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

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 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 the 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 sequencingmore » 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];  [2];  [1];  [3];  [3];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2] more »;  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [4];  [4];  [5];  [5];  [6];  [2];  [2];  [3];  [1];  [1];  [1];  [1];  [2] « less
  1. University of British Columbia, Vancouver
  2. Genome Sciences Centre, Vancouver, BC, Canada
  3. ORNL
  4. Cornell University
  5. Stanford University
  6. U.S. Department of Energy, Joint Genome Institute
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Oak Ridge National Environmental Research Park
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
931850
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, Readman, Shin, Heesun, Bosdet, Ian, Krywinski, Martin, Fjell, Chris, Wilkin, Jennifer, Yin, Tongming, DiFazio, Stephen P, Ali, Johar, Asano, Jennifer, Chan, Susanna, Cloutier, Alison, Girn, Noreen, Leach, Stephen, Lee, Darlene, Mathewson, Carrie, Olson, Teika, O'Connor, Katie, Prabhu, Anna-Liisa, Smailus, Duane, Stott, Jeffery, Tsai, Miranda, Wye, Natasaja, Yang, George, Zhuang, Jun, Holt, Robert A., Putnam, Nicholas, Vrebalov, Julia, Giovannoni, James, Grimwood, Jane, Schmutz, Jeremy, Rokhsar, Daniel, Jones, Steven, Marra, Marco, Tuskan, Gerald A, Bohlmann, J., Ellis, Brian, Ritland, Kermit, Douglas, Carl, and Schein, Jacqueline. A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation. United States: N. p., 2007. Web. doi:10.1111/j.1365-313X.2007.03112.x.
Kelleher, Colin, Chiu, Readman, Shin, Heesun, Bosdet, Ian, Krywinski, Martin, Fjell, Chris, Wilkin, Jennifer, Yin, Tongming, DiFazio, Stephen P, Ali, Johar, Asano, Jennifer, Chan, Susanna, Cloutier, Alison, Girn, Noreen, Leach, Stephen, Lee, Darlene, Mathewson, Carrie, Olson, Teika, O'Connor, Katie, Prabhu, Anna-Liisa, Smailus, Duane, Stott, Jeffery, Tsai, Miranda, Wye, Natasaja, Yang, George, Zhuang, Jun, Holt, Robert A., Putnam, Nicholas, Vrebalov, Julia, Giovannoni, James, Grimwood, Jane, Schmutz, Jeremy, Rokhsar, Daniel, Jones, Steven, Marra, Marco, Tuskan, Gerald A, Bohlmann, J., Ellis, Brian, Ritland, Kermit, Douglas, Carl, & Schein, Jacqueline. A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation. United States. doi:10.1111/j.1365-313X.2007.03112.x.
Kelleher, Colin, Chiu, Readman, Shin, Heesun, Bosdet, Ian, Krywinski, Martin, Fjell, Chris, Wilkin, Jennifer, Yin, Tongming, DiFazio, Stephen P, Ali, Johar, Asano, Jennifer, Chan, Susanna, Cloutier, Alison, Girn, Noreen, Leach, Stephen, Lee, Darlene, Mathewson, Carrie, Olson, Teika, O'Connor, Katie, Prabhu, Anna-Liisa, Smailus, Duane, Stott, Jeffery, Tsai, Miranda, Wye, Natasaja, Yang, George, Zhuang, Jun, Holt, Robert A., Putnam, Nicholas, Vrebalov, Julia, Giovannoni, James, Grimwood, Jane, Schmutz, Jeremy, Rokhsar, Daniel, Jones, Steven, Marra, Marco, Tuskan, Gerald A, Bohlmann, J., Ellis, Brian, Ritland, Kermit, Douglas, Carl, and Schein, Jacqueline. Mon . "A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation". United States. doi:10.1111/j.1365-313X.2007.03112.x.
@article{osti_931850,
title = {A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation},
author = {Kelleher, Colin and Chiu, Readman and Shin, Heesun and Bosdet, Ian and Krywinski, Martin and Fjell, Chris and Wilkin, Jennifer and Yin, Tongming and DiFazio, Stephen P and Ali, Johar and Asano, Jennifer and Chan, Susanna and Cloutier, Alison and Girn, Noreen and Leach, Stephen and Lee, Darlene and Mathewson, Carrie and Olson, Teika and O'Connor, Katie and Prabhu, Anna-Liisa and Smailus, Duane and Stott, Jeffery and Tsai, Miranda and Wye, Natasaja and Yang, George and Zhuang, Jun and Holt, Robert A. and Putnam, Nicholas and Vrebalov, Julia and Giovannoni, James and Grimwood, Jane and Schmutz, Jeremy and Rokhsar, Daniel and Jones, Steven and Marra, Marco and Tuskan, Gerald A and Bohlmann, J. and Ellis, Brian and Ritland, Kermit and Douglas, Carl and Schein, Jacqueline},
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 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 the 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.},
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}
}