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De novo sequencing of Astyanax mexicanus surface fish and Pachón cavefish transcriptomes reveals enrichment of mutations in cavefish putative eye genes.
- Source :
-
PloS one [PLoS One] 2013; Vol. 8 (1), pp. e53553. Date of Electronic Publication: 2013 Jan 09. - Publication Year :
- 2013
-
Abstract
- 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 Pachón 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.
- Subjects :
- Amino Acid Sequence
Animals
Base Sequence
Codon, Terminator genetics
Fish Proteins chemistry
Fish Proteins genetics
Gene Expression Regulation
Gene Library
Molecular Sequence Annotation
Molecular Sequence Data
Polymorphism, Genetic
RNA, Messenger genetics
RNA, Messenger metabolism
Caves
Characiformes genetics
Eye metabolism
Mutation genetics
Sequence Analysis, DNA methods
Transcriptome genetics
Subjects
Details
- Language :
- English
- ISSN :
- 1932-6203
- Volume :
- 8
- Issue :
- 1
- Database :
- MEDLINE
- Journal :
- PloS one
- Publication Type :
- Academic Journal
- Accession number :
- 23326453
- Full Text :
- https://doi.org/10.1371/journal.pone.0053553