ArticleIntegrative zoology2009
Differentially expressed genes identified by cross-species microarray in the blind cavefish Astyanax.
Article in Integrative zoology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 23 citations in OpenAlex.
- Microstructure and transcriptomics reveal rapid light-induced visual plasticity in the non-obligate cave dweller Oreolalax rhodostigmatus (Megophryidae, Anura).BMC genomics · 2025Article
- Parallel and convergent dynamics in the evolution of primary breast and lung adenocarcinomas.Communications biology · 2025Article
- Reduced adult stem cell fate specification led to eye reduction in cave planarians.Nature communications · 2025Article
- Dark-rearing uncovers novel gene expression patterns in an obligate cave-dwelling fish.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2020Article
- Dual roles of the retinal pigment epithelium and lens in cavefish eye degeneration.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2020Article
- Comparative Transcriptome Profiling of the LoachesFrontiers in genetics · 2019Article
- A Comparative Transcriptomic Analysis of Development in Two Astyanax Cavefish Populations.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2017Article
- Article
- Evolution of the eye transcriptome under constant darkness in Sinocyclocheilus cavefish.Molecular biology and evolution · 2013Article
- Differentially-expressedCurrent zoology · 2013Article
- Quantitative genetic analysis of retinal degeneration in the blind cavefish Astyanax mexicanus.PloS one · 2013Article
- An integrated transcriptome-wide analysis of cave and surface dwelling Astyanax mexicanus.PloS one · 2013Article
- Comparative genetics of the central nervous system in epigean and hypogean Astyanax mexicanus.Genetica · 2011Article
- Regressive evolution in Astyanax cavefish.Annual review of genetics · 2009Review
- Chapter 8. Evolution and development in the cavefish Astyanax.Current topics in developmental biology · 2009Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Changes in gene expression were examined by microarray analysis during development of the eyed surface dwelling (surface fish) and blind cave-dwelling (cavefish) forms of the teleost Astyanax mexicanus De Filippi, 1853. The cross-species microarray used surface and cavefish RNA hybridized to a DNA chip prepared from a closely related species, the zebrafish Danio rerio Hamilton, 1822. We identified a total of 67 differentially expressed probe sets at three days post-fertilization: six upregulated and 61 downregulated in cavefish relative to surface fish. Many of these genes function either in eye development and/or maintenance, or in programmed cell death. The upregulated probe set showing the highest mean fold change was similar to the human ubiquitin specific protease 53 gene. The downregulated probe sets showing some of the highest fold changes corresponded to genes with roles in eye development, including those encoding gamma crystallins, the guanine nucleotide binding proteins Gnat1 and Gant2, a BarH-like homeodomain transcription factor, and rhodopsin. Downregulation of gamma-crystallin and rhodopsin was confirmed by in situ hybridization and immunostaining with specific antibodies. Additional downregulated genes encode molecules that inhibit or activate programmed cell death. The results suggest that cross-species microarray can be used for identifying differentially expressed genes in cavefish, that many of these genes might be involved in eye degeneration via apoptotic processes, and that more genes are downregulated than upregulated in cavefish, consistent with the predominance of morphological losses over gains during regressive evolution.
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