利用体外方法进行染色体规模的远距离连锁的鸟枪组装
Chromosome-scale shotgun assembly using an in vitro method for long-range linkage
摘要：
从短读段数据中进行长距离和高度准确的从头组装是基因组学中最紧迫的挑战之一。最近，已经显示通过活组织的染色质中的DNA的邻近连接产生的读取对可以解决这个问题。这些数据显著增加了组装体的支架邻接性并提供了单倍型定相信息。在这里，我们描述了一个更简单的方法（“芝加哥”）的基础上，在体外重建染色质。我们用人类DNA生成了两个芝加哥数据集，并使用新的软件管道（“HiRise”）构建了高度准确的从头组装和具有30 Mb支架N50的人类基因组支架。我们还展示了芝加哥的效用，通过重新组装和支架的美洲短吻鳄的基因组，以改善现有的组件。利用单个文库和Illumina HiSeq测序的一个泳道，我们将美洲短吻鳄的支架N50从508 kb增加到10 Mb。我们的方法使用已建立的分子生物学程序，可用于分析任何基因组，因为它只需要约5微克的DNA作为起始材料。
英文摘要：
Long-range and highly accurate de novo assembly from short-read data is one of the most pressing challenges in genomics. Recently, it has been shown that read pairs generated by proximity ligation of DNA in chromatin of living tissue can address this problem. These data dramatically increase the scaffold contiguity of assemblies and provide haplotype phasing information. Here, we describe a simpler approach ("Chicago") based on in vitro reconstituted chromatin. We generated two Chicago datasets with human DNA and used a new software pipeline ("HiRise") to construct a highly accurate de novo assembly and scaffolding of a human genome with scaffold N50 of 30 Mb. We also demonstrated the utility of Chicago for improving existing assemblies by re-assembling and scaffolding the genome of the American alligator. With a single library and one lane of Illumina HiSeq sequencing, we increased the scaffold N50 of the American alligator from 508 kb to 10 Mb. Our method uses established molecular biology procedures and can be used to analyze any genome, as it requires only about 5 micrograms of DNA as the starting material.
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