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High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell

Author

Listed:
  • Todd P. Michael

    (J. Craig Venter Institute)

  • Florian Jupe

    (The Salk Institute for Biological Studies
    Monsanto Company)

  • Felix Bemm

    (Max Planck Institute for Developmental Biology)

  • S. Timothy Motley

    (J. Craig Venter Institute)

  • Justin P. Sandoval

    (The Salk Institute for Biological Studies)

  • Christa Lanz

    (Max Planck Institute for Developmental Biology)

  • Olivier Loudet

    (Université Paris-Saclay)

  • Detlef Weigel

    (Max Planck Institute for Developmental Biology)

  • Joseph R. Ecker

    (The Salk Institute for Biological Studies
    The Salk Institute for Biological Studies)

Abstract

The handheld Oxford Nanopore MinION sequencer generates ultra-long reads with minimal cost and time requirements, which makes sequencing genomes at the bench feasible. Here, we sequence the gold standard Arabidopsis thaliana genome (KBS-Mac-74 accession) on the bench with the MinION sequencer, and assemble the genome using typical consumer computing hardware (4 Cores, 16 Gb RAM) into chromosome arms (62 contigs with an N50 length of 12.3 Mb). We validate the contiguity and quality of the assembly with two independent single-molecule technologies, Bionano optical genome maps and Pacific Biosciences Sequel sequencing. The new A. thaliana KBS-Mac-74 genome enables resolution of a quantitative trait locus that had previously been recalcitrant to a Sanger-based BAC sequencing approach. In summary, we demonstrate that even when the purpose is to understand complex structural variation at a single region of the genome, complete genome assembly is becoming the simplest way to achieve this goal.

Suggested Citation

  • Todd P. Michael & Florian Jupe & Felix Bemm & S. Timothy Motley & Justin P. Sandoval & Christa Lanz & Olivier Loudet & Detlef Weigel & Joseph R. Ecker, 2018. "High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell," Nature Communications, Nature, vol. 9(1), pages 1-8, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-03016-2
    DOI: 10.1038/s41467-018-03016-2
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    Cited by:

    1. Haifei Hu & Armin Scheben & David Edwards, 2018. "Advances in Integrating Genomics and Bioinformatics in the Plant Breeding Pipeline," Agriculture, MDPI, vol. 8(6), pages 1-18, May.
    2. Gabriel E. Rech & Santiago Radío & Sara Guirao-Rico & Laura Aguilera & Vivien Horvath & Llewellyn Green & Hannah Lindstadt & Véronique Jamilloux & Hadi Quesneville & Josefa González, 2022. "Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    3. Yee Wen Low & Sitaram Rajaraman & Crystal M. Tomlin & Joffre Ali Ahmad & Wisnu H. Ardi & Kate Armstrong & Parusuraman Athen & Ahmad Berhaman & Ruth E. Bone & Martin Cheek & Nicholas R. W. Cho & Le Min, 2022. "Genomic insights into rapid speciation within the world’s largest tree genus Syzygium," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    4. Simone Scalabrin & Gabriele Magris & Mario Liva & Nicola Vitulo & Michele Vidotto & Davide Scaglione & Lorenzo Terra & Manuela Rosanna Ruosi & Luciano Navarini & Gloria Pellegrino & Jorge Carlos Berny, 2024. "A chromosome-scale assembly reveals chromosomal aberrations and exchanges generating genetic diversity in Coffea arabica germplasm," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

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