%0 Journal Article %A Trevor J. Krabbenhoft %A Thomas F. Turner %T Analytical considerations for comparative transcriptomics of wild organisms %D 2016 %R 10.1101/048652 %J bioRxiv %P 048652 %X Comparative transcriptomics can now be conducted on organisms in natural settings, which has greatly enhanced understanding of genome-environment interactions. However, important data handling and quality control challenges remain, particularly when working with non-model species outside of a controlled laboratory environment. Here, we demonstrate the utility and potential pitfalls of comparative transcriptomics of wild organisms, with an example from three cyprinid fish species (Teleostei:Cypriniformes). We present computational solutions for processing, annotating and summarizing comparative transcriptome data for assessing genome-environment interactions across species. The resulting bioinformatics pipeline addresses the following points: (1) the potential importance of “essential genes”, (2) the influence of microbiomes and other exogenous DNA, (3) potentially novel, species-specific genes, and (4) genomic rearrangements (e.g., whole genome duplication). Quantitative consideration of these points contributes to a firmer foundation for future comparative work across distantly related taxa for a variety of sub-disciplines, including stress and immune response, community ecology, ecotoxicology, and climate change. %U https://www.biorxiv.org/content/biorxiv/early/2016/05/09/048652.full.pdf