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Series GSE111508 Query DataSets for GSE111508
Status Public on Mar 23, 2018
Title Multi-environment fitness landscapes of a tRNA gene
Organism Saccharomyces cerevisiae
Experiment type Genome variation profiling by high throughput sequencing
Summary A fitness landscape (FL) describes the genotype-fitness relationship in a given environment. To explain and predict evolution, it is imperative to measure the FL in multiple environments because the natural environment changes frequently. Using a high-throughput method that combines precise gene replacement with next-generation sequencing, we determine the in vivo FL of a yeast tRNA gene comprising over 23,000 genotypes in four environments. Although genotype-by-environment interaction (G×E) is abundantly detected, its pattern is so simple that we can transform an existing FL to that in a new environment with fitness measures of only a few genotypes in the new environment. Under each environment, we observe prevalent, negatively biased epistasis between mutations (G×G). Epistasis-by-environment interaction (G×G×E) is also prevalent, but trends in epistasis difference between environments are predictable. Our study thus reveals simple rules underlying seemingly complex FLs, opening the door to understanding and predicting FLs in general.
 
Overall design We constructed a library of more than 100,000 yeast strains, each carrying a tR(CCU)J gene variant at its native genomic location. Three to five parallel competitions of this strain pool were conducted in each of four environments: 30°C in the rich medium YPD, 23°C in YPD, 37°C in YPD, and 30°C in YPD with 3% DMSO added.
 
Contributor(s) Li C, Zhang J
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Submission date Mar 07, 2018
Last update date Mar 13, 2019
Contact name Chuan Li
E-mail(s) chuanli@stanford.edu
Organization name Stanford University
Department Biology
Lab Dmitri Petrov lab
Street address 327 Campus Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platforms (1)
GPL13821 Illumina HiSeq 2000 (Saccharomyces cerevisiae)
Samples (5)
GSM3032438 tR(CCU)J_T0
GSM3032439 tR(CCU)J_23C
GSM3032440 tR(CCU)J_30C
Relations
BioProject PRJNA437246
SRA SRP134087

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE111508_FitnessDataMultiEnv.txt.gz 618.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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