Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

A Chromosome-level Sequence Assembly Reveals the Structure of the Arabidopsis thaliana Nd-1 Genome and its Gene Set

View ORCID ProfileBoas Pucker, View ORCID ProfileDaniela Holtgräwe, View ORCID ProfileKai Bernd Stadermann, View ORCID ProfileKatharina Frey, Bruno Huettel, Richard Reinhardt, View ORCID ProfileBernd Weisshaar
doi: https://doi.org/10.1101/407627
Boas Pucker
1Bielefeld University, Faculty of Biology & Center for Biotechnology, Bielefeld, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Boas Pucker
Daniela Holtgräwe
1Bielefeld University, Faculty of Biology & Center for Biotechnology, Bielefeld, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Daniela Holtgräwe
Kai Bernd Stadermann
1Bielefeld University, Faculty of Biology & Center for Biotechnology, Bielefeld, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Kai Bernd Stadermann
Katharina Frey
1Bielefeld University, Faculty of Biology & Center for Biotechnology, Bielefeld, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Katharina Frey
Bruno Huettel
2Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Richard Reinhardt
2Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Bernd Weisshaar
1Bielefeld University, Faculty of Biology & Center for Biotechnology, Bielefeld, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Bernd Weisshaar
  • For correspondence: bernd.weisshaar@uni-bielefeld.de
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

Background In addition to the BAC-based reference sequence of the accession Columbia-0 from the year 2000, several short read assemblies of THE plant model organism Arabidopsis thaliana were published during the last years. Also, a SMRT-based assembly of Landsberg erecta has been generated that identified translocation and inversion polymorphisms between two genotypes of the species.

Results Here we provide a chromosome-arm level assembly of the A. thaliana accession Niederzenz-1 (AthNd-1_v2c) based on SMRT sequencing data. The best assembly comprises 69 nucleome sequences and displays a contig length of up to 16 Mbp. Compared to an earlier Illumina short read-based NGS assembly (AthNd-1_v1), a 75 fold increase in contiguity was observed for AthNd-1_v2c. To assign contig locations independent from the Col-0 gold standard reference sequence, we used genetic anchoring to generate a de novo assembly. In addition, we assembled the chondrome and plastome sequences.

Conclusions Detailed analyses of AthNd-1_v2c allowed reliable identification of large genomic rearrangements between A. thaliana accessions contributing to differences in the gene sets that distinguish the genotypes. One of the differences detected identified a gene that is lacking from the Col-0 gold standard sequence. This de novo assembly extends the known proportion of the A. thaliana pan-genome.

Footnotes

  • Email addresses: BP: bpucker{at}cebitec.uni-bielefeld.de, DH: dholtgra{at}cebitec.uni-bielefeld.de, KS: kstaderm{at}cebitec.uni-bielefeld.de, KF: katharina.frey{at}uni-bielefeld.de., BH: huettel{at}mpipz.mpg.de, RR: reinhardt{at}mpipz.mpg.de, BW: bernd.weisshaar{at}uni-bielefeld.de

  • List of abbreviations

    NGS
    next generation sequencing
    NOR
    nucleolus organizing region
    RBH
    reciprocal best hit
    SMRT
    single molecule real time
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
    Back to top
    PreviousNext
    Posted April 14, 2019.
    Download PDF

    Supplementary Material

    Email

    Thank you for your interest in spreading the word about bioRxiv.

    NOTE: Your email address is requested solely to identify you as the sender of this article.

    Enter multiple addresses on separate lines or separate them with commas.
    A Chromosome-level Sequence Assembly Reveals the Structure of the Arabidopsis thaliana Nd-1 Genome and its Gene Set
    (Your Name) has forwarded a page to you from bioRxiv
    (Your Name) thought you would like to see this page from the bioRxiv website.
    CAPTCHA
    This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
    Share
    A Chromosome-level Sequence Assembly Reveals the Structure of the Arabidopsis thaliana Nd-1 Genome and its Gene Set
    Boas Pucker, Daniela Holtgräwe, Kai Bernd Stadermann, Katharina Frey, Bruno Huettel, Richard Reinhardt, Bernd Weisshaar
    bioRxiv 407627; doi: https://doi.org/10.1101/407627
    Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
    Citation Tools
    A Chromosome-level Sequence Assembly Reveals the Structure of the Arabidopsis thaliana Nd-1 Genome and its Gene Set
    Boas Pucker, Daniela Holtgräwe, Kai Bernd Stadermann, Katharina Frey, Bruno Huettel, Richard Reinhardt, Bernd Weisshaar
    bioRxiv 407627; doi: https://doi.org/10.1101/407627

    Citation Manager Formats

    • BibTeX
    • Bookends
    • EasyBib
    • EndNote (tagged)
    • EndNote 8 (xml)
    • Medlars
    • Mendeley
    • Papers
    • RefWorks Tagged
    • Ref Manager
    • RIS
    • Zotero
    • Tweet Widget
    • Facebook Like
    • Google Plus One

    Subject Area

    • Genomics
    Subject Areas
    All Articles
    • Animal Behavior and Cognition (2530)
    • Biochemistry (4972)
    • Bioengineering (3482)
    • Bioinformatics (15212)
    • Biophysics (6897)
    • Cancer Biology (5390)
    • Cell Biology (7738)
    • Clinical Trials (138)
    • Developmental Biology (4530)
    • Ecology (7147)
    • Epidemiology (2059)
    • Evolutionary Biology (10227)
    • Genetics (7512)
    • Genomics (9786)
    • Immunology (4844)
    • Microbiology (13215)
    • Molecular Biology (5138)
    • Neuroscience (29435)
    • Paleontology (203)
    • Pathology (837)
    • Pharmacology and Toxicology (1463)
    • Physiology (2138)
    • Plant Biology (4748)
    • Scientific Communication and Education (1013)
    • Synthetic Biology (1338)
    • Systems Biology (4012)
    • Zoology (768)