Related Experiment Video
Updated: Jul 6, 2026
06:53
In Vivo Monitoring of Transcriptional Activity During Metabolic Transition Using a Bioluminescent Reporter in Yeast
Published on: February 21, 2025
Co-evolutionary rates of functionally related yeast genes
Leonardo Mariño-Ramírez1, Olivier Bodenreider, Natalie Kantz
1National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, U.S.A.
Evolutionary Bioinformatics Online
|March 18, 2008
Summary
Gene evolutionary rates, specifically non-synonymous substitution rates (dN), correlate with gene function in yeast. This finding highlights the utility of evolutionary rates for predicting gene function and understanding natural selection.
Area of Science:
- Evolutionary Biology
- Computational Biology
- Genomics
Background:
- Evolutionary knowledge, particularly gene sequence divergence rates, aids computational gene function prediction.
- Understanding the relationship between evolutionary rates and gene function is crucial for biological research.
Purpose of the Study:
- To perform a genome-scale evaluation of the relationship between evolutionary rates and functional annotations in Saccharomyces cerevisiae.
- To investigate the connection between gene evolutionary rates and function using comparative genomics.
Main Methods:
- Calculated non-synonymous (dN) and synonymous (dS) substitution rates for 1,095 orthologous gene sets across seven yeast species.
- Compared differences in evolutionary rates (DeltadN, DeltadS) with functional similarities (sGO) derived from Gene Ontology annotations.
Main Results:
- Found substantial and significant correlations between DeltadN and sGO, indicating a link between protein-coding sequence evolution and function.
- Observed no apparent relationship between synonymous substitution rates (dS) and functional similarity (sGO).
- The correlation between evolutionary rates and function was stronger than that observed for phylogenetic profiles.
Conclusions:
- Functionally related genes in yeast exhibit co-evolution, suggesting natural selection acts on specific functions.
- Gene evolutionary rates are a valuable tool for predicting gene function, potentially outperforming other methods like phylogenetic profiling.
Related Concept Videos
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...
02:05Gene 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...
01:24Evolution of New Traits in Microbes
Microorganisms evolve rapidly due to their large population sizes and short generation times, often exhibiting measurable changes within days under laboratory conditions. Natural selection acts on standing genetic variation, enabling the retention and amplification of beneficial traits that confer fitness advantages in changing environments.Adaptive Pigment Regulation in RhodobacterIn Rhodobacter, a genus of purple non-sulfur bacteria, light-harvesting pigments such as bacteriochlorophyll and...
03:21Genome Size and the Evolution of New Genes
While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
03:21Genome Size and the Evolution of New Genes
While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
01:24Eukaryotic Evolution
The endosymbiont theory is the most widely accepted theory of eukaryotic evolution; however, its progression is still somewhat debated. According to the nucleus-first hypothesis, the ancestral prokaryote first evolved a membrane to enclose DNA and form the nucleus. Conversely, the mitochondria-first hypothesis suggests that the nucleus was formed after endosymbiosis of mitochondria.
Contrary to the endosymbiont theory, the eukaryote-first hypothesis proposes that the simpler prokaryotic and...
Contrary to the endosymbiont theory, the eukaryote-first hypothesis proposes that the simpler prokaryotic and...