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Gene Families

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...

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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...

Gene Evolution - Fast or Slow?

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
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The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...

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Related Experiment Video

Updated: May 27, 2025

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

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Published on: December 22, 2017

OrthoBrowser: gene family analysis and visualization.

Nolan T Hartwick¹, Todd P Michael¹

¹The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, United States.

Bioinformatics Advances

|February 17, 2025

Summary

OrthoBrowser simplifies the visualization and exploration of gene families across species. This tool enhances the usability of comparative genomics analyses, making evolutionary dynamics more accessible.

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Area of Science:

Comparative genomics
Evolutionary biology
Bioinformatics

Background:

Analyzing gene families across species is crucial for understanding evolutionary dynamics and functional genomics.
Current methods often demand substantial computational resources and user expertise.

Purpose of the Study:

To introduce OrthoBrowser, a novel static site generator designed to enhance the accessibility and usability of comparative genomic data.
To provide a user-friendly interface for exploring gene family evolution and synteny.

Main Methods:

OrthoBrowser is a static site generator that indexes and visualizes phylogenetic trees, gene trees, multiple sequence alignments, and multiple synteny alignments.
It employs a progressive hierarchical alignment approach in protein space, leveraging orthogroup membership for orthology determination.
The system is designed to scale to hundreds of genomes and allows users to filter and "zoom in" on specific subsets or subtrees.

Main Results:

OrthoBrowser significantly improves the visual accessibility of detailed results from tools like OrthoFinder.
It enables users to easily identify, interact with, explore, and share information on gene families.
The tool supports interactive filtering of large genomic datasets and exploration of orthogroup subtrees.

Conclusions:

OrthoBrowser offers a powerful and accessible solution for the analysis and visualization of gene families.
It democratizes the exploration of evolutionary dynamics and functional genomic landscapes for researchers.
The tool is readily available and easy to implement for comparative genomic studies.