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Reference Quality Assembly of the 3.5 Gb genome of Capsicum annuum from a Single Linked-Read Library

View ORCID ProfileAmanda M. Hulse-Kemp, Shamoni Maheshwari, Kevin Stoffel, Theresa A. Hill, David Jaffe, Stephen Williams, Neil Weisenfeld, Srividya Ramakrishnan, Vijay Kumar, Preyas Shah, Michael C. Schatz, Deanna M. Church, Allen Van Deynze
doi: https://doi.org/10.1101/152777
Amanda M. Hulse-Kemp
1 Department of Plant Sciences, University of California, Davis, CA
2 USDA-ARS, Genomics and Bioinformatics Research Unit, Raleigh, NC
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  • ORCID record for Amanda M. Hulse-Kemp
  • For correspondence: avandeynze@ucdavis.edu Amanda.hulse-kemp@ars.usda.gov
Shamoni Maheshwari
1 Department of Plant Sciences, University of California, Davis, CA
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Kevin Stoffel
1 Department of Plant Sciences, University of California, Davis, CA
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Theresa A. Hill
1 Department of Plant Sciences, University of California, Davis, CA
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David Jaffe
3 10x Genomics, Inc. 7068 Koll Center Parkway, Suite 401, Pleasanton, CA 94566
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Stephen Williams
3 10x Genomics, Inc. 7068 Koll Center Parkway, Suite 401, Pleasanton, CA 94566
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Neil Weisenfeld
3 10x Genomics, Inc. 7068 Koll Center Parkway, Suite 401, Pleasanton, CA 94566
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Srividya Ramakrishnan
4 Department of Computer Science, Johns Hopkins University, Baltimore, MD
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Vijay Kumar
3 10x Genomics, Inc. 7068 Koll Center Parkway, Suite 401, Pleasanton, CA 94566
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Preyas Shah
3 10x Genomics, Inc. 7068 Koll Center Parkway, Suite 401, Pleasanton, CA 94566
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Michael C. Schatz
4 Department of Computer Science, Johns Hopkins University, Baltimore, MD
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Deanna M. Church
3 10x Genomics, Inc. 7068 Koll Center Parkway, Suite 401, Pleasanton, CA 94566
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Allen Van Deynze
1 Department of Plant Sciences, University of California, Davis, CA
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  • For correspondence: avandeynze@ucdavis.edu Amanda.hulse-kemp@ars.usda.gov
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Abstract

Background Linked-Read sequencing technology has recently been employed successfully for de novo assembly of multiple human genomes, however the utility of this technology for complex plant genomes is unproven. We evaluated the technology for this purpose by sequencing the 3.5 gigabase (Gb) diploid pepper (Capsicum annuum) genome with a single Linked-Read library. Plant genomes, including pepper, are characterized by long, highly similar repetitive sequences. Accordingly, significant effort is used to ensure the sequenced plant is highly homozygous and the resulting assembly is a haploid consensus. With a phased assembly approach, we targeted a heterozygous F1 derived from a wide cross to assess the ability to derive both haplotypes for a pungency gene characterized by a large insertion/deletion.

Results The Supernova software generated a highly ordered, more contiguous sequence assembly than all currently available C. annuum reference genomes. Eighty-four percent of the final assembly was anchored and oriented using four de novo linkage maps. A comparison of the annotation of conserved eukaryotic genes indicated the completeness of assembly. The validity of the phased assembly is further demonstrated with the complete recovery of both 2.5 kb insertion/deletion haplotypes of the PUN1 locus in the F1 sample that represents pungent and non-pungent peppers.

Conclusions The most contiguous pepper genome assembly to date has been generated through this work which demonstrates that Linked-Read library technology provides a rapid tool to assemble de novo complex highly repetitive heterozygous plant genomes. This technology can provide an opportunity to cost-effectively develop high-quality reference genome assemblies for other complex plants and compare structural and gene differences through accurate haplotype reconstruction.

  • List of Abbreviations

    Gb
    Gigabase
    BAC
    Bacteria artificial chromosome
    Kb
    Kilobase
    Mb
    Megabase
    PAV
    Presence absence variant
    CM334
    Criollos del Morelos 334
    QTL
    Quantitative trait loci
    cM
    CentiMorgan
  • Copyright 
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    Posted June 20, 2017.
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    Reference Quality Assembly of the 3.5 Gb genome of Capsicum annuum from a Single Linked-Read Library
    Amanda M. Hulse-Kemp, Shamoni Maheshwari, Kevin Stoffel, Theresa A. Hill, David Jaffe, Stephen Williams, Neil Weisenfeld, Srividya Ramakrishnan, Vijay Kumar, Preyas Shah, Michael C. Schatz, Deanna M. Church, Allen Van Deynze
    bioRxiv 152777; doi: https://doi.org/10.1101/152777
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    Reference Quality Assembly of the 3.5 Gb genome of Capsicum annuum from a Single Linked-Read Library
    Amanda M. Hulse-Kemp, Shamoni Maheshwari, Kevin Stoffel, Theresa A. Hill, David Jaffe, Stephen Williams, Neil Weisenfeld, Srividya Ramakrishnan, Vijay Kumar, Preyas Shah, Michael C. Schatz, Deanna M. Church, Allen Van Deynze
    bioRxiv 152777; doi: https://doi.org/10.1101/152777

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