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

Evolutionary Relationships through Genome Comparisons02:54

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...
Bioreactor Controls-III01:22

Bioreactor Controls-III

Strain improvement is a foundational strategy in industrial microbiology aimed at maximizing microbial productivity, particularly because natural isolates typically yield commercially valuable products in very low concentrations. Although optimizing the culture medium and environmental conditions can improve yields, these adjustments are inherently limited by the organism’s genetic potential. As a result, the focus shifts toward genetic modifications to enhance biosynthetic capacity. The...

You might also read

Related Articles

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

Sort by
Same author

Allostery is a widespread cause of loss-of-function variant pathogenicity.

Nature communications·2026
Same author

Evolution of an Aurora Kinase A Inhibitor from an Essential tRNA Synthetase.

bioRxiv : the preprint server for biology·2026
Same author

Seven complete comparative maps of allosteric mutations in a protein family.

Nature communications·2026
Same author

The genetic architecture of an allosteric hormone receptor.

Nature communications·2026
Same author

Allosteric and energetic remodeling of a PDZ domain by protein domain extensions.

Nature communications·2026
Same author

The allosteric landscape of the Src kinase.

Science advances·2026

Related Experiment Video

Updated: May 27, 2026

High Throughput Yeast Strain Phenotyping with Droplet-Based RNA Sequencing
07:55

High Throughput Yeast Strain Phenotyping with Droplet-Based RNA Sequencing

Published on: May 21, 2020

Predicting phenotypic variation in yeast from individual genome sequences.

Rob Jelier1, Jennifer I Semple, Rosa Garcia-Verdugo

  • 1European Molecular Biology Laboratory, Centre for Genomic Regulation, Systems Biology Research Unit, Barcelona, Spain.

Nature Genetics
|November 15, 2011
PubMed
Summary

Predicting yeast (Saccharomyces cerevisiae) traits from genomes is challenging. Our study shows conservation-based methods can predict phenotypic variation, achieving 0.76 accuracy, especially when key genes are functionally connected.

More Related Videos

Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis
10:08

Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis

Published on: August 12, 2019

BEST: Barcode Enabled Sequencing of Tetrads
12:59

BEST: Barcode Enabled Sequencing of Tetrads

Published on: May 1, 2014

Related Experiment Videos

Last Updated: May 27, 2026

High Throughput Yeast Strain Phenotyping with Droplet-Based RNA Sequencing
07:55

High Throughput Yeast Strain Phenotyping with Droplet-Based RNA Sequencing

Published on: May 21, 2020

Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis
10:08

Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis

Published on: August 12, 2019

BEST: Barcode Enabled Sequencing of Tetrads
12:59

BEST: Barcode Enabled Sequencing of Tetrads

Published on: May 1, 2014

Area of Science:

  • Genetics and Genomics
  • Systems Biology
  • Computational Biology

Background:

  • Predicting phenotypic variation from genome sequences is a central challenge in genetics.
  • Understanding genotype-phenotype relationships is crucial for various biological applications.

Purpose of the Study:

  • To construct and evaluate phenotypic predictions for Saccharomyces cerevisiae strains using genome sequences.
  • To assess the accuracy of conservation-based methods in predicting gene function impact and resulting phenotypes.

Main Methods:

  • Utilized conservation-based approaches to predict the functional impact of protein-coding variations.
  • Developed a prediction score based on the sum of function-altering changes in relevant gene sets.
  • Evaluated predictions against experimentally observed growth rates and efficiencies across multiple conditions.

Main Results:

  • Achieved a median predictive performance (ROC AUC) of 0.76 across 15 Saccharomyces cerevisiae strains and 20 conditions.
  • Prediction accuracy improved when genes influencing a trait exhibited high connectivity within a functional gene network.

Conclusions:

  • Conservation-based methods offer a viable strategy for predicting phenotypic variation from genomic data in Saccharomyces cerevisiae.
  • The interconnectedness of genes within functional networks is a key factor influencing the accuracy of these predictions.