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...

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...

Genomic DNA in Eukaryotes

Genomic DNA in Eukaryotes

Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.

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...

Genomics

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...

Genome Size and the Evolution of New Genes

Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.

You might also read

Related Articles

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

Sort by

Same author

Closing the Complexity Gap of the Double Distance Problem.

IEEE transactions on computational biology and bioinformatics·2025

Same author

Reconstructing rearrangement phylogenies of natural genomes.

Algorithms for molecular biology : AMB·2025

Same author

Panacus: fast and exact pangenome growth and core size estimation.

Bioinformatics (Oxford, England)·2024

Same author

Applying rearrangement distances to enable plasmid epidemiology with pling.

Microbial genomics·2024

Same author

Panacus: fast and exact pangenome growth and core size estimation.

bioRxiv : the preprint server for biology·2024

Same author

Methods for Pangenomic Core Detection.

Methods in molecular biology (Clifton, N.J.)·2024

Same journal

Isolation of Mesenchymal Stem Cell-Derived Extracellular Vesicles.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Modeling Melanoma Immune Surveillance by CAR-T Cells in Human Skin Organoids.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Stepwise Optimization of a Matrigel-Based In Vitro Angiogenesis Assay for Reproducible and Quantifiable 2D-Tube Formation Using HUVECs.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Quantifying Mechanical Properties of Fresh Ovarian Tissue with Optical Brillouin Microscopy.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

3D Chromatin Architecture During Early Development: New Methods and New Findings.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Metabolic Plasticity in Embryogenesis Throughout the Lens of NAD<sup></sup>.

Methods in molecular biology (Clifton, N.J.)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jun 25, 2025

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells

Published on: April 4, 2016

Family-Free Genome Comparison.

Marilia D V Braga¹, Daniel Doerr², Diego P Rubert³

¹Faculty of Technology and Center for Biotechnology, Bielefeld University, Bielefeld, Germany.

Methods in Molecular Biology (Clifton, N.J.)

|May 31, 2024

Summary

This summary is machine-generated.

This study introduces FFGC, a novel genome comparison tool. FFGC analyzes large-scale genome structures and infers gene families without prior gene classification, aiding phylogenetic and genomic studies.

Keywords:

Common intervals Conserved adjacencies Double-cut-and-join Gene family-free Gene order analysis Gene orthology inference Genome distance Genome median Genome similarity

More Related Videos

Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing

Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing

Published on: July 28, 2017

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

Published on: March 22, 2018

Related Experiment Videos

Last Updated: Jun 25, 2025

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells

Published on: April 4, 2016

Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing

Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing

Published on: July 28, 2017

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

Published on: March 22, 2018

Area of Science:

Comparative genomics
Bioinformatics
Computational biology

Background:

Comparing large-scale genome structures aids understanding of species phylogeny, genome organization, and gene associations.
Existing methods often require prior gene classification, limiting comparative analyses.

Purpose of the Study:

To review the family-free genome comparison tool (FFGC).
To present FFGC's capabilities for analyzing genomes without pre-classified genes.
To highlight FFGC's utility in inferring gene families and genomic similarities.

Main Methods:

FFGC utilizes built-in interfaces with sequence comparison tools (BLAST+, DIAMOND) and ILP solvers (CPLEX, Gurobi).
The workflow accepts annotated genome sequences as input.
FFGC employs methods for similarity/dissimilarity computation and gene family inference.

Main Results:

FFGC enables genome comparison without prior gene classification.
It allows computation of similarity and dissimilarity measures between genomes.
FFGC facilitates the inference of gene families based on sequence similarity and genomic features.

Conclusions:

FFGC provides a comprehensive workflow for comparative genomics.
The tool supports robust phylogenetic and genome organization analyses.
FFGC advances the study of gene associations across species.