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Nat Commun. 2018 Feb 7;9(1):541. doi: 10.1038/s41467-018-03016-2.

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

Author information

1
J. Craig Venter Institute, La Jolla, CA, 92037, USA. tmichael@jcvi.org.
2
Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
3
Monsanto Company, Creve Coeur, MO, 63141, USA.
4
Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany.
5
J. Craig Venter Institute, La Jolla, CA, 92037, USA.
6
Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France.
7
Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.

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.

PMID:
29416032
PMCID:
PMC5803254
DOI:
10.1038/s41467-018-03016-2
[Indexed for MEDLINE]
Free PMC Article

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