ArticlePlasmid2020
ORF-based binarized structure network analysis of plasmids (OSNAp), a novel approach to core gene-independent plasmid phylogeny.
Article in Plasmid, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 17 citations in OpenAlex.
- pLAST-a tool for rapid comparison and classification of bacterial plasmid sequences.Bioinformatics (Oxford, England) · 2026Article
- Convergence of plasmid-driven virulence and antibiotic resistance in Escherichia coli.Nature communications · 2025Article
- Evaluation ofMicrobial genomics · 2024Article
- Taxonomic classification of genusFujita medical journal · 2024Article
- Genetic basis of I-complex plasmid stability and conjugation.PLoS genetics · 2023Article
- Assessment of plasmids for relating the 2020 Salmonella enterica serovar Newport onion outbreak to farms implicated by the outbreak investigation.BMC genomics · 2023Article
- Novel insights into genetic characteristics ofFrontiers in microbiology · 2023Article
- Characterization ofAntimicrobial agents and chemotherapy · 2020Article
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
objectivesSystematic comparison of multiple plasmids remains challenging. We aimed to develop a new method for phylogenetic analysis of plasmids, open reading frame (ORF)-based binarized structure network analysis of plasmids (OSNAp).
methodsWith the OSNAp, the genetic structures of plasmids in a given plasmid group are expressed as binary sequences based on the presence or absence of ORFs regardless of their positions or directions. As a proof-of-concept, ORFs were collected from 101 complete I1 plasmid sequences, and their corresponding binary sequences were generated. A tree was generated using the neighbor-net, an algorithm for constructing phylogenetic networks based on distance between taxa, to visualize the plasmid phylogeny drawn from binary sequences. The results were compared with those of plasmid sequence types (pSTs) defined by plasmid multilocus sequence typing (pMLST).
resultsAll I1 plasmids were placed on the phylogenetic tree constructed from the binary sequences. Most plasmids belonging to the same pSTs had Dice indices of ≥0.95 and were placed in the same OSNAp split. On the other hand, pST12 plasmids were distributed on separate splits due to differences in ORFs not used in pMLST, suggesting improved differentiation of the plasmids with OSNAp compared with pMLST.
conclusionOSNAp is a novel holistic approach to assess relatedness of a population of plasmids in a given plasmid group based on nucleotide sequence data. It provides higher discrimination than pMLST, which may prove useful in tracing bacteria that harbor plasmids of shared origins.
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