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Nanopore DNA Sequencing and Genome Assembly on the International Space Station.

TitleNanopore DNA Sequencing and Genome Assembly on the International Space Station.
Publication TypeJournal Article
Year of Publication2017
AuthorsCastro-Wallace SL, Chiu CY, John KK, Stahl SE, Rubins KH, McIntyre ABR, Dworkin JP, Lupisella ML, Smith DJ, Botkin DJ, Stephenson TA, Juul S, Turner DJ, Izquierdo F, Federman S, Stryke D, Somasekar S, Alexander N, Yu G, Mason CE, Burton AS
JournalSci Rep
Volume7
Issue1
Pagination18022
Date Published2017 Dec 21
ISSN2045-2322
Abstract

We evaluated the performance of the MinION DNA sequencer in-flight on the International Space Station (ISS), and benchmarked its performance off-Earth against the MinION, Illumina MiSeq, and PacBio RS II sequencing platforms in terrestrial laboratories. Samples contained equimolar mixtures of genomic DNA from lambda bacteriophage, Escherichia coli (strain K12, MG1655) and Mus musculus (female BALB/c mouse). Nine sequencing runs were performed aboard the ISS over a 6-month period, yielding a total of 276,882 reads with no apparent decrease in performance over time. From sequence data collected aboard the ISS, we constructed directed assemblies of the ~4.6 Mb E. coli genome, ~48.5 kb lambda genome, and a representative M. musculus sequence (the ~16.3 kb mitochondrial genome), at 100%, 100%, and 96.7% consensus pairwise identity, respectively; de novo assembly of the E. coli genome from raw reads yielded a single contig comprising 99.9% of the genome at 98.6% consensus pairwise identity. Simulated real-time analyses of in-flight sequence data using an automated bioinformatic pipeline and laptop-based genomic assembly demonstrated the feasibility of sequencing analysis and microbial identification aboard the ISS. These findings illustrate the potential for sequencing applications including disease diagnosis, environmental monitoring, and elucidating the molecular basis for how organisms respond to spaceflight.

DOI10.1038/s41598-017-18364-0
Alternate JournalSci Rep
PubMed ID29269933
PubMed Central IDPMC5740133
Grant ListR01 ES021006 / ES / NIEHS NIH HHS / United States
R01 HL105704 / HL / NHLBI NIH HHS / United States
R21 AI120977 / AI / NIAID NIH HHS / United States
R25 EB020393 / EB / NIBIB NIH HHS / United States