Meeting Abstract
Extreme environments frequently yield extreme characteristics in their inhabitants. The complex genetic changes that underlie these traits remain largely unknown. One extreme environment is the cave, which is marked by the complete absence of light. Here, we evaluate how varying lighting conditions influence gene expression in the blind Mexican cavefish, Astyanax mexicanus. These freshwater fish reside in 29 cave localities and countless surface localities in NE Mexico. Prior transcriptomic studies in this system have not accounted for photic rearing differences. To address this, we raised several cave and surface fish under 12:12hr light/dark conditions (“surface-like”, LD) or constant darkness (“cave-like”, DD) for 5+ years. Total RNA was extracted from head tissue, and poly-A primed, and subjected to Illumina HiSeq 2500 RNA-sequencing to a depth of ~10 million reads. Raw reads were aligned to the draft A. mexicanus genome to evaluate expression of 25,271 predicted genes. Intra-morphotypic gene expression changes were well correlated (R2=0.9599), however analyses of morphotypes under their “natural” lighting conditions (CDDxSLD) yielded dramatic expression level differences (R2=0.8597). A GO term analysis revealed many gene expression differences associated with ‘metabolism’ and ‘response to stimuli’. Moreover, several uniquely expressed genes were identified, which may inform how cave animals are able to survive life in total darkness. In sum, this work reveals dramatic changes in the RNA architecture of cave and surface fish raised under different lighting conditions. This gene expression analysis, paired with genetic association studies, will help inform how complex changes to the genome enable organisms to adapt to extreme environments.
