RT Journal Article
SR Electronic
T1 Nanopore DNA Sequencing and Genome Assembly on the International Space Station
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 077651
DO 10.1101/077651
A1 Sarah L. Castro-Wallace
A1 Charles Y. Chiu
A1 Kristen K. John
A1 Sarah E. Stahl
A1 Kathleen H. Rubins
A1 Alexa B. R. McIntyre
A1 Jason P. Dworkin
A1 Mark L. Lupisella
A1 David J Smith
A1 Douglas J. Botkin
A1 Timothy A. Stephenson
A1 Sissel Juul
A1 Daniel J. Turner
A1 Fernando Izquierdo
A1 Scot Federman
A1 Doug Stryke
A1 Sneha Somasekar
A1 Noah Alexander
A1 Guixia Yu
A1 Christopher E. Mason
A1 Aaron S Burton
YR 2016
UL http://biorxiv.org/content/early/2016/09/27/077651.abstract
AB The emergence of nanopore-based sequencers greatly expands the reach of sequencing into low-resource field environments, enabling in situ molecular analysis. In this work, we evaluated the performance of the MinION DNA sequencer (Oxford Nanopore Technologies) 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 mixtures of genomic DNA extracted from lambda bacteriophage, Escherichia coli (strain K12) and Mus musculus (BALB/c). The in-flight sequencing experiments generated more than 80,000 total reads with mean 2D accuracies of 85 – 90%, mean 1D accuracies of 75 – 80%, and median read lengths of approximately 6,000 bases. We were able to construct directed assemblies of the ~4.7 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% pairwise identity, respectively, and de novo assemblies of the lambda and E. coli genomes generated solely from nanopore reads yielded 100% and 99.8% genome coverage, respectively, at 100% and 98.5% pairwise identity. Across all surveyed metrics (base quality, throughput, stays/base, skips/base), no observable decrease in MinION performance was observed while sequencing DNA in space. Simulated runs of in-flight nanopore data using an automated bioinformatic pipeline and cloud or laptop based genomic assembly demonstrated the feasibility of real-time sequencing analysis and direct microbial identification in space. Applications of sequencing for space exploration include infectious disease diagnosis, environmental monitoring, evaluating biological responses to spaceflight, and even potentially the detection of extraterrestrial life on other planetary bodies.