Expression divergence measured by transcriptome sequencing of four yeast species

• Published in: BMC genomics 2011-12, Vol.12 (1), p.635-635, Article 635
• Main Authors: Busby, Michele A, Gray, Jesse M, Costa, Allen M, Stewart, Chip, Stromberg, Michael P, Barnett, Derek, Chuang, Jeffrey H, Springer, Michael, Marth, Gabor T
• Format: Article
• Language: English
• Subjects: Comparative transcriptomics; Confidence intervals; Data processing; Diploids; DNA sequencing; Evolution; Gene expression; Genetic aspects; Genetic transcription; Genetics; Genomes; Genomics; Methods; Neurosciences; Nucleotide sequencing; Polymerase Chain Reaction; RNA; RNA-Seq; S. bayanus; S. cerevisiae; S. mikatae; S. paradoxus; Saccharomyces; Saccharomyces - classification; Saccharomyces - genetics; Sampling; Species Specificity; Statistics; Transcriptome; Yeast fungi
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/1471-2164-12-635

The evolution of gene expression is a challenging problem in evolutionary biology, for which accurate, well-calibrated measurements and methods are crucial. 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). 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.