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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}
}
  • 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 andmore » 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.« less
  • We mapped and analyzed the microsatellites throughout 284295605 base pairs of the unambiguously assembled sequence scaffolds along 19 chromosomes of the haploid poplar genome. Totally, we found 150985 SSRs with repeat unit lengths between 2 and 5 bp. The established microsatellite physical map demonstrated that SSRs were distributed relatively evenly across the genome of Populus. On average, These SSRs occurred every 1883 bp within the poplar genome and the SSR densities in intergenic regions, introns, exons and UTRs were 85.4%, 10.7%, 2.7% and 1.2%, respectively. We took di-, tri-, tetra-and pentamers as the four classes of repeat units and foundmore » that the density of each class of SSRs decreased with the repeat unit lengths except for the tetranucleotide repeats. It was noteworthy that the length diversification of microsatellite sequences was negatively correlated with their repeat unit length and the SSRs with shorter repeat units gained repeats faster than the SSRs with longer repeat units. We also found that the GC content of poplar sequence significantly correlated with densities of SSRs with uneven repeat unit lengths (tri- and penta-), but had no significant correlation with densities of SSRs with even repeat unit lengths (di- and tetra-). In poplar genome, there were evidences that the occurrence of different microsatellites was under selection and the GC content in SSR sequences was found to significantly relate to the functional importance of microsatellites.« 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.