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Radiation Tolerance of Nanopore Sequencing Technology for Life Detection on Mars and Europa.

ABSTRACT: The search for life beyond Earth is a key motivator in space exploration. Informational polymers, like DNA and RNA, are key biosignatures for life as we know it. The MinION is a miniature DNA sequencer based on versatile nanopore technology that could be implemented on future planetary missions. A critical unanswered question is whether the MinION and its protein-based nanopores can withstand increased radiation exposure outside Earth's shielding magnetic field. We evaluated the effects of ionizing radiation on the MinION platform - including flow cells, reagents, and hardware - and discovered limited performance loss when exposed to ionizing doses comparable to a mission to Mars. Targets with harsher radiation environments, like Europa, would require improved radiation resistance via additional shielding or design refinements.

SUBMITTER: Sutton MA

PROVIDER: S-EPMC6441015 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

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Radiation Tolerance of Nanopore Sequencing Technology for Life Detection on Mars and Europa.

Sutton Mark A MA Burton Aaron S AS Zaikova Elena E Sutton Ryan E RE Brinckerhoff William B WB Bevilacqua Julie G JG Weng Margaret M MM Mumma Michael J MJ Johnson Sarah Stewart SS

Scientific reports 20190329 1

The search for life beyond Earth is a key motivator in space exploration. Informational polymers, like DNA and RNA, are key biosignatures for life as we know it. The MinION is a miniature DNA sequencer based on versatile nanopore technology that could be implemented on future planetary missions. A critical unanswered question is whether the MinION and its protein-based nanopores can withstand increased radiation exposure outside Earth's shielding magnetic field. We evaluated the effects of ioniz ...[more]

PMID: 30926841

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Project description:Transposables elements (TEs) contribute to both structural and functional dynamics of most eukaryotic genomes. Because of their propensity to densely populate plant and animal genomes, the precise estimation of the impact of transposition on genomic diversity has been considered as one of the main challenges of today's genomics. The recent development of NGS (next generation sequencing) technologies has open new perspectives in population genomics by providing new methods for high throughput detection of Transposable Elements-associated Structural Variants (TEASV). However, these have relied on Illumina platform that generates short reads (up to 350 nucleotides). This limitation in size of sequence reads can cause high false discovery rate (FDR) and therefore limit the power of detection of TEASVs, especially in the case of large, complex genomes. The newest sequencing technologies, such as Oxford Nanopore Technologies (ONT) can generate kilobases-long reads thus representing a promising tool for TEASV detection in plant and animals.We present the results of a pilot experiment for TEASV detection on the model plant species Arabidopsis thaliana using ONT sequencing and show that it can be used efficiently to detect TE movements. We generated a ~0.8X genome coverage of a met1-derived epigenetic recombinant inbred line (epiRIL) using a MinIon device with R7 chemistry. We were able to detect nine new copies of the LTR-retrotransposon Evadé (EVD). We also evidenced the activity of the DNA transposon CACTA, CAC1.Even at a low sequence coverage (0.8X), ONT sequencing allowed us to reliably detect several TE insertions in Arabidopsis thaliana genome. The long read length allowed a precise and un-ambiguous mapping of the structural variations caused by the activity of TEs. This suggests that the trade-off between read length and genome coverage for TEASV detection may be in favor of the former. Should the technology be further improved both in terms of lower error rate and operation costs, it could be efficiently used in diversity studies at population level.

Dataset Information

Radiation Tolerance of Nanopore Sequencing Technology for Life Detection on Mars and Europa.

Publications

Radiation Tolerance of Nanopore Sequencing Technology for Life Detection on Mars and Europa.

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