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PMID: 15060021 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S. Validation Study

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

Genome research ·Vol. 14 ·No. 4 ·2004-04-00 ·Pages 766-79

Krzywinski 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 AL, Shin H, Tänzer S, Thompson J, Tsai M, Walker J, Yang G, Sekhon M, Hillier L, 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

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.

MeSH Terms
Animals Automation Chromosomes/genetics Chromosomes, Artificial, Bacterial/genetics Chromosomes, Artificial, Yeast/genetics Cloning, Molecular/methods Computational Biology/methods,standards Contig Mapping/methods,standards DNA Fingerprinting/methods,standards Genetic Markers/genetics Genome Physical Chromosome Mapping/methods,standards Polymerase Chain Reaction/methods Rats Sequence Analysis, DNA/methods,standards
Chemicals
Genetic Markers
Authors & Affiliations
56 authors, click to expand affiliations / ORCID
Krzywinski Martin
Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada V5Z 4E6.
Wallis John
Gösele Claudia
Bosdet Ian
Chiu Readman
Graves Tina
Hummel Oliver
Layman Dan
Mathewson Carrie
Wye Natasja
Zhu Baoli
Albracht Derek
Asano Jennifer
Barber Sarah
Brown-John Mabel
Chan Susanna
Chand Steve
Cloutier Alison
Davito Jonathon
Fjell Chris
Gaige Tony
Ganten Detlev
Girn Noreen
Guggenheimer Kurtis
Himmelbauer Heinz
Kreitler Thomas
Leach Stephen
Lee Darlene
Lehrach Hans
Mayo Michael
Mead Kelly
Olson Teika
Pandoh Pawan
Prabhu Anna-Liisa
Shin Heesun
Tänzer Simone
Thompson Jason
Tsai Miranda
Walker Jason
Yang George
Sekhon Mandeep
Hillier LaDeana
Zimdahl Heike
Marziali Andre
Osoegawa Kazutoyo
Zhao Shaying
Siddiqui Asim
de Jong Pieter J
Warren Wes
Mardis Elaine
McPherson John D
Wilson Richard
Hübner Norbert
Jones Steven
Marra Marco
Schein Jacqueline
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.2336604
Published
2004-04-00
Pages
766-79
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC383324
Subset
IM
Grants
NHGRI NIH HHS · U01 HG002155 · United States
NHGRI NIH HHS · HG01165-06 · United States
NHGRI NIH HHS · U01 HG02155 · United States
External Links
PubMed source DOI: 10.1101/gr.2336604 PMC Full Text View journal details
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