Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

21.0K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
21.0K
From DNA to Protein03:06

From DNA to Protein

22.4K
The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma, which states that genes specify the sequence of mRNAs, which in turn specify the sequence of amino acids making up all proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis...
22.4K
Protein Complex Assembly02:41

Protein Complex Assembly

16.8K
Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
16.8K
Spindle Assembly02:50

Spindle Assembly

4.3K
Spindle assembly occurs through three, often coexisting, pathways – the centrosome-mediated pathway, the chromatin-mediated pathway, and the microtubule-mediated pathway – collectively contributing to form a robust spindle apparatus.
In most cells, centrosomes are the primary microtubule nucleation centers. In the centrosome-mediated pathway, the G2-prophase transition triggers centrosome maturation and increased microtubule nucleation. Progressive nucleation results in a...
4.3K
Oligosaccharide Assembly01:24

Oligosaccharide Assembly

3.7K
Protein glycosylation starts in the ER lumen and continues in the Golgi apparatus. Glycosyltransferases catalyze the addition of sugar molecules or glycosylation of proteins. Usually, these enzymes add sugars to the hydroxyl groups of selected serine or threonine residues to form O-linked glycans or the amino groups of asparagine residues to form N-linked glycans. Different positions on the same polypeptide chain can contain differently linked glycans.
Multiple sugar molecules that may or may...
3.7K
DNA Topoisomerases02:02

DNA Topoisomerases

35.5K
Topoisomerases are enzymes that relax overwound DNA molecules during various cell processes, including DNA replication and transcription. These enzymes regulate positive and negative DNA supercoiling without changing the nucleotide sequence. DNA overwinding in a clockwise direction results in positively supercoiled DNA, whereas underwinding in a counterclockwise direction produces negatively supercoiled DNA.
Types and Mechanism of action
Topoisomerases are divided into two main types. ...
35.5K

You might also read

Related Articles

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

Sort by
Same author

Professional Academies: The Duty to Lead.

Microbial biotechnology·2026
Same author

Living together: evolutionary and ecological dimensions of protist endosymbiosis.

microLife·2026
Same author

Scientists' Warning to Humanity: The Need to Begin Teaching Critical and Systems Thinking Early in Life.

Microbial biotechnology·2025
Same author

Reduced plastid genomes of colorless facultative pathogens Prototheca (Chlorophyta) are retained for membrane transport genes.

BMC biology·2024
Same author

Spatio-temporal changes of small protist and free-living bacterial communities in a temperate dimictic lake: insights from metabarcoding and machine learning.

FEMS microbiology ecology·2024
Same author

Genomics of Preaxostyla Flagellates Illuminates the Path Towards the Loss of Mitochondria.

PLoS genetics·2023
Same journal

Mapping the 3D Chromosome Organization of a Biosynthetic Gene Cluster by Capture Hi-C (CHi-C).

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

Mapping the 3D Chromosome Organization of Streptomyces by Hi-C.

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

CUT&Tag Epigenomic Profiling of Biosynthetic Gene Clusters in Arabidopsis thaliana.

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

Rhizobium rhizogenes-Mediated Hairy Root Transformation Protocol for Lotus japonicus and Other Legumes.

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

Characterization of Bioactive Saponins from Sea Cucumbers.

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

Methods for Functional Validation of Terpenoid Metabolic Clusters in Nicotiana benthamiana and Aspergillus oryzae.

Methods in molecular biology (Clifton, N.J.)·2026
See all related articles

Related Experiment Video

Updated: Feb 4, 2026

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells
14:26

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells

Published on: April 4, 2016

25.9K

Euglenid Extrachromosomal DNA: Assembly and Annotation.

Paweł Hałakuc1, Kacper Maciszewski2, Anna Karnkowska3

  • 1University of Warsaw, Faculty of Biology, Institute of Evolutionary Biology, Warsaw, Poland.

Methods in Molecular Biology (Clifton, N.J.)
|February 2, 2026
PubMed
Summary
This summary is machine-generated.

This study introduces a bioinformatics pipeline to assemble and annotate extrachromosomal DNA (ecDNA) from euglenids. The method efficiently recovers ribosomal DNA (rDNA), mitochondrial DNA (mtDNA), and plastid DNA (ptDNA) for evolutionary research.

Keywords:
EuglenidaEuglenozoaMitochondrial genomeNext-generation sequencingPlastid genomeRibosomal operon

More Related Videos

Automated Robotic Liquid Handling Assembly of Modular DNA Devices
11:22

Automated Robotic Liquid Handling Assembly of Modular DNA Devices

Published on: December 1, 2017

12.9K
Protocols for C-Brick DNA Standard Assembly Using Cpf1
12:03

Protocols for C-Brick DNA Standard Assembly Using Cpf1

Published on: June 15, 2017

8.7K

Related Experiment Videos

Last Updated: Feb 4, 2026

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells
14:26

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells

Published on: April 4, 2016

25.9K
Automated Robotic Liquid Handling Assembly of Modular DNA Devices
11:22

Automated Robotic Liquid Handling Assembly of Modular DNA Devices

Published on: December 1, 2017

12.9K
Protocols for C-Brick DNA Standard Assembly Using Cpf1
12:03

Protocols for C-Brick DNA Standard Assembly Using Cpf1

Published on: June 15, 2017

8.7K

Area of Science:

  • Genomics
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Euglenids possess diverse extrachromosomal DNA (ecDNA), including ribosomal DNA (rDNA), mitochondrial DNA (mtDNA), and plastid DNA (ptDNA).
  • These ecDNA elements are crucial for phylogenomic, metabarcoding, and evolutionary studies.
  • Accurate assembly and annotation of ecDNA are vital for understanding organismal evolution and diversity.

Purpose of the Study:

  • To present a robust and adaptable bioinformatics pipeline for the identification, assembly, and annotation of ecDNA from whole-genome datasets.
  • To specifically address the unique genomic features of euglenids while remaining adaptable for other protists.
  • To facilitate high-confidence recovery of organellar and rDNA sequences for various research applications.

Main Methods:

  • Development of a bioinformatics pipeline for processing whole-genome sequencing data.
  • Implementation of algorithms for the identification and assembly of extrachromosomal DNA elements.
  • Annotation of assembled sequences to identify rDNA, mtDNA, and ptDNA.

Main Results:

  • The pipeline successfully identifies, assembles, and annotates various ecDNA elements in euglenids.
  • Demonstrated high confidence in recovering organellar and rDNA sequences.
  • The method is effective even with limited sequencing data, such as single-cell or metagenomic datasets.

Conclusions:

  • The developed bioinformatics pipeline provides a reliable method for analyzing ecDNA in euglenids and other protists.
  • This tool enhances phylogenomic analyses, metabarcoding, and evolutionary studies by enabling efficient ecDNA recovery.
  • The pipeline supports both targeted research and large-scale environmental sequencing initiatives.