Plasmid detection and assembly in genomic and metagenomic datasets

D. Antipov, M. Raiko, A. Lapidus, P.A. Pevzner

Research output

1 Citation (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)961-968
Number of pages8
JournalGenome Research
Volume29
Issue number6
DOIs
Publication statusPublished - 1 Jan 2019

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Metagenomics
Plasmids
Datasets
Radar
Microbial Drug Resistance
Genome

Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Antipov, D. ; Raiko, M. ; Lapidus, A. ; Pevzner, P.A. / Plasmid detection and assembly in genomic and metagenomic datasets. In: Genome Research. 2019 ; Vol. 29, No. 6. pp. 961-968.
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Plasmid detection and assembly in genomic and metagenomic datasets. / Antipov, D.; Raiko, M.; Lapidus, A.; Pevzner, P.A.

In: Genome Research, Vol. 29, No. 6, 01.01.2019, p. 961-968.

Research output

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