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Series GSE81320 Query DataSets for GSE81320
Status Public on Jul 01, 2017
Title Intra- and inter-specific variations of gene expression levels in yeast are largely neutral
Organisms Saccharomyces cerevisiae; Saccharomyces paradoxus; Saccharomyces mikatae
Experiment type Expression profiling by high throughput sequencing
Summary It is commonly, although not universally, accepted that most intra- and inter-specific genome sequence variations are more or less neutral, whereas a large fraction of organism-level phenotypic variations are adaptive.  Gene expression levels are molecular phenotypes that bridge the gap between genotypes and corresponding organism-level phenotypes.  Yet, it is unknown whether natural variations in gene expression levels are mostly neutral or adaptive.  Here we address this fundamental question by genome-wide profiling and comparison of gene expression levels in nine yeast strains belonging to three closely related Saccharomyces species and originating from five different ecological environments.
Overall design To answer whether variations in gene expression levels within and between species are largely neutral or adaptive, we compared the transcriptomes of nine yeast strains belonging to three closely related species sampled from five different ecological environments. Importantly, we selected strains such that their genomic phylogenetic relationships mismatch their relationships at the environmental level. For instance, some strains are phylogenetically relatively distant from one another but have similar ecological environments, whereas others are phylogenetically relatively close to one another but live in ecologically distinct environments. If gene expression variations among these strains result from the accumulation of neutral mutations, the relationships of their transcriptomes should mimic the genome-based phylogenetic tree. On the contrary, if the expression variations among these strains are largely shaped by adaptations to their respective environments, their transcriptomes should cluster according to their ecological environments. Thus, our design allows a distinction between the neutral and adaptive hypotheses. Raw short read data available on SRA under accession SRP074509.
Contributor(s) Zhang J, Yang J
Citation(s) 28575451
BioProject PRJNA320926
Submission date May 11, 2016
Last update date May 15, 2019
Contact name Jian-Rong Yang
Organization name Sun Yat-sen University
Street address No. 74, Zhongshan 2nd Road
City Guangzhou
ZIP/Postal code 510080
Country China
Platforms (3)
GPL9377 Illumina Genome Analyzer II (Saccharomyces cerevisiae)
GPL21861 Illumina Genome Analyzer II (Saccharomyces mikatae)
GPL21862 Illumina Genome Analyzer II (Saccharomyces paradoxus)
Samples (10)
GSM2150319 IFO1815
GSM2150320 N17
GSM2150321 N44
SRA SRP074509

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE81320_RAW.tar 370.0 Kb (http)(custom) TAR (of TXT)
GSE81320_allExpr.matrix.txt.gz 235.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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