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Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome

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Item Type:Article
Title:Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome
Creators Name:Krzywinski, M. and Wallis, J. and Goesele, C. and Bosdet, I. and Chiu, R. and Graves, T. and Hummel, O. and Layman, D. and Mathewson, C. and Wye, N. and Zhu, B. and Albracht, D. and Asano, J. and Barber, S. and Brown-John, M. and Chan, S. and Chand, S. and Cloutier, A. and Davito, J. and Fjell, C. and Gaige, T. and Ganten, D. and Girn, N. and Guggenheimer, K. and Himmelbauer, H. and Kreitler, T. and Leach, S. and Lee, D. and Lehrach, H. and Mayo, M. and Mead, K. and Olson, T. and Pandoh, P. and Prabhu, A.L. and Shin, H. and Taenzer, S. and Thompson, J. and Tsai, M. and Walker, J. and Yang, G. and Sekhon, M. and Hillier, L. and Zimdahl, H. and Marziali, A. and Osoegawa, K. and Zhao, S. and Siddiqui, A. and de Jong, P.J. and Warren, W. and Mardis, E. and McPherson, J.D. and Wilson, R. and Huebner, N. and Jones, S. and Marra, M. and Schein, J.
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.
Keywords:Automation, Bacterial Artificial Chromosomes, Chromosomes, Computational Biology, Contig Mapping, DNA Fingerprinting, DNA Sequence Analysis, Genetic Markers, Genome, Molecular Cloning, Physical Chromosome Mapping, Polymerase Chain Reaction, Yeast Artificial Chromosomes, Animals, Rats
Source:Genome Research
Publisher:Cold Spring Harbor Laboratory Press
Page Range:766-779
Date:April 2004
Official Publication:https://doi.org/10.1101/gr.2336604
PubMed:View item in PubMed

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