May 9, 2016

Analytical considerations for comparative transcriptomics of wild organisms.

BioRxiv : the Preprint Server for Biology
Trevor J Krabbenhoft, Thomas F Turner

Abstract

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.

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Mentioned in this Paper

Immune Response
Genome
Genes
Cyprinidae
Environment
Genome Assembly Sequence
Bio-Informatics
Laboratory
Cytochrome-c Oxidase Deficiency
Genomics

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