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Title: PolyCRACKER, a robust method for the unsupervised partitioning of polyploid subgenomes by signatures of repetitive DNA evolution

Abstract

Our understanding of polyploid genomes is limited by our inability to definitively assign sequences to a specific subgenome without extensive prior knowledge like high resolution genetic maps or genome sequences of diploid progenitors. In theory, existing methods for assigning sequences to individual species from metagenome samples could be used to separate subgenomes in polyploid organisms, however, these methods rely on differences in coarse genome properties like GC content or sequences from related species. Thus, these approaches do not work for subgenomes where gross features are indistinguishable and related genomes are lacking. Here we describe a method that uses rapidly evolving repetitive DNA to circumvent these limitations. RESULTS:By using short, repetitive, DNA sequences as species-specific signals we separated closely related genomes from test datasets and subgenomes from two polyploid plants, tobacco and wheat, without any prior knowledge. CONCLUSION:This approach is ideal for separating the subgenomes of polyploid species with unsequenced or unknown progenitor genomes.

Authors:
; ; ORCiD logo
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1546694
Grant/Contract Number:  
[AC02-05CH11231]
Resource Type:
Accepted Manuscript
Journal Name:
BMC Genomics
Additional Journal Information:
[ Journal Volume: 20; Journal Issue: 1]; Journal ID: ISSN 1471-2164
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Gordon, Sean P., Levy, Joshua J., and Vogel, John P. PolyCRACKER, a robust method for the unsupervised partitioning of polyploid subgenomes by signatures of repetitive DNA evolution. United States: N. p., 2019. Web. doi:10.1186/s12864-019-5828-5.
Gordon, Sean P., Levy, Joshua J., & Vogel, John P. PolyCRACKER, a robust method for the unsupervised partitioning of polyploid subgenomes by signatures of repetitive DNA evolution. United States. doi:10.1186/s12864-019-5828-5.
Gordon, Sean P., Levy, Joshua J., and Vogel, John P. Fri . "PolyCRACKER, a robust method for the unsupervised partitioning of polyploid subgenomes by signatures of repetitive DNA evolution". United States. doi:10.1186/s12864-019-5828-5. https://www.osti.gov/servlets/purl/1546694.
@article{osti_1546694,
title = {PolyCRACKER, a robust method for the unsupervised partitioning of polyploid subgenomes by signatures of repetitive DNA evolution},
author = {Gordon, Sean P. and Levy, Joshua J. and Vogel, John P.},
abstractNote = {Our understanding of polyploid genomes is limited by our inability to definitively assign sequences to a specific subgenome without extensive prior knowledge like high resolution genetic maps or genome sequences of diploid progenitors. In theory, existing methods for assigning sequences to individual species from metagenome samples could be used to separate subgenomes in polyploid organisms, however, these methods rely on differences in coarse genome properties like GC content or sequences from related species. Thus, these approaches do not work for subgenomes where gross features are indistinguishable and related genomes are lacking. Here we describe a method that uses rapidly evolving repetitive DNA to circumvent these limitations. RESULTS:By using short, repetitive, DNA sequences as species-specific signals we separated closely related genomes from test datasets and subgenomes from two polyploid plants, tobacco and wheat, without any prior knowledge. CONCLUSION:This approach is ideal for separating the subgenomes of polyploid species with unsequenced or unknown progenitor genomes.},
doi = {10.1186/s12864-019-5828-5},
journal = {BMC Genomics},
number = [1],
volume = [20],
place = {United States},
year = {2019},
month = {7}
}

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Works referenced in this record:

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Reproductive Isolation of Hybrid Populations Driven by Genetic Incompatibilities
journal, March 2015


Large-scale genome clustering across life based on a linguistic approach
journal, September 2005


Genome sequence of the progenitor of the wheat D genome Aegilops tauschii
journal, November 2017

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De novo identification of repeat families in large genomes
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    Works referencing / citing this record:

    Large-scale genome clustering across life based on a linguistic approach
    journal, September 2005


    Ancient WGD events as drivers of key innovations in angiosperms
    journal, April 2016


    Draft genome of the wheat A-genome progenitor Triticum urartu
    journal, March 2013

    • Ling, Hong-Qing; Zhao, Shancen; Liu, Dongcheng
    • Nature, Vol. 496, Issue 7443
    • DOI: 10.1038/nature11997

    Clonal dynamics of native haematopoiesis
    journal, October 2014

    • Sun, Jianlong; Ramos, Azucena; Chapman, Brad
    • Nature, Vol. 514, Issue 7522
    • DOI: 10.1038/nature13824

    Genome sequence of the progenitor of the wheat D genome Aegilops tauschii
    journal, November 2017

    • Luo, Ming-Cheng; Gu, Yong Q.; Puiu, Daniela
    • Nature, Vol. 551, Issue 7681
    • DOI: 10.1038/nature24486

    The tobacco genome sequence and its comparison with those of tomato and potato
    journal, May 2014

    • Sierro, Nicolas; Battey, James N. D.; Ouadi, Sonia
    • Nature Communications, Vol. 5, Issue 1
    • DOI: 10.1038/ncomms4833

    Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution
    journal, November 2014

    • Geering, Andrew D. W.; Maumus, Florian; Copetti, Dario
    • Nature Communications, Vol. 5, Issue 1
    • DOI: 10.1038/ncomms6269

    Disentangling a polyploid genome
    journal, August 2017


    Haplotype-resolved sweet potato genome traces back its hexaploidization history
    journal, August 2017


    De novo identification of repeat families in large genomes
    journal, June 2005


    shinyCircos: an R/Shiny application for interactive creation of Circos plot
    journal, November 2017


    Dissection of the Octoploid Strawberry Genome by Deep Sequencing of the Genomes of Fragaria Species
    journal, November 2013


    The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum
    journal, October 2017


    Next Generation Sequencing Reveals Genome Downsizing in Allotetraploid Nicotiana tabacum, Predominantly through the Elimination of Paternally Derived Repetitive DNAs
    journal, April 2011

    • Renny-Byfield, S.; Chester, M.; Kovarik, A.
    • Molecular Biology and Evolution, Vol. 28, Issue 10
    • DOI: 10.1093/molbev/msr112

    Automated De Novo Identification of Repeat Sequence Families in Sequenced Genomes
    journal, July 2002


    Ancient hybridization and genomic stabilization in a swordtail fish
    journal, April 2016

    • Schumer, Molly; Cui, Rongfeng; Powell, Daniel L.
    • Molecular Ecology, Vol. 25, Issue 11
    • DOI: 10.1111/mec.13602

    A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency
    journal, June 2017


    Reproductive Isolation of Hybrid Populations Driven by Genetic Incompatibilities
    journal, March 2015


    MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
    journal, January 2015