Integrated and Sequence-Ordered BAC- and YAC-Based Physical Maps for the Rat Genome

  1. Martin Krzywinski1,
  2. John Wallis2,
  3. Claudia Gösele3,4,
  4. Ian Bosdet1,
  5. Readman Chiu1,
  6. Tina Graves2,
  7. Oliver Hummel3,
  8. Dan Layman2,
  9. Carrie Mathewson1,
  10. Natasja Wye1,
  11. Baoli Zhu5,
  12. Derek Albracht2,
  13. Jennifer Asano1,
  14. Sarah Barber1,
  15. Mabel Brown-John1,
  16. Susanna Chan1,
  17. Steve Chand1,
  18. Alison Cloutier1,
  19. Jonathon Davito2,
  20. Chris Fjell1,
  21. Tony Gaige2,
  22. Detlev Ganten3,
  23. Noreen Girn1,
  24. Kurtis Guggenheimer6,
  25. Heinz Himmelbauer4,
  26. Thomas Kreitler3,4,
  27. Stephen Leach1,
  28. Darlene Lee1,
  29. Hans Lehrach4,
  30. Michael Mayo1,
  31. Kelly Mead2,
  32. Teika Olson1,
  33. Pawan Pandoh1,
  34. Anna-Liisa Prabhu1,
  35. Heesun Shin1,
  36. Simone Tänzer7,
  37. Jason Thompson6,
  38. Miranda Tsai1,
  39. Jason Walker2,
  40. George Yang1,
  41. Mandeep Sekhon2,
  42. LaDeana Hillier2,
  43. Heike Zimdahl3,4,
  44. Andre Marziali6,
  45. Kazutoyo Osoegawa5,
  46. Shaying Zhao8,
  47. Asim Siddiqui1,
  48. Pieter J. de Jong5,
  49. Wes Warren2,
  50. Elaine Mardis2,
  51. John D. McPherson2,
  52. Richard Wilson2,
  53. Norbert Hübner3,
  54. Steven Jones1,
  55. Marco Marra1, and
  56. Jacqueline Schein1,9
  1. 1 Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada V5Z 4E6
  2. 2 Genome Sequencing Centre, Washington University School of Medicine, St. Louis, Missouri 63108, USA
  3. 3 Max-Delbruck-Center for Molecular Medicine (MDC), 13125 Berlin-Buch, Germany
  4. 4 Max-Planck Institute for Molecular Genetics, 14195 Berlin, Germany
  5. 5 BACPAC Resources, Children's Hospital Oakland Research Institute, Oakland, California 94609, USA
  6. 6 Department of Physics and Astronomy, University of British Columbia, Vancouver, Canada V6T 1Z1
  7. 7 Department of Genome Analysis, Institute of Molecular Biotechnology, 07745 Jena, Germany
  8. 8 The Institute for Genomic Research, Rockville, Maryland 20850, USA

Abstract

As part of the effort to sequence the genome of Rattus norvegicus, we constructed a physical map comprised of fingerprinted bacterial artificial chromosome (BAC) clones from the CHORI-230 BAC library. These BAC clones provide ∼13-fold redundant coverage of the genome and have been assembled into 376 fingerprint contigs. A yeast artificial chromosome (YAC) map was also constructed and aligned with the BAC map via fingerprinted BAC and P1 artificial chromosome clones (PACs) sharing interspersed repetitive sequence markers with the YAC-based physical map. We have annotated 95% of the fingerprint map clones in contigs with coordinates on the version 3.1 rat genome sequence assembly, using BAC-end sequences and in silico mapping methods. These coordinates have allowed anchoring 358 of the 376 fingerprint map contigs onto the sequence assembly. Of these, 324 contigs are anchored to rat genome sequences localized to chromosomes, and 34 contigs are anchored to unlocalized portions of the rat sequence assembly. The remaining 18 contigs, containing 54 clones, still require placement. The fingerprint map is a high-resolution integrative data resource that provides genome-ordered associations among BAC, YAC, and PAC clones and the assembled sequence of the rat genome.

Footnotes

  • [Supplemental material is available online at www.genome.org.]

  • Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.2336604.

  • ↵9 Corresponding author. E-MAIL jschein{at}bcgsc.ca; FAX (604) 877-6085.

    • Accepted February 16, 2004.
    • Received January 5, 2004.
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  1. doi: 10.1101/gr.2336604 Genome Res. 14: 766-779 Cold Spring Harbor Laboratory Press

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