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

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.
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

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...
Genomics02:02

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...

You might also read

Related Articles

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

Sort by
Same author

Rational engineering of facultative anaerobiosis enables commensal survival in the oxygenated gut.

bioRxiv : the preprint server for biology·2026
Same author

Endurance exercise elicits temporal and sexual dimorphic multi-omics remodeling of liver metabolism revealed by MoTrPAC.

Cell reports·2026
Same author

Reduced Oxygen Condition Is Associated with Genome-Wide Expression Changes in Mastitis-Lineage <i>Staphylococcus aureus</i> During In Vitro Invasion into a Mammary Cell Line.

International journal of molecular sciences·2026
Same author

Metabolomic Profiling of Squid Chromatophores Reveals Differential Biochemical Fingerprints across Red, Yellow, and Brown Colors.

Journal of proteome research·2026
Same author

Dehydration promotes intracellular lipid synthesis and accumulation.

Nature communications·2026
Same author

Multi-Omic, Multi-Tissue Responses to Acute Exercise in Sedentary Adults: Findings from the Molecular Transducers of Physical Activity Consortium.

bioRxiv : the preprint server for biology·2026
Same journal

Analysis of strength degradation of coal and rock masses and stability of mined areas under long term immersion environment.

PloS one·2026
Same journal

Biogenic Silver-Selenium nanocomposite with anticancer activity and potent efficacy against vancomycin-resistant Staphylococcus aureus.

PloS one·2026
Same journal

Preparation and physicochemical characterization of a biodegradable chitosan/carboxymethyl cellulose hydrogel synthesized in NaOH/urea medium.

PloS one·2026
Same journal

Action-guilt, survivor-guilt, and depression in combat-related PTSD.

PloS one·2026
Same journal

Explainable machine learning for predicting activities of daily living at discharge in stroke patients: A retrospective study using SHAP interpretability.

PloS one·2026
Same journal

Deep learning based two-way feature depiction model for brain tumor detection.

PloS one·2026
See all related articles

Related Experiment Video

Updated: May 23, 2026

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens
09:14

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Published on: June 28, 2018

Comparative omics-driven genome annotation refinement: application across Yersiniae.

Alexandra C Schrimpe-Rutledge1, Marcus B Jones, Sadhana Chauhan

  • 1Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America.

Plos One
|April 6, 2012
PubMed
Summary
This summary is machine-generated.

This study introduces a comparative omic-based approach to refine genome annotations. Proteogenomic data revealed novel and incorrect protein-coding sequences in Yersiniae genomes, improving accuracy.

More Related Videos

Analysis of Yersinia enterocolitica Effector Translocation into Host Cells Using Beta-lactamase Effector Fusions
12:23

Analysis of Yersinia enterocolitica Effector Translocation into Host Cells Using Beta-lactamase Effector Fusions

Published on: October 13, 2015

Quantifying Yersinia pseudotuberculosis Type III Secretion System Activity Following Iron Starvation and Anaerobic Growth
08:36

Quantifying Yersinia pseudotuberculosis Type III Secretion System Activity Following Iron Starvation and Anaerobic Growth

Published on: May 31, 2024

Related Experiment Videos

Last Updated: May 23, 2026

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens
09:14

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Published on: June 28, 2018

Analysis of Yersinia enterocolitica Effector Translocation into Host Cells Using Beta-lactamase Effector Fusions
12:23

Analysis of Yersinia enterocolitica Effector Translocation into Host Cells Using Beta-lactamase Effector Fusions

Published on: October 13, 2015

Quantifying Yersinia pseudotuberculosis Type III Secretion System Activity Following Iron Starvation and Anaerobic Growth
08:36

Quantifying Yersinia pseudotuberculosis Type III Secretion System Activity Following Iron Starvation and Anaerobic Growth

Published on: May 31, 2024

Area of Science:

  • Genomics
  • Proteomics
  • Bioinformatics

Background:

  • Automated genome annotation pipelines struggle with accuracy due to the high volume of sequence data.
  • Integrating omics measurements (transcriptomic and proteomic) offers a path to reduce errors in computational genome annotations.
  • Comparative genome assessment across closely related species can enhance annotation refinement.

Purpose of the Study:

  • To develop and demonstrate a comprehensive comparative omic-based annotation methodology.
  • To refine genome annotations of closely related pathogenic Yersiniae species using proteogenomic data.
  • To identify novel and incorrect protein-coding sequences missed by current automated annotation pipelines.

Main Methods:

  • Utilized transcriptomic and proteomic data from three highly similar pathogenic Yersiniae strains (Y. pestis CO92, Y. pestis Pestoides F, and Y. pseudotuberculosis PB1/+).
  • Applied a proteogenomic-based approach to integrate omics measurements with genome sequences for annotation refinement.
  • Conducted comparative assessment of genomes across these closely related species.

Main Results:

  • Experimentally validated expression for nearly 40% of the predicted proteome across the three strains using peptide and oligo measurements.
  • Identified 28 novel protein-coding sequences and 68 incorrect sequences (frameshifts, extended start sites, translated pseudogenes) within existing genome annotations.
  • Discovered several potentially essential genes, including a ribosomal protein, virulence factors, a transcriptional regulator, and numerous hypothetical proteins.

Conclusions:

  • Comparative omic-based annotation significantly improves the accuracy and completeness of genome annotations.
  • The identification of translated pseudogenes highlights the role of gene loss in Yersinia pestis virulence and necessitates further functional analysis.
  • This methodology successfully uncovered previously missed genes crucial for understanding pathogen divergence and function.