2003) Curr. Opin. Plant Biol. 6: 343. Sequencing strategy.

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Medicago genome sequencing initiative

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  1. Medicago genome sequencing initiative Nevin Dale Young January 2007

  2. Medicago as a model legume Photo: R. Guerts, Wageningen Choi HK, et al (2004) PNAS 101:15289-15294. Limpens & Bisseling (2003) Curr. Opin. Plant Biol. 6: 343 Nevin Dale Young January 2007

  3. Sequencing strategy • BAC-by-BAC sequencing of the entire euchromatin of Medicago truncatula, originally estimated at 200 Mbp, now estimated at ~300 Mbp. • >2000 BACs sequenced as of January 2007. • Goal is high quality “Bermuda standards” sequence throughout the euchromatin. • Strategy chosen to optimize the utility of the M. truncatula sequence in comparative genomics. • International consortium of genome centers are responsible for sequencing, distributed by chromosome. • Initial coordinated, genome-wide assembly generated in August 2006. Analysis is underway and release is planned for early 2007. Nevin Dale Young January 2007

  4. www.medicago.org/genome M. truncatula assembly — Release 1.0 Nevin Dale Young January 2007

  5. M. truncatula genome assembly Nevin Dale Young January 2007

  6. M. truncatula genome assembly Nevin Dale Young January 2007

  7. IMGAG Annotation Nevin Dale Young January 2007

  8. Confidence of gene models Nevin Dale Young January 2007

  9. Confidence of gene models Nevin Dale Young January 2007

  10. M. truncatula – Genome statistics Nevin Dale Young January 2007

  11. M. truncatula – Genome statistics Nevin Dale Young January 2007

  12. Mth2-139k124-S border Mth2-20l08 4-N border Gene density Gypsy density Copia density Total TE density Pericentromere Centromeres & pericentromeres Nevin Dale Young January 2007

  13. Legume phylogeny Nevin Dale Young January 2007

  14. Medicago & Lotus Nevin Dale Young January 2007

  15. Medicago & Glycine Nevin Dale Young January 2007

  16. Arabidopsis Medicago Poplar Arabidopsis Medicago Poplar Multi-species synteny comparisons Nevin Dale Young January 2007

  17. Multi-species synteny comparisons Nevin Dale Young January 2007

  18. Synteny on different chromosomes Nevin Dale Young January 2007

  19. Synteny on differentchromosomes Nevin Dale Young January 2007

  20. Summary: The Medicago genome • BAC-by-BAC sequence by end of 2008 • Release 1.0 (~60% complete) in early 2007 • Genome features • Lots of genes; many short, but probably expressed • Recombination drops nears ends of chromosomes • Chromosome 6 is very different from others • Comparative & evolutionary genomics • Ten large synteny blocks between Medicago & Lotus • Less internal duplication than At/Pt • Many short, scattered synteny blocks with At/Pt • Synteny varies greatly from region to region • For more information, visit posters P7 & P221 Nevin Dale Young January 2007

  21. EU Medicago Sequencing Christine Nicholson (Sanger) Frederic Debelle (Toulouse) Jerome Gouzy (Toulouse) Rene Guerts (Wageningen) Sean Humphray (Sanger) Gyorgy Kiss (Hungary) Klaus Mayer (MIPS) Giles Oldroyd (JIC) Frances Quetier (Genoscope) Stephane Rombauts (Ghent) Jane Rogers (Sanger) Thomas Schiex (Toulouse) Heiko Schoof (MIPS) Yves van de Peer (Ghent) Many others… Also Perry Cregan (Beltsville) David Hyten (Beltsville) Sequencing the Medicago genome • TIGR • Chris Town • Ryan Althoff • Tammy Arbogast • Foo Cheung • Doug Fadrosch • Erin Hine • Hean Koo • Erin Monaghan • Luke Tallon • CCGB (Minnesota) • Ernie Retzel • John Crow • Chris Dwan • Michael Heuer • Anne-Francoise Lamblin • UC-Davis • Doug Cook • Dongjin Kim • Hong-Kyu Choi • Andrew Cook • Young Lab (Minnesota) • Carine Ameline-Torregrosa • Eric Boehlke • Ryan Bretzel • Steven Cannon (now @ ISU) • Ethy Cannon (now @ ISU) • Ben Chacko • Roxanne Denny • Joann Mudge • Libby Shoop • Bing-Bing Wang • Min Wang • Shelley Wang • Ariel Abell • Atif Ahmed • Chris Alley • Daniel Feldman • Andrew Homan • Shara Johnson • Dana Larsen-Howe • Michael Kantar • Nyaling Moorosi • Michael O’Toole • Jake Pemberton • Diana Rommelfanger • Erica Savage Nevin Dale Young January 2007

  22. Mandi Aycock Amy Dickey Kayci Hale Randy Hine Aisha Hines Courtney Johnson Joey Klebba Julia Kim Xiangfei Kong Karen Marichal Goldameir Osisanya Stephen Snow Aleksandra Stojanoska, Yonas Tesfai Graham Wiley Erica Willis Sequencing the Medicago genome • Steve Kenton • Hongshing Lai • Sean Qian • Jim White • Axin Hua • Fares Najar • Shweta Deshpande • Majesta Seigfried • Irena Vasylenko • Ying Yi • Tammy Womack • KayLynn Hale University of Oklahoma • Bruce Roe • Anh Do • Trang Do • Sara Downard • Mounir Elharam • Ying Fu • Shaoping Lin • Phoebe Loh, • Rose Morales-Diaz • Sulan Qi • Baifang Qin • Chunmei Qu • Ziyun Zao • Doug White • Keqin Wang • Limei Yang • Yang Ye • Liping Zhao Nevin Dale Young January 2007

  23. Medicago genome sequencing initiative Nevin Dale Young January 2007

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