Nation-scale recovery of complete environmental plasmids pushes the boundaries of plasmid diversity through long-read sequencing
- 1Center for Microbial Communities, University of Aalborg, Denmark
Abstract
Plasmids are important agents of prokaryotic evolution and yet existing reference databases remain biased towards cultivable species, limiting our knowledge of their function and ecology in the environment. Here we present a major expansion of known plasmid diversity, through curation and annotation of 8,744 topologically complete plasmids from 9,972 short- and 154 long-read metagenomes as part of the Microflora Danica project. These were found to increase plasmid taxonomic unit diversity by 15% and 99% relative to all and environmental plasmids, respectively, from public sources. In particular, we identify a novel lineage of plasmids in the genus Methanosarcina, encoding genes associated with methanogenesis and cell surface properties, expanding our understanding of chromosome-plasmid complementarity and its potential contribution to host biology. Combining our plasmids with public sources, we curated a set of 17 replication-associated proteins that could be found in 82% of known plasmids and can serve as hallmarks for future detection of plasmids. We present this resource, and a tool for confirming topological completeness of plasmid assemblies, as a toolkit for future plasmid discovery.
Related
- Genetic diversity of Legionella species in culture-negative clinical and environmental specimens by sequencing the 23S-5S ribosomal intergenic spacer region
- A meta-analysis of environmental sequencing data reveals the global distribution and hidden diversity of marine anaerobic ciliates
- Genotyping by Sequencing (GBS) uncovers genetic diversity and population structure for salicornia breeding programs in Iran
- Sequencing of 10 complete Curvularia genomes isolated from rice in Burkina Faso
- Complete chloroplast genome sequencing of Morus alba var. pendula Dippel, 1753 from North China.
BibTeX
@misc{sorensen2026nationscale,
title = {{Nation-scale recovery of complete environmental plasmids pushes the boundaries of plasmid diversity through long-read sequencing}},
author = {B. Sorensen and C. L. Brown and M. Sereika and S. Heidelbach and P. Hugenholtz and M. Albertsen and F. Delogu},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.06.756670},
url = {https://www.biorxiv.org/content/10.64898/2026.10.06.756670v1},
note = {CC BY-NC},
}
RIS
TY - UNPB
TI - Nation-scale recovery of complete environmental plasmids pushes the boundaries of plasmid diversity through long-read sequencing
AU - B. Sorensen
AU - C. L. Brown
AU - M. Sereika
AU - S. Heidelbach
AU - P. Hugenholtz
AU - M. Albertsen
AU - F. Delogu
PY - 2026
DA - 2026/10/06
PB - bioRxiv
DO - 10.64898/2026.10.06.756670
UR - https://www.biorxiv.org/content/10.64898/2026.10.06.756670v1
AB - Plasmids are important agents of prokaryotic evolution and yet existing reference databases remain biased towards cultivable species, limiting our knowledge of their function and ecology in the environment. Here we present a major expansion of known plasmid diversity, through curation and annotation of 8,744 topologically complete plasmids from 9,972 short- and 154 long-read metagenomes as part of the Microflora Danica project. These were found to increase plasmid taxonomic unit diversity by 15% and 99% relative to all and environmental plasmids, respectively, from public sources. In particular, we identify a novel lineage of plasmids in the genus Methanosarcina, encoding genes associated with methanogenesis and cell surface properties, expanding our understanding of chromosome-plasmid complementarity and its potential contribution to host biology. Combining our plasmids with public sources, we curated a set of 17 replication-associated proteins that could be found in 82% of known plasmids and can serve as hallmarks for future detection of plasmids. We present this resource, and a tool for confirming topological completeness of plasmid assemblies, as a toolkit for future plasmid discovery.
ER -