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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}
}
  • 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 first maps of an undomesticated, highly heterozygous plant species. The physical map, consisting of 2,802 contigs, was constructed from fingerprinted bacterial artificial chromosome (BAC) clones. The map represents approximately 9.4-fold coverage of the 485+10 Mb Populus genome, as estimated from the genome sequence assembly. BAC ends were sequenced to aid in long-range assembly of whole genome shotgun sequence scaffolds and to anchor the physical map to themore » genome sequence. Simple sequence repeat (SSR)-based markers were derived from the end sequences and used to initiate integration of the BAC and genetic maps. 2,411 physical map contigs, representing 97% of all clones assigned to contigs, were aligned to the sequence assembly (JGI Populus trichocarpa v1.0). 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.« less
  • There have been concerted efforts in the past 5 years to create a high-resolution genetic map for all of the human chromosomes that contain markers that can be analyzed using the polymerase chain reaction technique. In 1992, a second-generation genetic linkage map of the human genome was presented that was composed of such markers. Additional genetic linkage maps have also been described that are mostly composed of simple-tandem repeat markers. And recently, Gyapay et al. expanded their initial genetic map and described the generation of a higher resolution human genetic map that was composed of over 2000 genetic markers. Unfortunately,more » most published genetic maps contain minimal information about the physical location of the markers. Since the physical location of most diseases are described based on where they map relative to a G-banded chromosome, it would be of use to determine the physical location of all genetic markers. 9 refs., 1 fig.« less
  • No abstract prepared.
  • A total of 992,682 single-nucleotide polymorphisms (SNPs) was identified as ideal for Illumina Infinium II BeadChip design after sequencing a diverse set of 17 common bean (Phaseolus vulgaris L) varieties with the aid of next-generation sequencing technology. From these, two BeadChips each with >5000 SNPs were designed. The BARCBean6K_1 BeadChip was selected for the purpose of optimizing polymorphism among market classes and, when possible, SNPs were targeted to sequence scaffolds in the Phaseolus vulgaris 14× genome assembly with sequence lengths >10 kb. The BARCBean6K_2 BeadChip was designed with the objective of anchoring additional scaffolds and to facilitate orientation of largemore » scaffolds. Analysis of 267 F2 plants from a cross of varieties Stampede × Red Hawk with the two BeadChips resulted in linkage maps with a total of 7040 markers including 7015 SNPs. With the linkage map, a total of 432.3 Mb of sequence from 2766 scaffolds was anchored to create the Phaseolus vulgaris v1.0 assembly, which accounted for approximately 89% of the 487 Mb of available sequence scaffolds of the Phaseolus vulgaris v0.9 assembly. A core set of 6000 SNPs (BARCBean6K_3 BeadChip) with high genotyping quality and polymorphism was selected based on the genotyping of 365 dry bean and 134 snap bean accessions with the BARCBean6K_1 and BARCBean6K_2 BeadChips. The BARCBean6K_3 BeadChip is a useful tool for genetics and genomics research and it is widely used by breeders and geneticists in the United States and abroad.« less