De Novo Sequencing of Astyanax mexicanus Surface Fish and Pachon Cavefish Transcriptomes Reveals Enrichment of Mutations in Cavefish Putative Eye Genes
- Authors
- Hinaux, H., Poulain, J., Da Silva, C., Noirot, C., Jeffery, W.R., Casane, D., and Retaux, S.
- ID
- ZDB-PUB-130125-15
- Date
- 2013
- Source
- PLoS One 8(1): e53553 (Journal)
- Registered Authors
- Casane, Didier, Jeffery, William R.
- Keywords
- none
- MeSH Terms
-
- Amino Acid Sequence
- Animals
- Base Sequence
- Caves*
- Characiformes/genetics*
- Codon, Terminator/genetics
- Eye/metabolism*
- Fish Proteins/chemistry
- Fish Proteins/genetics
- Gene Expression Regulation
- Gene Library
- Molecular Sequence Annotation
- Molecular Sequence Data
- Mutation/genetics*
- Polymorphism, Genetic
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Sequence Analysis, DNA/methods*
- Transcriptome/genetics*
- PubMed
- 23326453 Full text @ PLoS One
Astyanax mexicanus, a teleost species with surface dwelling (surface fish) and cave adapted (cavefish) morphs, is an important model system in evolutionary developmental biology (evodevo). Astyanax cavefish differ from surface fish in numerous traits, including the enhancement of non-visual sensory systems, and the loss of eyes and pigmentation. The genetic bases for these differences are not fully understood as genomic and transcriptomic data are lacking. We here present de novo transcriptome sequencing of embryonic and larval stages of a surface fish population and a cavefish population originating from the Pachon cave using the Sanger method. This effort represents the first large scale sequence and clone resource for the Astyanax research community. The analysis of these sequences show low levels of polymorphism in cavefish compared to surface fish, confirming previous studies on a small number of genes. A high proportion of the genes mutated in cavefish are known to be expressed in the zebrafish visual system. Such a high number of mutations in cavefish putative eye genes may be explained by relaxed selection for vision during the evolution in the absence of light. Based on these sequence differences, we provide a list of 11 genes that are potential candidates for having a role in cavefish visual system degeneration.