质粒
基因组
生物
基因组
遗传学
计算生物学
基因
作者
Dmitry Antipov,Mikhail Raiko,Alla Lapidus,Pavel A. Pevzner
出处
期刊:Genome Research
[Cold Spring Harbor Laboratory]
日期:2019-05-02
卷期号:29 (6): 961-968
被引量:105
标识
DOI:10.1101/gr.241299.118
摘要
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.
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