Plasmid detection and assembly in genomic and metagenomic data sets
Plasmid detection and assembly in genomic and metagenomic data sets
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DOI：
10.1101/gr.241299.118
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发表时间：
2019-06-01
期刊：
影响因子：
7
通讯作者：
Pevzner, Pavel A.
中科院分区：
文献类型：
--
作者：
Antipov, Dmitry;Raiko, Mikhail;Pevzner, Pavel A.
尽管质粒对于细菌的存活和适应是重要的，但是从基因组样品（更不用说宏基因组样品）中检测和组装质粒仍然具有挑战性。最近开发的plasmidSPAdes组装器解决了分离基因组的一些挑战，但没有检测到宏基因组组装中的质粒，这是一个尚未开发的尚未发现的质粒来源。我们提出了metaplasmidSPAdes工具，用于宏基因组数据集中的质粒组装，与最先进的方法相比，降低了质粒检测的假阳性率。我们在不同的数据集中组装了质粒，并表明在已经完成的基因组和宏基因组研究中，数千种质粒仍然处于雷达之下。我们的分析揭示了质粒的极端变异性，并导致发现了许多新的质粒（包括许多携带耐药基因的质粒），这些质粒与目前已知的质粒没有显著的相似性。
Although plasmids are important for bacterial survival and adaptation, plasmid detection and assembly from genomic, let alone metagenomic, samples remain challenging. The recently developed plasmidSPAdes assembler addressed some of these challenges in the case of isolate genomes but stopped short of detecting plasmids in metagenomic assemblies, an untapped source of yet to be discovered plasmids. We present the metaplasmidSPAdes tool for plasmid assembly in metagenomic data sets that reduced the false positive rate of plasmid detection compared with the state-of-the-art approaches. We assembled plasmids in diverse data sets and have shown that thousands of plasmids remained below the radar in already completed genomic and metagenomic studies. Our analysis revealed the extreme variability of plasmids and has led to the discovery of many novel plasmids (including many plasmids carrying antibiotic-resistance genes) without significant similarities to currently known ones.