The detection of mobile genetic elements is crucial for exploring the ecology and evolution of microbial communities, and it has diverse implications in biotechnology and public health. geNomad is a computational framework that enables researchers to precisely identifiy and annotate plasmids and viruses in sequencing data on a large scale.
This is a preview of subscription content, access via your institution
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Rent or buy this article
Prices vary by article type
from$1.95
to$39.95
Prices may be subject to local taxes which are calculated during checkout
References
Koonin, E. V. Viruses and mobile elements as drivers of evolutionary transitions. Phil. Trans. R. Soc. B 371, 20150442 (2016). A review that discusses how MGEs function as genetic reservoirs that allow major evolutionary transitions.
Durrant, M. G. et al. Systematic discovery of recombinases for efficient integration of large DNA sequences into the human genome. Nat Biotechnol. 41, 488–499 (2023). This paper reports the discovery of thousands of MGE-encoded large serine integrases with recombination activity in human cells.
San Millan, A. Evolution of plasmid-mediated antibiotic resistance in the clinical context. Trends Microbiol. 26, 978–985 (2018). A review discussing the role of plasmids in the spread of antibiotic resistance genes in clinical settings.
Paez-Espino, D. et al. Uncovering Earth’s virome. Nature 536, 425–430 (2016). This paper identifies over a hundred thousand virus genomes in metagenomic sequencing data, expanding the number of known viral genes at that time by 16-fold.
Camargo, A. P. et al. IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata. Nuc. Acids Res. 51, D733–D743 (2023). This paper describes the IMG/VR v4 database, which was created using geNomad and includes more than 15 million sequences of viral genomes.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
This is a summary of: Camargo, A. P. et al. Identification of mobile genetic elements with geNomad. Nat. Biotechnol. https://doi.org/10.1038/s41587-023-01953-y (2023).
Rights and permissions
About this article
Cite this article
Fast and accurate identification of plasmids and viruses in sequencing data using geNomad. Nat Biotechnol (2023). https://doi.org/10.1038/s41587-023-01982-7
Published:
DOI: https://doi.org/10.1038/s41587-023-01982-7
