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

Todd P. Michael (), Florian Jupe, Felix Bemm, S. Timothy Motley, Justin P. Sandoval, Christa Lanz, Olivier Loudet, Detlef Weigel and Joseph R. Ecker
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Todd P. Michael: J. Craig Venter Institute
Florian Jupe: The Salk Institute for Biological Studies
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

Nature Communications, 2018, vol. 9, issue 1, 1-8

Abstract: 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.

Date: 2018
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DOI: 10.1038/s41467-018-03016-2

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