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

21.4K
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.
21.4K
Applications of Molecular Taxonomy01:20

Applications of Molecular Taxonomy

652
Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
652
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

827
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...
827
RNA-seq03:21

RNA-seq

12.4K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
12.4K

You might also read

Related Articles

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

Sort by
Same author

Chromosomal fusions shaped the genome of the greater hornwrack bryozoan (Flustra foliacea) (Linnaeus, 1758).

The Journal of heredity·2026
Same author

International Symposium on Ruminant Physiology: Current perspective on rumen microbial ecology to improve fiber digestibility.

Journal of dairy science·2024
Same author

Haploflow: Strain-resolved <i>de novo</i> assembly of viral genomes.

bioRxiv : the preprint server for biology·2021
Same author

Characterization of an AA9 LPMO from Thielavia australiensis, TausLPMO9B, under industrially relevant lignocellulose saccharification conditions.

Biotechnology for biofuels·2020
Same author

Integration of absolute multi-omics reveals dynamic protein-to-RNA ratios and metabolic interplay within mixed-domain microbiomes.

Nature communications·2020
Same author

Author Correction: Structural Features of a Bacteroidetes-Affiliated Cellulase Linked with a Polysaccharide Utilization Locus.

Scientific reports·2020
Same journal

MT-MRI for detection of renal interstitial fibrosis in renovascular disease.

Scientific reports·2026
Same journal

Detection of underground objects from GPR data using a lightweight YOLO-based approach.

Scientific reports·2026
Same journal

Early systemic inflammatory-metabolic trajectory phenotypes are associated with survival outcomes in metastatic renal cell carcinoma treated with nivolumab.

Scientific reports·2026
Same journal

Water balance components in a dry-seeded rice-wheat system: Untangling the effects of tillage and mulching practices.

Scientific reports·2026
Same journal

Topological approaches to quantum tensor train compression via ZX-calculus and SVD.

Scientific reports·2026
Same journal

determinants of flood impacts and adaptive capacity among market vendors in Walukuba-Masese, Jinja city, Uganda.

Scientific reports·2026
See all related articles

Related Experiment Video

Updated: Mar 21, 2026

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

5.9K

Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data.

J A Frank1, Y Pan2, A Tooming-Klunderud3

  • 1Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, 1432 Norway.

Scientific Reports
|May 10, 2016
PubMed
Summary
This summary is machine-generated.

Pacific Biosciences circular consensus sequencing (CCS) reads significantly improve metagenomic assembly and genome reconstruction. This long-read technology enhances microbial community analysis, outperforming traditional short-read sequencing alone.

More Related Videos

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing
07:21

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Published on: August 25, 2018

13.6K
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

24.2K

Related Experiment Videos

Last Updated: Mar 21, 2026

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

5.9K
Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing
07:21

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Published on: August 25, 2018

13.6K
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

24.2K

Area of Science:

  • Genomics
  • Microbiology
  • Bioinformatics

Background:

  • Metagenomic DNA assembly is crucial for understanding microbial communities.
  • Short-read sequencing (e.g., Illumina HiSeq) has limitations in reconstructing complex genomes.
  • Long-read sequencing offers potential improvements for metagenomic analysis.

Purpose of the Study:

  • To evaluate the utility of Pacific Biosciences (PacBio) long and high-accuracy circular consensus sequencing (CCS) reads in metagenomic projects.
  • To compare the performance of PacBio CCS reads against Illumina HiSeq data for DNA assembly and taxonomic binning.
  • To assess the impact of hybrid assembly strategies combining both data types.

Main Methods:

  • Generated PacBio CCS reads (94 Mb, 1319 nt average length, 99.7% accuracy) from a biogas reactor microbiome sample.
  • Compared assembly and taxonomic binning using PacBio CCS data, Illumina HiSeq data (~18 Gb), and hybrid assemblies.
  • Utilized established assembly and binning algorithms for comparative analysis.

Main Results:

  • PacBio CCS assembly yielded a comparable number of large contigs (>1 kb) to a much larger HiSeq dataset.
  • Hybrid assemblies improved contig length and the number of large contigs.
  • Incorporation of CCS data significantly enhanced taxonomic binning and genome reconstruction of dominant microbial phylotypes.

Conclusions:

  • PacBio CCS reads are valuable for metagenomic applications, particularly for improving genome assembly and reconstruction.
  • Long-read sequencing complements short-read data, offering enhanced insights into microbial community structure and function.
  • Hybrid assembly strategies combining long and short reads provide superior metagenomic assembly statistics.