Abstract
BackgroundThe evolution of gene expression is a challenging problem in evolutionary biology, for which accurate, well-calibrated measurements and methods are crucial.ResultsWe 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).ConclusionWe 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
Highlights
The evolution of gene expression is a challenging problem in evolutionary biology, for which accurate, well-calibrated measurements and methods are crucial
We grew two independent cultures of each the following prototophic, diploid strains: S. cerevisiae (FY4 (MAT a) and FY5 (MAT alpha) [16] which we mated to get a diploid, S. paradoxus (Y-17217), S. mikatae (IFO1815), and S. bayanus (MCYC623) according to the protocols described in Methods
The reference genome and annotations for S. cerevisiae were downloaded from the Saccharomyces Genome Database
Summary
The evolution of gene expression is a challenging problem in evolutionary biology, for which accurate, well-calibrated measurements and methods are crucial. Previous studies have found that gene expression diverges as the distance between species increases, and that this divergence is linearly related to the time since divergence (Reviewed in [1]) This expression evolution has been reported to be slow enough that orthologous genes still have highly correlated expression, even in species that diverged up to 400 million years ago [2,3]. The gross inter-species measurement of gene expression by RNA-Seq contains four components: (1) true inter-species gene expression difference; (2) expression differences caused by environmental variance; (3) variance from technical measurement imprecision; and (4) Poisson sampling noise Because of these alternate sources of variance, it is possible for a gene without true interspecies gene expression changes to be measured with different values in different species
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