Nature子刊:超长DNA片段提取助力纳米孔测序对复杂环境单菌基因组的组装
  • 虽然基因组中重复元件结构对于理解基因组功能至关重要,但使用常规短读长的测序去组装重复元件非常困难;
  • 本文提出一套测序流程(Lathe)结合长读长序列组装和短读长序列纠错可以从复杂的微生物群落中组装完整的基因组;
  • 这套流程成功在12种细菌的模拟群落中组装出7个完整基因组,在13个人类粪便样本中组装了20个环状基因组;
  • 这一方法将在研究微生物功能尤其是重复元件的作用等方面具有广阔应用前景。
主编推荐语
刘永鑫-中科院-宏基因组
基于二代测序让我们对复杂环境微生物群落组成和功能有了进一步的认识,然而更深层次的研究就需要从复杂环境中组装得到完整基因组,虽然三代测序准确率有待提升,但是却帮助我们将序列读长扩展到足够用的地步,可我们却还是无法从复杂环境中得到可用于三代测序的大片段DNA。因此,从复杂环境中组装完整基因组的工作,从样本提取就开始困难重重,本文提出了一整套方案,从样本提取到下游的生物信息学分析,带我们跨越障碍,组装高质量基因组。
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Complete, closed bacterial genomes from microbiomes using nanopore sequencing

使用纳米孔测序从微生物组中得到完整成环的细菌基因组

10.1038/s41587-020-0422-6

02-10, Editorial Material

Abstract & Authors:展开

Abstract:收起
Microbial genomes can be assembled from short-read sequencing data, but the assembly contiguity of these metagenome-assembled genomes is constrained by repeat elements. Correct assignment of genomic positions of repeats is crucial for understanding the effect of genome structure on genome function. We applied nanopore sequencing and our workflow, named Lathe, which incorporates long-read assembly and short-read error correction, to assemble closed bacterial genomes from complex microbiomes. We validated our approach with a synthetic mixture of 12 bacterial species. Seven genomes were completely assembled into single contigs and three genomes were assembled into four or fewer contigs. Next, we used our methods to analyze metagenomics data from 13 human stool samples. We assembled 20 circular genomes, including genomes of Prevotella copri and a candidate Cibiobacter sp. Despite the decreased nucleotide accuracy compared with alternative sequencing and assembly approaches, our methods improved assembly contiguity, allowing for investigation of the role of repeat elements in microbial function and adaptation.

First Authors:
Eli L Moss

Correspondence Authors:
Ami S Bhatt

All Authors:
Eli L Moss,Dylan G Maghini,Ami S Bhatt

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