Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome.
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.
Krzywinski
Martin
M
Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada V5Z 4E6.
Wallis
John
J
Gösele
Claudia
C
Bosdet
Ian
I
Chiu
Readman
R
Graves
Tina
T
Hummel
Oliver
O
Layman
Dan
D
Mathewson
Carrie
C
Wye
Natasja
N
Zhu
Baoli
B
Albracht
Derek
D
Asano
Jennifer
J
Barber
Sarah
S
Brown-John
Mabel
M
Chan
Susanna
S
Chand
Steve
S
Cloutier
Alison
A
Davito
Jonathon
J
Fjell
Chris
C
Gaige
Tony
T
Ganten
Detlev
D
Girn
Noreen
N
Guggenheimer
Kurtis
K
Himmelbauer
Heinz
H
Kreitler
Thomas
T
Leach
Stephen
S
Lee
Darlene
D
Lehrach
Hans
H
Mayo
Michael
M
Mead
Kelly
K
Olson
Teika
T
Pandoh
Pawan
P
Prabhu
Anna-Liisa
AL
Shin
Heesun
H
Tänzer
Simone
S
Thompson
Jason
J
Tsai
Miranda
M
Walker
Jason
J
Yang
George
G
Sekhon
Mandeep
M
Hillier
LaDeana
L
Zimdahl
Heike
H
Marziali
Andre
A
Osoegawa
Kazutoyo
K
Zhao
Shaying
S
Siddiqui
Asim
A
de Jong
Pieter J
PJ
Warren
Wes
W
Mardis
Elaine
E
McPherson
John D
JD
Wilson
Richard
R
Hübner
Norbert
N
Jones
Steven
S
Marra
Marco
M
Schein
Jacqueline
J
D000818:Animals; D001331:Automation; D002875:Chromosomes / Q000235:genetics; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D018244:Chromosomes, Artificial, Yeast / Q000235:genetics*; D003001:Cloning, Molecular / Q000379:methods; D019295:Computational Biology / Q000379:methods / Q000592:standards; D020451:Contig Mapping / Q000379:methods / Q000592:standards; D016172:DNA Fingerprinting / Q000379:methods / Q000592:standards; D005819:Genetic Markers / Q000235:genetics; D016678:Genome; D020161:Physical Chromosome Mapping / Q000379:methods* / Q000592:standards; D016133:Polymerase Chain Reaction / Q000379:methods; D051381:Rats; D017422:Sequence Analysis, DNA / Q000379:methods / Q000592:standards
D005819:Genetic Markers