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

Export of Mitochondrial and Chloroplast Genes02:19

Export of Mitochondrial and Chloroplast Genes

3.8K
A eukaryotic cell can have up to three different types of genetic systems: nuclear, mitochondrial, and chloroplast. During evolution, organelles have exported many genes to the nucleus; this transfer is still ongoing in some plant species. Approximately 18% of the Arabidopsis thaliana nuclear genome is thought to be derived from the chloroplast’s cyanobacterial ancestor, and around 75% of the yeast genome derived from the mitochondria’s bacterial ancestor. This export has occurred...
3.8K
Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

13.4K
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...
13.4K
Assembly of Complex Microtubule Structures01:32

Assembly of Complex Microtubule Structures

1.9K
Complex microtubule structures are present in resting cells and in dividing cells. In resting cells, they are responsible for maintaining the cellular architecture, tracks for intracellular transport, positioning of organelles, assembly of cilia and flagella. They mediate the bipolar spindle assembly for chromosomal segregation and positioning of the cell division plate in dividing cells. The formation of microtubule complex structures depends on the cell type, cell stage, and cell function.
1.9K
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

19.3K
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.
19.3K
Assembly of Cytoskeletal Filaments01:18

Assembly of Cytoskeletal Filaments

21.4K
Cytoskeletal filaments are polymeric forms of smaller protein subunits. However, individual cytoskeletal filaments may easily disassemble or associate with other similar filaments to form rigid structures. Microfilaments, made of actin monomers, rely on actin-binding proteins to form bundles and create networks of individual actin filaments. Microtubules rely on microtubule-associated proteins (MAPs) to form sturdy cylindrical structures. However, the proteins involved in forming complex...
21.4K
Protein Complex Assembly02:41

Protein Complex Assembly

2.1K
2.1K

You might also read

Related Articles

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

Sort by
Same author

Functional divergence of MADS-box genes and the dual regulatory role of a long noncoding RNA underlie sex determination in Ginkgo biloba.

BMC plant biology·2026
Same author

Accurate Identification of <i>Ilex</i> (Aquifoliaceae) Taxa Based on Leaf Morphology Using Deep Learning.

Plants (Basel, Switzerland)·2026
Same author

MMGS: a novel genomic prediction framework to integrate genotype, environment and their interactions for multi-environment breeding trials.

Horticulture research·2026
Same author

Combined NMR and MRI Assessment of Water Status and Migration in <i>Quercus texana</i> Seeds During Dehydration.

Plants (Basel, Switzerland)·2026
Same author

Improving genomic selection accuracy using a dual-path convolutional neural network framework: a terpenoid case study.

The New phytologist·2025
Same author

Cross-kingdom RNA trafficking from bacteria to fungi enables plant protection against fungal pathogens.

Molecular plant·2025

Related Experiment Video

Updated: Sep 10, 2025

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

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

Published on: December 7, 2021

2.3K

PMAT2: An efficient graphical assembly toolkit for comprehensive organellar genomes.

Fuchuan Han1,2, Changwei Bi1,3, Yicun Chen2

  • 1State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province Nanjing Forestry University Nanjing China.

Imeta
|August 27, 2025
PubMed
Summary

We created PMAT2, a new bioinformatics tool for assembling plant, animal, and fungal mitochondrial and plant chloroplast genomes. It provides complete and accurate assemblies using PacBio HiFi reads, outperforming other tools.

More Related Videos

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

17.8K
Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

10.6K

Related Experiment Videos

Last Updated: Sep 10, 2025

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

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

Published on: December 7, 2021

2.3K
A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

17.8K
Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

10.6K

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Organellar genomes (mitochondrial and chloroplast) are crucial for understanding cellular function and evolution.
  • De novo assembly of these genomes presents unique challenges due to their structure and repetitive elements.
  • Accurate assembly is essential for downstream analyses, including population genetics and phylogenomics.

Discussion:

  • PMAT2 utilizes optimized graph-based strategies specifically designed for organellar genome complexity.
  • The toolkit demonstrates high performance even with low-coverage, highly accurate PacBio HiFi sequencing data.
  • Comparative analyses show PMAT2 achieves superior assembly completeness compared to existing methods.

Key Insights:

  • PMAT2 enables lineage-specific de novo assembly of plant, animal, and fungal mitochondrial genomes.
  • It also facilitates the assembly of plant chloroplast genomes.
  • The tool ensures complete and accurate genome reconstruction, validated across 150 diverse organellar genomes.

Outlook:

  • PMAT2 is expected to accelerate research in evolutionary biology, population genetics, and functional genomics by providing a robust assembly solution.
  • Future developments may focus on expanding its applicability to other types of non-model organism genomes.
  • The open-source availability of PMAT2 promotes wider adoption and collaborative advancements in the field.