Species-level deconvolution of metagenome assemblies with Hi-C-based contact probability maps.
Species-level deconvolution of metagenome assemblies with Hi-C-based contact probability maps.
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DOI：
10.1534/g3.114.011825
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发表时间：
2014-05-22
期刊：
影响因子：
--
通讯作者：
Shendure J
中科院分区：
文献类型：
--
作者：
Burton JN;Liachko I;Dunham MJ;Shendure J
微生物群落由生物体的混合种群组成，包括丰度未知的未知物种。这些群落通常通过宏基因组鸟枪法测序进行研究，但标准的文库构建方法会删除远程邻接信息；因此，鸟枪法测序和宏基因组的从头组装通常会产生不能轻易按物种分组的重叠群集合。用于生成染色质水平接触概率图的方法，例如通过 Hi-C 方法生成的方法，提供了完全细胞内的连续信号，并且包含染色体内和染色体间信息。在这里，我们演示了如何利用该信号来重建混合样本中存在的微生物物种的个体基因组。我们将此方法应用于两个合成宏基因组样本，成功对真菌、细菌和古细菌物种的基因组内容进行聚类，与已发布的参考基因组的一致性超过 99%。我们还表明，Hi-C 信号其次可用于创建微生物群落中存在的单个真核物种的支架基因组组装，其连续性水平高于某些物种已发表的参考基因组。
Microbial communities consist of mixed populations of organisms, including unknown species in unknown abundances. These communities are often studied through metagenomic shotgun sequencing, but standard library construction methods remove long-range contiguity information; thus, shotgun sequencing and de novo assembly of a metagenome typically yield a collection of contigs that cannot readily be grouped by species. Methods for generating chromatin-level contact probability maps, e.g., as generated by the Hi-C method, provide a signal of contiguity that is completely intracellular and contains both intrachromosomal and interchromosomal information. Here, we demonstrate how this signal can be exploited to reconstruct the individual genomes of microbial species present within a mixed sample. We apply this approach to two synthetic metagenome samples, successfully clustering the genome content of fungal, bacterial, and archaeal species with more than 99% agreement with published reference genomes. We also show that the Hi-C signal can secondarily be used to create scaffolded genome assemblies of individual eukaryotic species present within the microbial community, with higher levels of contiguity than some of the species’ published reference genomes.
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影响因子：
64.8
作者：
通讯作者：
--
DOI：
10.1038/nrg3454
发表时间：
2013-06
期刊：
Nature reviews. Genetics
影响因子：
--
作者：
通讯作者：
--
DOI：
10.1073/pnas.1402564111
发表时间：
2014-04-01
影响因子：
11.1
作者：
Howe, Adina Chuang;Jansson, Janet K.;Brown, C. Titus
通讯作者：
Brown, C. Titus
影响因子：
5
作者：
Renouf, Vincent;Claisse, Olivier;Lonvaud-Funel, Aline
通讯作者：
Lonvaud-Funel, Aline
影响因子：
11
作者：
Narasingarao, Priya;Podell, Sheila;Allen, Eric E.
通讯作者：
Allen, Eric E.