A chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping.
A chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping.
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DOI：
10.1038/s41467-018-07271-1
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发表时间：
2018-11-19
影响因子：
16.6
通讯作者：
Lin H
中科院分区：
文献类型：
--
作者：
Deschamps S;Zhang Y;Llaca V;Ye L;Sanyal A;King M;May G;Lin H
长读段测序技术极大地促进了大型真核基因组的组装。在本文中，MinION测序仪上生成的Oxford Nanopore序列与Bionano Genomics直接标记和染色（DLS）光学图谱相结合，以生成富含重复序列的Sorbicolor Tx430基因组的染色体规模从头组装。最终组装由29个支架组成，在大多数情况下包含整个染色体臂。它的支架N50为33.28 Mbps，覆盖了预期基因组长度的90%。在将组装体与Illumina Tx430数据比对后获得99.85%的序列准确度，并且34，211个公共基因模型中的99.6%与组装体比对。Tx430和BTx623 DLS图谱与公开的BTx623 v3.0.1基因组组装的比较表明存在实质性差异，其起源仍有待确定。总之，这项研究表明，可以通过将纳米孔测序与DLS光学图谱相结合来生成复杂植物基因组的信息组装。大的、重复序列丰富的真核基因组的组装仍然具有挑战性。在这里，作者使用BioNano Genomics DLS光学作图和单分子纳米孔测序来生成新Sorbicolor登录的染色体规模组装，并与公开可用的S.双色基因组
Long-read sequencing technologies have greatly facilitated assemblies of large eukaryotic genomes. In this paper, Oxford Nanopore sequences generated on a MinION sequencer are combined with Bionano Genomics Direct Label and Stain (DLS) optical maps to generate a chromosome-scale de novo assembly of the repeat-rich Sorghum bicolor Tx430 genome. The final assembly consists of 29 scaffolds, encompassing in most cases entire chromosome arms. It has a scaffold N50 of 33.28 Mbps and covers 90% of the expected genome length. A sequence accuracy of 99.85% is obtained after aligning the assembly against Illumina Tx430 data and 99.6% of the 34,211 public gene models align to the assembly. Comparisons of Tx430 and BTx623 DLS maps against the public BTx623 v3.0.1 genome assembly suggest substantial discrepancies whose origin remains to be determined. In summary, this study demonstrates that informative assemblies of complex plant genomes can be generated by combining nanopore sequencing with DLS optical maps. Assembly of large, repeat-rich eukaryotic genomes remains challenging. Here, the authors use BioNano Genomics DLS optical mapping and single-molecule nanopore sequencing to generate a chromosome-scale assembly of a new Sorghum bicolor accession and identify variation compared to the publicly available S. bicolor genome.
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影响因子：
64.8
作者：
Luo MC;Gu YQ;Puiu D;Wang H;Twardziok SO;Deal KR;Huo N;Zhu T;Wang L;Wang Y;McGuire PE;Liu S;Long H;Ramasamy RK;Rodriguez JC;Van SL;Yuan L;Wang Z;Xia Z;Xiao L;Anderson OD;Ouyang S;Liang Y;Zimin AV;Pertea G;Qi P;Bennetzen JL;Dai X;Dawson MW;Müller HG;Kugler K;Rivarola-Duarte L;Spannagl M;Mayer KFX;Lu FH;Bevan MW;Leroy P;Li P;You FM;Sun Q;Liu Z;Lyons E;Wicker T;Salzberg SL;Devos KM;Dvořák J
通讯作者：
Dvořák J
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
16.6
作者：
Michael TP;Jupe F;Bemm F;Motley ST;Sandoval JP;Lanz C;Loudet O;Weigel D;Ecker JR
通讯作者：
Ecker JR
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：
5.8
作者：
Li, Heng
通讯作者：
Li, Heng