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

Phylogeny01:23

Phylogeny

56.6K
Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.
56.6K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

6.8K
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...
6.8K
Phylogenetic Trees03:21

Phylogenetic Trees

49.1K
Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
49.1K
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

20.5K
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.
20.5K
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

548
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...
548
Synteny and Evolution02:31

Synteny and Evolution

3.7K
John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral...
3.7K

You might also read

Related Articles

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

Sort by
Same author

The MicrobeAtlas database: Global trends and insights into Earth's microbial ecosystems.

Cell·2026
Same author

Enhanced semantic classification of microbiome sample origins using large language models (LLMs).

GigaScience·2026
Same author

Uncovering Cas9 PAM diversity through metagenomic mining and machine learning.

Nature communications·2026
Same author

Root growth promotion by <i>Penicillium melinii</i> : mechanistic insights and agricultural applications.

bioRxiv : the preprint server for biology·2026
Same author

Community conservatism is widespread across microbial phyla and environments.

Nature ecology & evolution·2026
Same author

PaxDb v6.0: reprocessed, LLM-selected, curated protein abundance data across organisms.

Nucleic acids research·2025

Related Experiment Video

Updated: Jan 9, 2026

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
09:37

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Published on: August 15, 2019

10.3K

eggNOG v7: phylogeny-based orthology predictions and functional annotations.

Ana Hernández-Plaza1, Ziqi Deng1, Fabian Robledo-Yagüe2

  • 1Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo-UPM, 28223 Madrid, Spain.

Nucleic Acids Research
|December 8, 2025
PubMed
Summary
This summary is machine-generated.

The eggNOG v7 database enhances evolutionary gene analysis with a new phylogenetic, domain-centric workflow. This phylogenomic resource improves orthologous group reconstruction and functional annotation accuracy for millions of proteins.

More Related Videos

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

16.4K
A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

36.0K

Related Experiment Videos

Last Updated: Jan 9, 2026

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
09:37

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Published on: August 15, 2019

10.3K
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

16.4K
A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

36.0K

Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • The eggNOG database provides orthology inference and functional annotation across diverse species.
  • Previous versions faced computational and accuracy limitations in orthologous group reconstruction.

Purpose of the Study:

  • To introduce eggNOG v7, featuring a novel phylogenetic, domain-centric workflow.
  • To enhance orthologous group (OG) reconstruction, evolutionary dating, and functional annotation accuracy.

Main Methods:

  • Implemented a domain-centric pipeline involving sequence pre-clustering, multiple sequence alignment, and phylogenetic tree inference.
  • Utilized a noise-tolerant algorithm for speciation and duplication event detection to build hierarchically consistent OGs.
  • Applied the workflow to 59.3 million proteins from 12,535 species.

Main Results:

  • Generated 3.18 million orthologous groups (OGs) with reduced fragmentation and improved consistency compared to previous versions.
  • Demonstrated higher functional consistency against manually curated KEGG OGs.
  • Released updated protein functional annotations and a redesigned web interface with enhanced search and visualization tools.

Conclusions:

  • eggNOG v7 represents a significant advancement in phylogenomic analysis through its robust phylogenetic, domain-centric approach.
  • The new version offers improved accuracy, consistency, and usability for evolutionary and functional genomics research.