Resolving plasmid structures in Enterobacteriaceae using the MinION nanopore sequencer: assessment of MinION and MinION/Illumina hybrid data assembly approaches.
Resolving plasmid structures in Enterobacteriaceae using the MinION nanopore sequencer: assessment of MinION and MinION/Illumina hybrid data assembly approaches.
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使用 MinION 纳米孔测序仪解析肠杆菌科中的质粒结构：MinION 和 MinION/Illumina 混合数据组装方法的评估。
DOI：
10.1099/mgen.0.000118
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发表时间：
2017-08
影响因子：
3.9
通讯作者：
Phan HTT
中科院分区：
文献类型：
--
作者：
George S;Pankhurst L;Hubbard A;Votintseva A;Stoesser N;Sheppard AE;Mathers A;Norris R;Navickaite I;Eaton C;Iqbal Z;Crook DW;Phan HTT
本研究旨在评估使用Oxford Nanopore Technologies (ONT) MinION长读测序仪重建6个不同种类肠杆菌科8株质粒完全封闭序列的可行性，这些质粒群体具有不同的复杂性。所代表的物种有大肠杆菌、肺炎克雷伯菌、弗氏柠檬酸杆菌、阴沟肠杆菌、粘质沙雷菌和氧化克雷伯菌，质粒数量为1 ~ 11个，大小为2 ~ 330 kb。使用Illumina（短读）和ONT的MinION（长读）平台对分离株进行测序，并与相同分离株的完全解析PacBio（长读）序列片段进行比较。通过与金标准PacBio参考序列对比，比较了SPAdes、plasmidSPAdes、hybridSPAdes、Canu、Canu+Pilon （canuPilon）和npScarf等不同组装方法在恢复这些分离株质粒结构方面的性能。总体而言，canuPilon在装配统计（N50， contigs数量）和装配精度（相对于参考序列的单核苷酸多态性(snp)/索引的存在）方面都提供了一致的高质量装配。对于质粒重建，Canu在完整的contigs中恢复了70%的质粒，结合三种组装方法（Canu或canuPilon， hybridSPAdes和plasmidSPAdes），所有质粒的总回收率为78%。该分析证明了使用MinION测序技术在独立于Illumina测序数据或与Illumina测序数据结合的情况下解决肠杆菌科物种重要质粒结构的潜力。从几种组装方法中得出的共识组装可以在准确地解决最多数量的质粒结构方面提供显着的好处。
This study aimed to assess the feasibility of using the Oxford Nanopore Technologies (ONT) MinION long-read sequencer in reconstructing fully closed plasmid sequences from eight Enterobacteriaceae isolates of six different species with plasmid populations of varying complexity. Species represented were Escherichia coli, Klebsiella pneumoniae, Citrobacter freundii, Enterobacter cloacae, Serratia marcescens and Klebsiella oxytoca, with plasmid populations ranging from 1–11 plasmids with sizes of 2–330 kb. Isolates were sequenced using Illumina (short-read) and ONT’s MinION (long-read) platforms, and compared with fully resolved PacBio (long-read) sequence assemblies for the same isolates. We compared the performance of different assembly approaches including SPAdes, plasmidSPAdes, hybridSPAdes, Canu, Canu+Pilon (canuPilon) and npScarf in recovering the plasmid structures of these isolates by comparing with the gold-standard PacBio reference sequences. Overall, canuPilon provided consistently good quality assemblies both in terms of assembly statistics (N50, number of contigs) and assembly accuracy [presence of single nucleotide polymorphisms (SNPs)/indels with respect to the reference sequence]. For plasmid reconstruction, Canu recovered 70 % of the plasmids in complete contigs, and combining three assembly approaches (Canu or canuPilon, hybridSPAdes and plasmidSPAdes) resulted in a total 78 % recovery rate for all the plasmids. The analysis demonstrated the potential of using MinION sequencing technology to resolve important plasmid structures in Enterobacteriaceae species independent of and in conjunction with Illumina sequencing data. A consensus assembly derived from several assembly approaches could present significant benefit in accurately resolving the greatest number of plasmid structures.
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影响因子：
3.7
作者：
Walker BJ;Abeel T;Shea T;Priest M;Abouelliel A;Sakthikumar S;Cuomo CA;Zeng Q;Wortman J;Young SK;Earl AM
通讯作者：
Earl AM
影响因子：
1.7
作者：
Bankevich, Anton;Nurk, Sergey;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.
影响因子：
4.6
作者：
Deschamps, Stephane;Mudge, Joann;May, Gregory
通讯作者：
May, Gregory
影响因子：
3.9
作者：
Judge, Kim;Hunt, Martin;Peacock, Sharon J.
通讯作者：
Peacock, Sharon J.
影响因子：
17.1
作者：
Conlan S;Thomas PJ;Deming C;Park M;Lau AF;Dekker JP;Snitkin ES;Clark TA;Luong K;Song Y;Tsai YC;Boitano M;Dayal J;Brooks SY;Schmidt B;Young AC;Thomas JW;Bouffard GG;Blakesley RW;NISC Comparative Sequencing Program;Mullikin JC;Korlach J;Henderson DK;Frank KM;Palmore TN;Segre JA
通讯作者：
Segre JA