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

TitleIntegrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome.
Publication TypeJournal Article
Year of Publication2004
AuthorsKrzywinski, M, Wallis, J, Gösele, C, Bosdet, I, Chiu, R, Graves, T, Hummel, O, Layman, D, Mathewson, C, Wye, N, Zhu, B, Albracht, D, Asano, J, Barber, S, Brown-John, M, Chan, S, Chand, S, Cloutier, A, Davito, J, Fjell, C, Gaige, T, Ganten, D, Girn, N, Guggenheimer, K, Himmelbauer, H, Kreitler, T, Leach, S, Lee, D, Lehrach, H, Mayo, M, Mead, K, Olson, T, Pandoh, P, Prabhu, A-L, Shin, H, Tänzer, S, Thompson, J, Tsai, M, Walker, J, Yang, G, Sekhon, M, Hillier, LD, Zimdahl, H, Marziali, A, Osoegawa, K, Zhao, S, Siddiqui, A, De Jong, PJ, Warren, W, Mardis, E, McPherson, JD, Wilson, R, Hübner, N, Jones, S, Marra, M, Schein, J
JournalGenome Res
Volume14
Issue4
Pagination766-79
Date Published2004 Apr
ISSN1088-9051
KeywordsAnimals, Automation, Chromosomes, Chromosomes, Artificial, Bacterial, Chromosomes, Artificial, Yeast, Cloning, Molecular, Computational Biology, Contig Mapping, DNA Fingerprinting, Genetic Markers, Genome, Physical Chromosome Mapping, Polymerase Chain Reaction, Rats, Sequence Analysis, DNA
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 approximately 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.

DOI10.1101/gr.2336604
Alternate JournalGenome Res.
PubMed ID15060021
PubMed Central IDPMC383324
Grant ListU01 HG002155 / HG / NHGRI NIH HHS / United States
HG01165-06 / HG / NHGRI NIH HHS / United States
U01 HG02155 / HG / NHGRI NIH HHS / United States