Natural populations subjected to strong environmental selection pressures offer a window into the genetic underpinnings of evolutionary change. Cavefish populations, Astyanax mexicanus (Teleostei: Characiphysi), exhibit repeated, independent evolution for a variety of traits including eye degeneration, pigment loss, increased size and number of taste buds and mechanosensory organs, and shifts in many behavioural traits. Surface and cave forms are interfertile making this system amenable to genetic interrogation; however, lack of a reference genome has hampered efforts to identify genes responsible for changes in cave forms of A. mexicanus. Here we present the first de novo genome assembly for Astyanax mexicanus cavefish, contrast repeat elements to other teleost genomes, identify candidate genes underlying quantitative trait loci (QTL), and assay these candidate genes for potential functional and expression differences. We expect the cavefish genome to advance understanding of the evolutionary process, as well as, analogous human disease including retinal dysfunction.
Bibliographical noteFunding Information:
This work was supported by NIH grant R24 RR032658-01 to W.C.W. and The Genome Institute at Washington University School of Medicine. Collections were conducted with Mexican Permit Number 040396-213-03 granted to W.R.J. This work was also supported by the Wellcome Trust (grant numbers WT095908 and WT098051) and the European Molecular Biology Laboratory. Shisa2 qPCR work benefited from the facilities and expertise of the QPCR platform of IMAGIF (Centre de Recherche de Gif-www. imagif.cnrs.fr). This work was supported in part by the National Institutes of Health (NIDCR) grant DE022403 to J.B.G. We thank J. Tabin for technical assistance. We are grateful for resources from the University of Minnesota Supercomputing Institute.
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