De Novo Sequencing of Astyanax mexicanus Surface Fish and Pachón Cavefish Transcriptomes Reveals Enrichment of Mutations in Cavefish Putative Eye Genes
Open Access
- 9 January 2013
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLOS ONE
- Vol. 8 (1), e53553
- https://doi.org/10.1371/journal.pone.0053553
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.Keywords
This publication has 39 references indexed in Scilit:
- Gene flow and population structure in the Mexican blind cavefish complex (Astyanax mexicanus)BMC Ecology and Evolution, 2012
- Ensembl 2012Nucleic Acids Research, 2011
- Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiationBMC Ecology and Evolution, 2011
- MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony MethodsMolecular Biology and Evolution, 2011
- Quality control and preprocessing of metagenomic datasetsBioinformatics, 2011
- CDD: a Conserved Domain Database for the functional annotation of proteinsNucleic Acids Research, 2010
- ZFIN: enhancements and updates to the zebrafish model organism databaseNucleic Acids Research, 2010
- Evolution of a Behavioral Shift Mediated by Superficial Neuromasts Helps Cavefish Find Food in DarknessCurrent Biology, 2010
- Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 EnhancerScience, 2010
- Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics researchBioinformatics, 2005