| Title |
De Novo Sequencing of Astyanax mexicanus Surface Fish and Pachón Cavefish Transcriptomes Reveals Enrichment of Mutations in Cavefish Putative Eye Genes
|
|---|---|
| Published in |
PLOS ONE, January 2013
|
| DOI | 10.1371/journal.pone.0053553 |
| Pubmed ID | |
| Authors |
Hélène Hinaux, Julie Poulain, Corinne Da Silva, Céline Noirot, William R. Jeffery, Didier Casane, Sylvie Rétaux |
| 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. |
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Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Mexico | 1 | 17% |
| United States | 1 | 17% |
| United Kingdom | 1 | 17% |
| Unknown | 3 | 50% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 4 | 67% |
| Scientists | 1 | 17% |
| Science communicators (journalists, bloggers, editors) | 1 | 17% |
Mendeley readers
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Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United Kingdom | 2 | 2% |
| United States | 2 | 2% |
| Spain | 1 | <1% |
| Italy | 1 | <1% |
| Unknown | 96 | 94% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 26 | 25% |
| Researcher | 20 | 20% |
| Student > Master | 13 | 13% |
| Professor > Associate Professor | 6 | 6% |
| Student > Bachelor | 6 | 6% |
| Other | 17 | 17% |
| Unknown | 14 | 14% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 52 | 51% |
| Biochemistry, Genetics and Molecular Biology | 16 | 16% |
| Environmental Science | 5 | 5% |
| Neuroscience | 4 | 4% |
| Arts and Humanities | 1 | <1% |
| Other | 4 | 4% |
| Unknown | 20 | 20% |