Subterranean Fishes of the World

3281

2017

AIM 2017

Elucidating the physiological mechanisms of adaptation to different environmental condition remains a major task, especially in non-model organisms. High-throughput sequencing technologies have transformed the quantification of genome-wide gene expression patterns in natural systems through the use of RNA-seq. Here, we performed an RNA-seq study on three different organs of fish adapted to H2S rich environments and caves to quantify patterns of gene expression. We specifically asked: (1) How do gene expression and functional responses vary among populations and organs? (2) Is there evidence of shared expression responses in populations exposed to the same environments, and how do shared responses vary among levels of organization? (3) What inferences can analyses of differential expression provide about potential molecular mechanisms underlying adaptation? To address this, we assembled and annotated transcriptomes of Poecilia mexicana based on transcripts from 16 wild-caught individuals with four individuals and three tissue types per ecotype. We mapped all reads to the Poecilia mexicana genome and identified variation in gene expression patterns between ecotypes and tissues. We uncovered rampant variation in gene expression. Organ type was the major driver of expression among samples illuminating the importance of choosing focal organs in the study of gene expression in nature. We also identified variation in the amount of shared differentially expressed genes, where shared responses increased with level of biological organization. Nonetheless, shared responses were more common in the sulfidic habitats, highlighting the effects of H2S on gene regulation. Overall, our analyses provided insights into transcriptional variation in a unique system with coinciding sources of selection, and functional annotation of differentially expressed genes provide a springboard for investigating physiological modifications associated with adaptation to extreme environments.

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