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

Gene Families

Gene Families

Homologous Recombination

Homologous Recombination

Polytene Chromosomes

Polytene Chromosomes

Evolutionary Relationships through Genome Comparisons

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...

Phylogeny

Phylogeny

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.

Phylogenetic Trees

Phylogenetic Trees

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.

You might also read

Related Articles

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

Sort by

Same author

An overview of computational methods for gene prediction in eukaryotes: strengths, limitations, and future directions.

Bioinformatics advances·2025

Same author

TranscriptDB: a transcript-centric database to study eukaryotic transcript conservation and evolution.

Nucleic acids research·2024

Same author

SimSpliceEvol2: alternative splicing-aware simulation of biological sequence evolution and transcript phylogenies.

BMC bioinformatics·2024

Same author

Median and small parsimony problems on RNA trees.

Bioinformatics (Oxford, England)·2024

Same author

Toward a Better Understanding of G4 Evolution in the 3 Living Kingdoms.

Evolutionary bioinformatics online·2023

Same author

OpenProt 2.0 builds a path to the functional characterization of alternative proteins.

Nucleic acids research·2023

Same journal

Mosquito Species and Gender Identification System Based on Artificial Intelligence and Image Processing Methods.

Journal of computational biology : a journal of computational molecular cell biology·2026

Same journal

GMSA: A Graph Matching and Point Cloud Registration-Based Method for Spatial Transcriptomics Data Alignment.

Journal of computational biology : a journal of computational molecular cell biology·2026

Same journal

Investigations on Multiple Protein Scaffold Filling.

Journal of computational biology : a journal of computational molecular cell biology·2026

Same journal

Cell Type Prediction for Single-Cell RNA Sequencing Utilizing Unsupervised Domain Adaptation and Semi-Supervised Learning.

Journal of computational biology : a journal of computational molecular cell biology·2026

Same journal

PPIGAN: Prediction of Protein-Protein Interactions Using Generative Adversarial Networks.

Journal of computational biology : a journal of computational molecular cell biology·2026

Same journal

Deep Structure-Enhanced Cell Clustering Model for Single-Cell RNA Sequencing Data.

Journal of computational biology : a journal of computational molecular cell biology·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jun 28, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Orthology and Paralogy Relationships at Transcript Level.

Wend Yam D D Ouedraogo¹, Aida Ouangraoua¹

¹Department of Computer Science, Université de Sherbrooke, Sherbrooke, Quebec, Canada.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology

|April 15, 2024

Summary

This summary is machine-generated.

This study defines orthology and paralogy for transcripts, developing an algorithm to cluster conserved homologous transcripts. This method aids in understanding transcriptome diversity and evolutionary relationships between gene families.

Keywords:

isoorthology orthology and paralogy transcript phylogeny transcriptome

More Related Videos

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Related Experiment Videos

Last Updated: Jun 28, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Area of Science:

Molecular Biology
Bioinformatics
Evolutionary Genetics

Background:

Eukaryotic gene alternative processing generates transcriptome diversity, producing multiple transcripts from a single gene.
Over half of human genes are affected by alternative processing, with conserved transcripts across species.
Understanding transcript homology is crucial for deciphering gene evolution and function.

Purpose of the Study:

To define orthology and paralogy for transcripts of homologous genes.
To develop an algorithm for clustering conserved orthologous and paralogous transcripts.
To explore transcript conservation beyond strict orthologs.

Main Methods:

Utilized gene-level homology to define transcript homology relationships.
Employed a Reciprocal Best Hits approach for inferring isoorthologous and paralogous transcript clusters.
Applied the algorithm to simulated and Ensembl-Compara real gene families.

Main Results:

Successfully computed clusters of conserved orthologous and paralogous transcripts.
Results align with previous studies comparing orthologous gene transcripts.
Demonstrated the value of searching for conserved transcripts among homologous genes, not just orthologs.

Conclusions:

The developed algorithm effectively clusters conserved homologous transcripts.
Findings support the significance of alternative processing in generating transcriptome diversity.
Investigating transcript conservation across homologous genes offers valuable evolutionary insights.