Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

Plasmids

Plasmids

Plasmids are extrachromosomal DNA molecules found in bacteria, archaea, and some eukaryotic microbes like yeast. These small, circular DNA structures typically contain fewer than 30 genes, although some may exist linearly. Plasmids vary in their number within a cell, known as copy number. Single-copy plasmids are present in one copy per cell and multi-copy plasmids are present in multiple copies, reaching over 100 copies per cell.Plasmids usually replicate independently of the chromosomal DNA...

Modern Molecular Taxonomy

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...

Microbial Phylogeny

Microbial Phylogeny

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...

Genomic DNA in Prokaryotes

Genomic DNA in Prokaryotes

The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
Genomic Diversity in Bacteria
Although bacterial genomes are much...

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Think pink 2.0 - Description of Roseobacter cerffii sp. nov., isolated from the chromerid alga Vitrella brassicaformis, and reclassification of Sulfitobacter sabulilitoris as Billmartinia sabulilitoris, gen. nov., comb. nov.

Systematic and applied microbiology·2026

Same author

Marine Rhodobacterales as Drivers of Ulva Growth: From Macroalgal-Bacterial Interactions to Bioactive Factor Enrichment.

Journal of chemical ecology·2026

Same author

The microbiome of marine mat-forming cyanobacteria-a microcosm of taxonomic novelty and phototrophic diversity.

ISME communications·2026

Same author

Structural and regulatory determinants of flagellar motility in <i>Rhodobacterales</i>-the archetypal flagellum of <i>Phaeobacter inhibens</i> DSM 17395.

mSystems·2025

Same author

Structural and regulatory determinants of flagellar motility in <i>Rhodobacterales</i> - The archetypal flagellum of <i>Phaeobacter inhibens</i> DSM 17395.

bioRxiv : the preprint server for biology·2025

Same author

Erratum: The genus <i>Limnospira</i> contains only two species, both unable to produce microcystins: <i>L. maxima</i> and <i>L. platensis</i>.

iScience·2025

Search research articles

Related Experiment Video

Updated: Jun 3, 2026

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

Phylogeny and compatibility: plasmid classification in the genomics era.

Jörn Petersen¹

¹DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany. joern.petersen@dsmz.de

Archives of Microbiology

|March 5, 2011

Summary

This study introduces a new phylogenetic method for classifying plasmids, which are mobile genetic elements. This approach aids in understanding plasmid evolution and predicting their compatibility within microbial communities.

More Related Videos

Testing the Role of Multicopy Plasmids in the Evolution of Antibiotic Resistance

Testing the Role of Multicopy Plasmids in the Evolution of Antibiotic Resistance

Published on: May 2, 2018

Quantification of Plasmid-Mediated Antibiotic Resistance in an Experimental Evolution Approach

Quantification of Plasmid-Mediated Antibiotic Resistance in an Experimental Evolution Approach

Published on: December 14, 2019

Related Experiment Videos

Last Updated: Jun 3, 2026

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

Testing the Role of Multicopy Plasmids in the Evolution of Antibiotic Resistance

Testing the Role of Multicopy Plasmids in the Evolution of Antibiotic Resistance

Published on: May 2, 2018

Quantification of Plasmid-Mediated Antibiotic Resistance in an Experimental Evolution Approach

Quantification of Plasmid-Mediated Antibiotic Resistance in an Experimental Evolution Approach

Published on: December 14, 2019

Area of Science:

Microbiology
Genomics
Evolutionary Biology

Background:

Plasmids are crucial extrachromosomal elements for microbial evolution and adaptation.
Traditional plasmid classification relies on laborious compatibility testing, which is insufficient for the growing volume of sequence data.
Comparative genomics is limited for plasmids due to high recombination rates.

Purpose of the Study:

To present a novel phylogenetic approach for classifying plasmids.
To enable in silico prediction of plasmid compatibility.
To facilitate systematic assessment of the increasing plasmid sequence data.

Main Methods:

Phylogenetic analysis focusing on genes within the plasmid replication module (replicase and partitioning genes).
Exemplification of the method using four plasmid types from Alphaproteobacteria.
In silico prediction of plasmid compatibility based on phylogenetic classification.

Main Results:

The proposed phylogenetic method reliably classifies plasmid replicons.
The approach allows for accurate in silico prediction of plasmid compatibility.
Demonstrated effectiveness for plasmid classification within Alphaproteobacteria.

Conclusions:

Phylogenetic analysis of replication module genes offers a robust method for plasmid classification.
This strategy addresses the limitations of experimental compatibility testing for large-scale plasmid data.
A general classification scheme is essential for understanding extrachromosomal element distribution and evolution.