|
| Status |
Public on Jul 02, 2017 |
| Title |
Experimental assay of a fitness landscape on a macroevolutionary scale |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Genome variation profiling by high throughput sequencing
|
| Summary |
Characterization of the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted to create functional organisms. Here, we reconstruct the evolutionarily-relevant segment of the fitness landscape of His3, a gene coding for an enzyme in the histidine synthesis pathway, focusing on combinations of amino acid states found at orthologous sites of extant species. We find that the His3 fitness landscape is dominated by synergistic epistasis, such that the cumulative effect of amino acid substitutions causes a dramatic decline in fitness. Furthermore, in 63% of sites substitutions were strongly positive in one genetic background and strongly negative in another, with 41% of sites showing reciprocal sign epistasis. This sign epistasis, present in proportionally few genotypes, was caused by simultaneous interaction of multiple sites with demonstrating a complex multidimensional nature of the His3 fitness landscape.
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| |
|
| Overall design |
PCR amplification of mutated loci inside S. cerevisiae His3 gene.
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| |
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| Contributor(s) |
Pokusaeva VO, Espinar Calvo LM, Usmanova DR, Filion GJ, Carey LB, Kondrashov FA |
| Citation(s) |
30969963 |
| Submission date |
Jun 13, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Guillaume J Filion |
| E-mail(s) |
guillaume.filion@gmail.com
|
| Phone |
+33783006131
|
| Organization name |
UTSC
|
| Department |
Biological Sciences
|
| Street address |
1265 Military Trail
|
| City |
Scarborough |
| State/province |
Ontario |
| ZIP/Postal code |
M1C1A4 |
| Country |
Canada |
| |
|
| Platforms (1) |
| GPL13821 |
Illumina HiSeq 2000 (Saccharomyces cerevisiae) |
|
| Samples (24)
|
|
| Relations |
| BioProject |
PRJNA390287 |
| SRA |
SRP109110 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE99990_RAW.tar |
1.6 Gb |
(http)(custom) |
TAR (of TXT) |
| GSE99990_S01_fitness.txt.gz |
3.3 Mb |
(ftp)(http) |
TXT |
| GSE99990_S02_fitness.txt.gz |
3.2 Mb |
(ftp)(http) |
TXT |
| GSE99990_S03_fitness.txt.gz |
2.6 Mb |
(ftp)(http) |
TXT |
| GSE99990_S04_fitness.txt.gz |
1.9 Mb |
(ftp)(http) |
TXT |
| GSE99990_S05_fitness.txt.gz |
2.8 Mb |
(ftp)(http) |
TXT |
| GSE99990_S06_fitness.txt.gz |
2.2 Mb |
(ftp)(http) |
TXT |
| GSE99990_S07_fitness.txt.gz |
704.3 Kb |
(ftp)(http) |
TXT |
| GSE99990_S08_fitness.txt.gz |
1.7 Mb |
(ftp)(http) |
TXT |
| GSE99990_S09_fitness.txt.gz |
2.1 Mb |
(ftp)(http) |
TXT |
| GSE99990_S10_fitness.txt.gz |
2.2 Mb |
(ftp)(http) |
TXT |
| GSE99990_S11_fitness.txt.gz |
791.8 Kb |
(ftp)(http) |
TXT |
| GSE99990_S12_fitness.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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