A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation.
As part of a larger project to sequence the Populus genome and generate genomic resources for this emerging model tree, we constructed a physical map of the Populus genome, representing one of the few such maps of an undomesticated, highly heterozygous plant species. The physical map, consisting of 2802 contigs, was constructed from fingerprinted bacterial artificial chromosome (BAC) clones. The map represents approximately 9.4-fold coverage of the Populus genome, which has been estimated from the genome sequence assembly to be 485 +/- 10 Mb in size. BAC ends were sequenced to assist long-range assembly of whole-genome shotgun sequence scaffolds and to anchor the physical map to the genome sequence. Simple sequence repeat-based markers were derived from the end sequences and used to initiate integration of the BAC and genetic maps. A total of 2411 physical map contigs, representing 97% of all clones assigned to contigs, were aligned to the sequence assembly (JGI Populus trichocarpa, version 1.0). These alignments represent a total coverage of 384 Mb (79%) of the entire poplar sequence assembly and 295 Mb (96%) of linkage group sequence assemblies. A striking result of the physical map contig alignments to the sequence assembly was the co-localization of multiple contigs across numerous regions of the 19 linkage groups. Targeted sequencing of BAC clones and genetic analysis in a small number of representative regions showed that these co-aligning contigs represent distinct haplotypes in the heterozygous individual sequenced, and revealed the nature of these haplotype sequence differences.
Kelleher
Colin T
CT
Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
Chiu
Readman
R
Shin
Heesun
H
Bosdet
Ian E
IE
Krzywinski
Martin I
MI
Fjell
Chris D
CD
Wilkin
Jennifer
J
Yin
Tongming
T
DiFazio
Stephen P
SP
Ali
Johar
J
Asano
Jennifer K
JK
Chan
Susanna
S
Cloutier
Alison
A
Girn
Noreen
N
Leach
Stephen
S
Lee
Darlene
D
Mathewson
Carrie A
CA
Olson
Teika
T
O'connor
Katie
K
Prabhu
Anna-Liisa
AL
Smailus
Duane E
DE
Stott
Jeffery M
JM
Tsai
Miranda
M
Wye
Natasja H
NH
Yang
George S
GS
Zhuang
Jun
J
Holt
Robert A
RA
Putnam
Nicholas H
NH
Vrebalov
Julia
J
Giovannoni
James J
JJ
Grimwood
Jane
J
Schmutz
Jeremy
J
Rokhsar
Daniel
D
Jones
Steven J M
SJ
Marra
Marco A
MA
Tuskan
Gerald A
GA
Bohlmann
Jörg
J
Ellis
Brian E
BE
Ritland
Kermit
K
Douglas
Carl J
CJ
Schein
Jacqueline E
JE
D022202:Chromosomes, Artificial, Bacterial; D018745:Genome, Plant; D006239:Haplotypes; D018598:Minisatellite Repeats; D020161:Physical Chromosome Mapping; D011110:Polymorphism, Genetic; D032107:Populus / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA