Subterranean Fishes of the World

3197

2013

AIM 2013

The blind Mexican tetra, Astyanax mexicanus, is a powerful system for evolutionary and developmental studies owing to our ability to directly compare “ancestral” surface morphs to cave morphs. Utilizing this comparative approach, a wealth of prior research has established that a number of obvious differences in adult phenotype between these two forms arise during embryogenesis. Dramatic differences in gene expression levels likely accompany many of the phenotypic changes occurring during development. To investigate the nature of these expression level differences, we adapted an RNA sequencing (mRNA-seq) approach to assess transcriptome-wide changes occurring during a critical developmental period. We interrogated gene expression changes from pooled RNA derived from groups of whole embryos ranging from 10 hours post-fertilization (hpf) through 3 days post-fertilization (dpf). A prior analysis using normalized next-generation sequencing libraries indicated that many genes in the adult of one morphotype are undetectable in the other morphotype. For instance, cave morphs express a number of genes involved in metabolism that are not evident from surface fish. Conversely, surface fish express a number of genes relevant for the visual system that are not expressed in cavefish. We adopted a similar approach by investigating gene sets from non-normalized libraries, subjected to high-throughput Illumina sequencing, that demonstrated “exclusive” expression in one morphotype but not the other. To understand the function of these groups of genes, we performed enrichment analyses for gene ontology (GO) terms associated with exclusively expressed genes at each developmental stage. As a parallel approach, we also identified and assessed genes associated with a variety of traits categorically defined in past studies as “regressive” or “constructive”. Herein, we sought to determine whether genes associated with these traits demonstrate dramatic gene expression differences between morphotypes. Transcriptome-level studies such as this provide an additional tool for identifying essential genes that accompanied evolution of cave-associated characteristics in the subterranean habitat.

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