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Title: A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map

Abstract

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 contigsmore » 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.« less

Authors:
 [1];  [2];  [2];  [2];  [2];  [1];  [3];  [4]
  1. University of British Columbia, Vancouver
  2. Genome Sciences Centre, Vancouver, BC, Canada
  3. ORNL
  4. West Virginia University
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Laboratory Directed Research and Development (LDRD) Program
OSTI Identifier:
936835
DOE Contract Number:  
DE-AC05-00OR22725
Resource Type:
Journal Article
Resource Relation:
Journal Name: Plant Journal, The; Journal Volume: 50; Journal Issue: 6
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; CHROMOSOMES; CONTIGS; GENETICS; POPLARS

Citation Formats

Kelleher, Colin, CHIU, Dr. R., Shin, Dr. H., Krywinski, Martin, Fjell, Chris, Wilkin, Jennifer, Yin, Tongming, and Difazio, Stephen P.. A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map. United States: N. p., 2007. Web. doi:10.1111/j.1365-313X.2007.03112.x.
Kelleher, Colin, CHIU, Dr. R., Shin, Dr. H., Krywinski, Martin, Fjell, Chris, Wilkin, Jennifer, Yin, Tongming, & Difazio, Stephen P.. A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map. United States. doi:10.1111/j.1365-313X.2007.03112.x.
Kelleher, Colin, CHIU, Dr. R., Shin, Dr. H., Krywinski, Martin, Fjell, Chris, Wilkin, Jennifer, Yin, Tongming, and Difazio, Stephen P.. Mon . "A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map". United States. doi:10.1111/j.1365-313X.2007.03112.x.
@article{osti_936835,
title = {A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map},
author = {Kelleher, Colin and CHIU, Dr. R. and Shin, Dr. H. and Krywinski, Martin and Fjell, Chris and Wilkin, Jennifer and Yin, Tongming and Difazio, Stephen P.},
abstractNote = {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.},
doi = {10.1111/j.1365-313X.2007.03112.x},
journal = {Plant Journal, The},
number = 6,
volume = 50,
place = {United States},
year = {Mon Jan 01 00:00:00 EST 2007},
month = {Mon Jan 01 00:00:00 EST 2007}
}