High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell.
High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell.
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DOI：
10.1038/s41467-018-03016-2
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发表时间：
2018-02-07
影响因子：
16.6
通讯作者：
Ecker JR
中科院分区：
文献类型：
--
作者：
Michael TP;Jupe F;Bemm F;Motley ST;Sandoval JP;Lanz C;Loudet O;Weigel D;Ecker JR
手持式Oxford Nanopore MinION测序仪以最低的成本和时间要求生成超长读数，这使得在实验台上对基因组进行测序变得可行。在这里，我们用MinION测序仪在工作台上对金标准拟南芥基因组（KBS-Mac-74登录）进行测序，并使用典型的消费者计算硬件（4个核心，16 Gb RAM）将基因组组装成染色体臂（62个重叠群，N50长度为12.3 Mb）。我们用两种独立的单分子技术，Bionano光学基因组图谱和Pacific Biosciences Sequel测序验证了组装的连续性和质量。新的A. thaliana KBS-Mac-74基因组能够解析先前被基于Sanger的BAC测序方法排除的数量性状基因座。总之，我们证明，即使目的是了解基因组单个区域的复杂结构变异，完整的基因组组装也成为实现这一目标的最简单方法。长读段测序技术促进高效和高质量的基因组组装。在这里，Michael等人使用手持式Oxford Nanopore MinION测序仪和消费者计算硬件实现了拟南芥KBS-Mac-74登录的快速参考组装，并证明了其在解决复杂结构变异方面的有用性。
The handheld Oxford Nanopore MinION sequencer generates ultra-long reads with minimal cost and time requirements, which makes sequencing genomes at the bench feasible. Here, we sequence the gold standard Arabidopsis thaliana genome (KBS-Mac-74 accession) on the bench with the MinION sequencer, and assemble the genome using typical consumer computing hardware (4 Cores, 16 Gb RAM) into chromosome arms (62 contigs with an N50 length of 12.3 Mb). We validate the contiguity and quality of the assembly with two independent single-molecule technologies, Bionano optical genome maps and Pacific Biosciences Sequel sequencing. The new A. thaliana KBS-Mac-74 genome enables resolution of a quantitative trait locus that had previously been recalcitrant to a Sanger-based BAC sequencing approach. In summary, we demonstrate that even when the purpose is to understand complex structural variation at a single region of the genome, complete genome assembly is becoming the simplest way to achieve this goal. Long-read sequencing technologies facilitate efficient and high quality genome assembly. Here Michael et al. achieve a fast reference assembly for Arabidopsis thaliana KBS-Mac-74 accession using the handheld Oxford Nanopore MinION sequencer and consumer computing hardware, and demonstrate its usefulness in resolving complex structural variation.
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影响因子：
64.5
作者：
Kawakatsu T;Huang SC;Jupe F;Sasaki E;Schmitz RJ;Urich MA;Castanon R;Nery JR;Barragan C;He Y;Chen H;Dubin M;Lee CR;Wang C;Bemm F;Becker C;O'Neil R;O'Malley RC;Quarless DX;1001 Genomes Consortium;Schork NJ;Weigel D;Nordborg M;Ecker JR
通讯作者：
Ecker JR
影响因子：
64.8
作者：
Gan X;Stegle O;Behr J;Steffen JG;Drewe P;Hildebrand KL;Lyngsoe R;Schultheiss SJ;Osborne EJ;Sreedharan VT;Kahles A;Bohnert R;Jean G;Derwent P;Kersey P;Belfield EJ;Harberd NP;Kemen E;Toomajian C;Kover PX;Clark RM;Rätsch G;Mott R
通讯作者：
Mott R
影响因子：
5.8
作者：
Li, Heng
通讯作者：
Li, Heng
影响因子：
46.9
作者：
通讯作者：
--
影响因子：
11.6
作者：
Schmidt, Maximilian H. -W.;Vogel, Alexander;Usadel, Bjorn
通讯作者：
Usadel, Bjorn