Subterranean Fishes of the World

3202

2013

AIM 2013

Astyanax mexicanus, a freshwater fish species native to the northeastern region of Mexico, is an emerging model for the study of regressive evolution due to its support of multiple cave-adapted populations in addition to an ancestral surface population. The geographically isolated cave populations are phenotypically distinct from their surface-dwelling counterparts, having converged on a striking suite of traits including reduced pigmentation and a highly regressed visual system within the confines of a nutrient-poor subterranean environment, though interbreeding remains possible. To address the limited amount of genetic information available for this system, we utilized Roche/454 pyrosequencing for an integrated de novo assembly of the adult A. mexicanus transcriptome, using whole-fish RNA collected from two surface-form fish and two fish from the Pachón cave. 22,596 high-quality contiguous sequences were generated using this approach, then identified using the NCBI’s BlastX database, with the integrated nature of the assembly allowing for rapid identification of sequence polymorphisms between morphotypes. Sequences were assigned a wide variety of Gene Ontology (GO) terms using Blast2Go, indicating that this transcriptome effectively represents the genetic makeup of A. mexicanus. We adapted our dataset for an RNA-seq study to reveal that certain genes showed expression that was exclusive to just one of the morphotypes. We detected the expression of several genes involved in visual system maintenance in surface-form fish that were not expressed in the cave-form fish. Additionally, many genes related to metabolism that showed expression in cavefish, which previous studies have shown to possess more efficient metabolisms, could not be detected in surface fish. Our results serve as a resource that will enable powerful genetic and genomic analyses in the future that will better clarify the heritable genetic changes governing adaptation to the cave environment.

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