Expression divergence measured by transcriptome sequencing of four yeast species.
BACKGROUND
The evolution of gene expression is a challenging problem in evolutionary biology, for which accurate, well-calibrated measurements and methods are crucial.


RESULTS
We quantified gene expression with whole-transcriptome sequencing in four diploid, prototrophic strains of Saccharomyces species grown under the same condition to investigate the evolution of gene expression. We found that variation in expression is gene-dependent with large variations in each gene's expression between replicates of the same species. This confounds the identification of genes differentially expressed across species. To address this, we developed a statistical approach to establish significance bounds for inter-species differential expression in RNA-Seq data based on the variance measured across biological replicates. This metric estimates the combined effects of technical and environmental variance, as well as Poisson sampling noise by isolating each component. Despite a paucity of large expression changes, we found a strong correlation between the variance of gene expression change and species divergence (R² = 0.90).


CONCLUSIONS
We provide an improved methodology for measuring gene expression changes in evolutionary diverged species using RNA Seq, where experimental artifacts can mimic evolutionary effects.GEO Accession Number: GSE32679.
Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467-3961, USA.
Michele A
MA
Busby
Jesse M
JM
Gray
Allen M
AM
Costa
Chip
C
Stewart
Michael P
MP
Stromberg
Derek
D
Barnett
Jeffrey H
JH
Chuang
Michael
M
Springer
Gabor T
GT
Marth
D016133:Polymerase Chain Reaction; D012440:Saccharomyces / Q000145:classification / Q000235:genetics*; D013045:Species Specificity; D059467:Transcriptome