Nanopore DNA Sequencing and Genome Assembly on the International Space Station.
Nanopore DNA Sequencing and Genome Assembly on the International Space Station.
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DOI：
10.1038/s41598-017-18364-0
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发表时间：
2017-12-21
影响因子：
4.6
通讯作者：
Burton AS
中科院分区：
文献类型：
--
作者：
Castro-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
我们评估了MinION DNA测序仪在国际空间站（ISS）飞行中的性能，并将其性能与地面实验室中的MinION，Illumina MiSeq和PacBio RS II测序平台进行了基准测试。样品含有来自λ噬菌体、大肠杆菌（菌株K12，MG 1655）和小家鼠（雌性BALB/c小鼠）的基因组DNA的等摩尔混合物。在6个月的时间内，在ISS上进行了9次测序运行，总共产生了276，882个读数，随着时间的推移，性能没有明显下降。从国际空间站上收集的序列数据，我们构建了~4.6 Mb E. coli基因组、~ 48.5kb λ基因组和代表性的M. musculus序列（~ 16.3kb线粒体基因组）的同源性分别为100%、100%和96.7%;来自原始读段的大肠杆菌基因组产生包含99.9%的基因组的单一重叠群，具有98.6%的共有成对同一性。使用自动化生物信息学管道和基于笔记本电脑的基因组组装对飞行中序列数据进行模拟实时分析，证明了国际空间站上测序分析和微生物鉴定的可行性。这些发现说明了测序应用的潜力，包括疾病诊断，环境监测和阐明生物体如何对太空飞行作出反应的分子基础。
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.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
--
作者：
Kinross, James M;von Roon, Alexander C;Nicholson, Jeremy K
通讯作者：
Nicholson, Jeremy K
影响因子：
11.8
作者：
Hoenen T;Groseth A;Rosenke K;Fischer RJ;Hoenen A;Judson SD;Martellaro C;Falzarano D;Marzi A;Squires RB;Wollenberg KR;de Wit E;Prescott J;Safronetz D;van Doremalen N;Bushmaker T;Feldmann F;McNally K;Bolay FK;Fields B;Sealy T;Rayfield M;Nichol ST;Zoon KC;Massaquoi M;Munster VJ;Feldmann H
通讯作者：
Feldmann H
影响因子：
48
作者：
Rand AC;Jain M;Eizenga JM;Musselman-Brown A;Olsen HE;Akeson M;Paten B
通讯作者：
Paten B
影响因子：
7
作者：
Naccache SN;Federman S;Veeraraghavan N;Zaharia M;Lee D;Samayoa E;Bouquet J;Greninger AL;Luk KC;Enge B;Wadford DA;Messenger SL;Genrich GL;Pellegrino K;Grard G;Leroy E;Schneider BS;Fair JN;Martínez MA;Isa P;Crump JA;DeRisi JL;Sittler T;Hackett J Jr;Miller S;Chiu CY
通讯作者：
Chiu CY