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

Genome Annotation and Assembly

Genome Annotation and Assembly

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.

Modern Molecular Taxonomy

Modern Molecular Taxonomy

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...

You might also read

Related Articles

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

Sort by

Same author

Novel cell wall polysaccharide genotypes and structures of lactococcal strains isolated from milk and fermented foods.

International journal of food microbiology·2024

Same author

Maternal gut Bifidobacterium breve modifies fetal brain metabolism in germ-free mice.

Molecular metabolism·2024

Same author

Discovery of antiphage systems in the lactococcal plasmidome.

Nucleic acids research·2024

Same author

Pseudocin 196, a novel lantibiotic produced by <i>Bifidobacterium pseudocatenulatum</i> elicits antimicrobial activity against clinically relevant pathogens.

Gut microbes·2024

Same author

Unveiling metabolic pathways of selected plant-derived glycans by <i>Bifidobacterium pseudocatenulatum</i>.

Frontiers in microbiology·2024

Same author

Viromic and Metagenomic Analyses of Commercial Spirulina Fermentations Reveal Remarkable Microbial Diversity.

Viruses·2024

Search research articles

Related Experiment Video

Updated: Nov 15, 2025

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

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

Bifidobacterium Genome Assembly and Methylome Analysis Using Pacbio SMRT Sequencing.

Francesca Bottacini¹, Douwe van Sinderen²

¹APC Microbiome Ireland, University College Cork, Cork, Ireland. f.bottacini@umail.ucc.ie.

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

|March 2, 2021

Summary

This study introduces a method for de novo genome assembly and methylome analysis in Bifidobacterium using Pacbio SMRT sequencing. This approach aids in predicting restriction-modification systems for genetic engineering applications.

Keywords:

Base modification Bifidobacteria Probiotic SMRT sequencing

More Related Videos

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

Methyl-binding DNA capture Sequencing for Patient Tissues

Methyl-binding DNA capture Sequencing for Patient Tissues

Published on: October 31, 2016

Related Experiment Videos

Last Updated: Nov 15, 2025

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

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

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

Methyl-binding DNA capture Sequencing for Patient Tissues

Methyl-binding DNA capture Sequencing for Patient Tissues

Published on: October 31, 2016

Area of Science:

Microbiology
Genomics
Bioinformatics

Background:

Bifidobacterium species are crucial in gut health and industrial applications.
Complete genome sequences and understanding of their methylomes are essential for genetic manipulation.
Existing methods may not provide complete genome assemblies or detailed methylome information.

Purpose of the Study:

To present a generic method for de novo genome assembly of Bifidobacterium.
To enable comprehensive methylome analysis for Bifidobacterium strains.
To facilitate the prediction of active restriction-modification systems.

Main Methods:

Utilizing Pacbio Single Molecule, Real-Time (SMRT) sequencing technology.
Employing the SMRT Link pipeline for genome assembly and analysis.
Performing de novo Pacbio or hybrid Illumina-Pacbio assembly.
Detecting base modifications and analyzing the methylome.

Main Results:

Achieved complete genome sequences for Bifidobacterium.
Successfully identified DNA motifs through methylome analysis.
Predicted active restriction-modification (RM) systems within Bifidobacterium strains.

Conclusions:

The presented method provides a robust approach for Bifidobacterium genome and methylome characterization.
Identified RM systems and their target motifs can guide the selection of appropriate genetic tools.
This work supports advancements in the genetic engineering of Bifidobacterium for various applications.