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

18.8K
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.
18.8K

You might also read

Related Articles

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

Sort by
Same author

Interpretable spatial multi-omics data integration and dimensionality reduction with SpaMV.

Nature communications·2026
Same author

Amino acid-based biological age clock and its implications for human health and aging.

Nature communications·2026
Same author

Cross-species comparison of amniote single-cell transcriptomes reveals evolutionary conservation and divergence in the chicken immune system.

Nature communications·2026
Same author

A little longer, a lot better: simulation-guided exploration of extended-length single-end barcoded reads for structural variant detection.

bioRxiv : the preprint server for biology·2026
Same author

Osteoblastic sclerostin loop3-LRP4 interaction required by sclerostin to inhibit bone formation.

Bone research·2026
Same author

The Extreme Environment Microbiome Catalog (EEMC): a global resource for microbial diversity and antimicrobial discovery.

Nature communications·2026

Related Experiment Video

Updated: Jun 24, 2025

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
12:08

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

5.0K

Exploring high-quality microbial genomes by assembling short-reads with long-range connectivity.

Zhenmiao Zhang1, Jin Xiao1, Hongbo Wang1

  • 1Department of Computer Science, Hong Kong Baptist University, Hong Kong, China.

Nature Communications
|May 31, 2024
PubMed
Summary

Pangaea enhances microbial genome assembly from short-read sequencing data with long-range connectivity. This cost-effective bioinformatic approach improves the recovery of near-complete metagenome-assembled genomes (NCMAGs).

More Related Videos

Ultra-long Read Sequencing for Whole Genomic DNA Analysis
10:34

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

22.8K
High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq
09:06

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

10.2K

Related Experiment Videos

Last Updated: Jun 24, 2025

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
12:08

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

5.0K
Ultra-long Read Sequencing for Whole Genomic DNA Analysis
10:34

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

22.8K
High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq
09:06

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

10.2K

Area of Science:

  • Metagenomics
  • Bioinformatics
  • Microbial Genomics

Background:

  • Long-read sequencing offers complete microbial genomes but is costly for large studies.
  • Assembling short-reads with long-range connectivity presents a cost-effective alternative for high-quality genome generation.

Purpose of the Study:

  • To develop Pangaea, a novel bioinformatic approach for enhanced metagenome assembly using short-reads with long-range connectivity.
  • To improve the generation of high-quality microbial genomes from complex metagenomic data.

Main Methods:

  • Pangaea utilizes physical (linked-reads) or virtual barcodes (short-read to long-read alignment) for read connectivity.
  • A deep learning-based read binning algorithm assembles co-barcoded reads with similar sequence contexts and abundances.
  • A multi-thresholding strategy refines assembly for low-abundance microbes.

Main Results:

  • Pangaea significantly improves contig continuity and the number of near-complete metagenome-assembled genomes (NCMAGs) compared to existing assemblers.
  • The method was benchmarked on simulated data, mock communities, and human gut metagenomes.
  • Three complete and circular NCMAGs were successfully generated from human gut microbiomes.

Conclusions:

  • Pangaea offers a powerful and cost-effective solution for assembling microbial genomes from metagenomic data.
  • The approach effectively enhances the recovery of both high- and low-abundance microbial genomes.
  • Pangaea advances the potential for large-scale metagenomic studies and microbial genome reconstruction.