Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1153026 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:we report a transcriptome-wide comparative investigation between surface and cave species in Sinocyclocheilus. De novo transcriptome assemblies were performed on surface and cave species; then the Sinocyclocheilus contigs were annotated with Gene Ontology. RNA-Seq assays revealed reduced transcription of a series of visual phototransduction and retinal disease related genes in cave-dwelling species compared with surface species. Degeneration of the retina in Sinocyclocheilus cavefish might occur in a lens-independent way by the down-regulation of several transcriptional factors, which have direct roles in retina development and maintenance, such as crx, rorb and Wnt pathway members. Examination of 2 different eye samples in 2 Sinocyclocheilus species.
2013-03-31 | E-GEOD-40446 | biostudies-arrayexpress
Project description:we report a transcriptome-wide comparative investigation between surface and cave species in Sinocyclocheilus. De novo transcriptome assemblies were performed on surface and cave species; then the Sinocyclocheilus contigs were annotated with Gene Ontology. RNA-Seq assays revealed reduced transcription of a series of visual phototransduction and retinal disease related genes in cave-dwelling species compared with surface species. Degeneration of the retina in Sinocyclocheilus cavefish might occur in a lens-independent way by the down-regulation of several transcriptional factors, which have direct roles in retina development and maintenance, such as crx, rorb and Wnt pathway members.
2013-03-31 | GSE40446 | GEO
Project description:We found higher substitution rates in cavefish compared with surface fish, in accordance with a smaller cavefish population size which has allowed more rapid fixation of derived alleles present in the ancestral population. This result also implies that the Pachn cave population is much younger than previously estimated. The comparison of these data with simulations suggests that the Pachn cavefish population has probably been underground less than 30,000 years. This new time frame, together with other evidence, indicate that the evolution of cave phenotypes mainly involves the fixation of cryptic genetic variants present in surface fish populations within a short period of time.
2016-06-27 | E-MTAB-5142 | biostudies-arrayexpress
Project description:The muscle composition of cave dwelling and surface fish was analyzed by proteomics. Specifically, the composition of the myosin heavy chain was determined by in-gel digestion followed by reversed phase LC-MS/MS. The proteome of the different muscle types was analyzed by tandem mass tags and phosphorylation differences were determined by enriching for the modification.
2021-02-12 | MSV000086857 | MassIVE
Project description:Studying how different genotypes respond to environmental variation is essential to understand the genetic basis of adaptation. The Mexican tetra, Astyanax mexicanus, has cave and surface‐dwelling morphotypes that have adapted to entirely different environments in the wild, and are now successfully maintained in lab conditions. While this has enabled the identification of genetic adaptations underlying a variety of physiological processes, few studies have directly compared morphotypes between lab‐reared and natural populations. Such comparative approaches could help dissect the varying effects of environment and morphotype, and determine the extent to which phenomena observed in the lab are generalizable to conditions in the field. To this end, we take a transcriptomic approach to compare the Pachón cavefish and their surface fish counterparts in their natural habitats and the lab environment. We identify key changes in expression of genes implicated in metabolism and physiology between groups of fish, suggesting that morphotype (surface or cave) and environment (natural or lab) both alter gene expression. We find gene expression differences between cave and surface fish in their natural habitats are much larger than differences in expression between morphotypes in the lab environment. However, lab‐raised cave and surface fish still exhibit numerous gene expression changes, supporting genetically encoded changes in livers of this species. From this, we conclude that a controlled laboratory environment may serve as an ideal setting to study the genetic underpinnings of metabolic and physiological differences between the cavefish and surface fish.
2020-02-19 | GSE139490 | GEO
Project description:O. rhodostigmatus are non-obligative cave dwellers, whose tadpoles keep albinistic phenotype in caves but rapidly darken in light within 24 hours. Their coloration system is an excellent model for exploring the processes and mechanisms of light-induced pigmentation and revealing the genetic adaptation for non-obligative cave dwelling due to complicated life history. Using comparative transcriptomics, we found that melanocyte MCC (including melanogenesis and melanocytes proliferation) was responsible for the rapid skin darkening in was activated in O. rhodostigmatus. Light exposure induced robust activation of growth signals (including growth factor signals, MAPK signal pathways and PIK3-Akt signal pathways) at transcriptional levels, which were likely the upstream activation signals of melanocyte MCC in O. rhodostigmatus tadpoles. These results evidenced that amphibians and mammals likely share similar regulatory signals for light-induced melanocyte MCC. The conservation of pigmentation mechanisms across lower vertebrates and mammals imply that knowledge based on simpler models could also provide implications for causations and therapies of human pigmentation disorders and pigmented tumors. In aspect of genetic adaptation, an in-frame deletion of four amino acids in the membrane/extracellular junctions of the second and third transmembrane domains of O. rhodostigmatus MC1R, the receptor for melanogenesis signal, was identified. This mutation increases the negative charge of the ligand pocket of MC1R and results stereo-tandem of three aspartate residues aligning towards its ligand pocket. The ligand pocket of O. rhodostigmatus MC1R resembles a trap for positively charged ligands (α-MSH and ACTH) and likely increases the ligands-dependent activity of MC1R, providing an explanation for the rapid MCC of O. rhodostigmatus in light. Meanwhile, increased negative charge of ligand pocket likely decreased the constitutive activity of MC1R, in in supporting the albinistic phenotype of cave dwelling tadpoles. Therefore, genetic change of MC1R explains, at least to some extent, how the pigmentation system of O. rhodostigmatus coordinates the capacity of rapid melanogenesis (or other types of pigment production) and pigment regression, a couple of seemingly contradictory coloration requirements. To our knowledge, this is the first study reporting the association between pigmentation phenotype adaptation and MC1R mutations in amphibians or in non-obligative cave dwellers.
2018-06-07 | GSE106622 | GEO
Project description:cave-dwelling Leptonetela species. Raw sequence reads
| PRJNA912070 | ENA