Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data.
Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data.
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DOI：
10.1101/gr.213652.116
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发表时间：
2017-05
期刊：
影响因子：
7
通讯作者：
Schneeberger K
中科院分区：
文献类型：
--
作者：
Jiao WB;Accinelli GG;Hartwig B;Kiefer C;Baker D;Severing E;Willing EM;Piednoel M;Woetzel S;Madrid-Herrero E;Huettel B;Hümann U;Reinhard R;Koch MA;Swan D;Clavijo B;Coupland G;Schneeberger K
长读段测序可以克服真核基因组组装中短读段的弱点;然而，目前需要额外的支架来实现染色体水平的组装。我们生成了Pacific Biosciences（PacBio）的模式植物拟南芥的三个亲戚的基因组的长读数据，并将所有三个基因组组装成只有几百个重叠群。为了提高这些组件的连续性，我们生成了BioNano Genomics光学作图和Dovetail Genomics染色体构象捕获数据用于基因组支架。尽管它们的技术差异，光学定位和染色体构象捕获表现相似，并使N50值加倍。改进这两种整合方法后，组装邻近性达到了染色体臂水平。我们使用Illumina配对文库和遗传图谱信息严格评估了重叠群和支架的质量。这表明PacBio组装具有高序列准确性，但可能包含几个错误组装，这些错误组装连接了基因组的未连接区域。在光学作图和染色体构象捕获数据的整合过程中，去除了这些错位中的大部分，但不是全部。尽管没有一个着丝粒完全组装，但支架显示了一些着丝粒区域的大部分，甚至包括一些异染色质区域，这些区域在金标准参考序列中不存在。
Long-read sequencing can overcome the weaknesses of short reads in the assembly of eukaryotic genomes; however, at present additional scaffolding is needed to achieve chromosome-level assemblies. We generated Pacific Biosciences (PacBio) long-read data of the genomes of three relatives of the model plant Arabidopsis thaliana and assembled all three genomes into only a few hundred contigs. To improve the contiguities of these assemblies, we generated BioNano Genomics optical mapping and Dovetail Genomics chromosome conformation capture data for genome scaffolding. Despite their technical differences, optical mapping and chromosome conformation capture performed similarly and doubled N50 values. After improving both integration methods, assembly contiguity reached chromosome-arm-levels. We rigorously assessed the quality of contigs and scaffolds using Illumina mate-pair libraries and genetic map information. This showed that PacBio assemblies have high sequence accuracy but can contain several misassemblies, which join unlinked regions of the genome. Most, but not all, of these misjoints were removed during the integration of the optical mapping and chromosome conformation capture data. Even though none of the centromeres were fully assembled, the scaffolds revealed large parts of some centromeric regions, even including some of the heterochromatic regions, which are not present in gold standard reference sequences.