Related Experiment Video
Updated: Jul 21, 2026
12:00
A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
GeneContent: software for whole-genome phylogenetic analysis.
Xun Gu1, Wei Huang, Dongping Xu
1Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA. xgu@iastate.edu
Bioinformatics (Oxford, England)
|December 16, 2004
Summary
GeneContent software infers genome phylogeny using gene content data, analyzing gene family presence, absence, and duplication across species to reveal evolutionary patterns of gene loss and proliferation.
Area of Science:
- Computational Biology
- Genomics
- Evolutionary Biology
Background:
- Gene content data provides genome-wide information including gene family absence, single copy presence, or duplications across multiple species.
- Understanding gene content evolution is crucial for phylogenetic analysis and evolutionary pattern exploration.
Purpose of the Study:
- To introduce GeneContent, a novel software system for inferring genome phylogeny.
- To enable the exploration of genome-wide evolutionary patterns, specifically gene loss and proliferation.
Main Methods:
- Utilizes an additive genome distance estimated from extended gene content data.
- Analyzes genome-wide information on gene family status (absence, single copy, duplicates) across species.
Main Results:
- Successfully infers genome phylogeny based on estimated additive genome distance.
- Provides a framework for exploring evolutionary dynamics of gene content.
Conclusions:
- GeneContent offers a robust method for phylogenetic inference using gene content.
- The system facilitates deeper insights into the evolutionary history of gene loss and gain in genomes.
Related Concept Videos
01:23Phylogeny
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...
02:02Genomics
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...
02:05Gene 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.
In contrast, regions which code...
In contrast, regions which code...
02:54Evolutionary 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...
03:00Next-generation Sequencing
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
02:05Gene 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.
In contrast, regions which code...
In contrast, regions which code...