Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1007611 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25708943_1.fastq.gz | Fastqsanger.gz | |||
| SRR25708943_2.fastq.gz | Fastqsanger.gz | |||
| SRR25708944_1.fastq.gz | Fastqsanger.gz | |||
| SRR25708944_2.fastq.gz | Fastqsanger.gz | |||
| SRR25708945_1.fastq.gz | Fastqsanger.gz |
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Project description:Anableps anableps (Largescale four-eyed fish) genome, fAnaAna1, primary haplotype
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Project description:Anableps anableps (Largescale four-eyed fish) genome, fAnaAna1, alternate haplotype
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Project description:Evolutionary remodeling of the ventral retina enables aerial vision in the four-eyed fish Anableps anableps
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Project description:The emergence of evolutionary novelties remains a central challenge in biology, particularly for complex organs such as the vertebrate eye. While visual systems have repeatedly undergone degeneration or loss, examples of innovation are rare and poorly understood. Mechanistic insight into such gains requires tractable systems in which novel visual functions have evolved. Here we leverage the four-eyed fish Anableps anableps to uncover the cellular and molecular basis of adaptation to simultaneous aerial and aquatic light. Combining single-nucleus and spatial transcriptomics, we show that the Anableps ventral retina has been developmentally and functionally reconfigured for aerial vision. In fully aquatic teleosts such as zebrafish, ventral photoreceptors are tuned to red-shifted, downwelling light. In contrast, we show that Anableps exhibits an expanded and diversified ventral cone population encompassing ultraviolet-, blue-, green-, and red-sensitive types, enabling broad-spectrum, high-intensity vision from above water. To estimate Anableps opsin spectral properties, we employed OPTICS, a machine-learning model of opsin spectral tuning, which predicts that the ventrally expressed opn1mw2 opsin is red-shifted relative to typical green-sensitive pigments. Analysis of dorsal-ventral patterning markers reveals an overrepresentation of ventral retinal cell types. Consistent with this, comparative spatial transcriptomic profiling of developing and adult Anableps and the killifish (Fundulus heteroclitus) indicates a dorsal displacement of the dorsal-ventral boundary in Anableps, resulting in a proportionally larger ventral retinal domain. Collectively, our results reveal that Anableps achieved its unique dual visual capacity by developmentally expanding and functionally reprogramming the ventral retina for aerial light detection, an evolutionary innovation that redefines how retinal domains can adapt to radically different visual environments.
2025-11-18 | GSE306418 | GEO
Project description:The emergence of evolutionary novelties remains a central challenge in biology, particularly for complex organs such as the vertebrate eye. While visual systems have repeatedly undergone degeneration or loss, examples of innovation are rare and poorly understood. Mechanistic insight into such gains requires tractable systems in which novel visual functions have evolved. Here we leverage the four-eyed fish Anableps anableps to uncover the cellular and molecular basis of adaptation to simultaneous aerial and aquatic light. Combining single-nucleus and spatial transcriptomics, we show that the Anableps ventral retina has been developmentally and functionally reconfigured for aerial vision. In fully aquatic teleosts such as zebrafish, ventral photoreceptors are tuned to red-shifted, downwelling light. In contrast, we show that Anableps exhibits an expanded and diversified ventral cone population encompassing ultraviolet-, blue-, green-, and red-sensitive types, enabling broad-spectrum, high-intensity vision from above water. To estimate Anableps opsin spectral properties, we employed OPTICS, a machine-learning model of opsin spectral tuning, which predicts that the ventrally expressed opn1mw2 opsin is red-shifted relative to typical green-sensitive pigments. Analysis of dorsal-ventral patterning markers reveals an overrepresentation of ventral retinal cell types. Consistent with this, comparative spatial transcriptomic profiling of developing and adult Anableps and the killifish (Fundulus heteroclitus) indicates a dorsal displacement of the dorsal-ventral boundary in Anableps, resulting in a proportionally larger ventral retinal domain. Collectively, our results reveal that Anableps achieved its unique dual visual capacity by developmentally expanding and functionally reprogramming the ventral retina for aerial light detection, an evolutionary innovation that redefines how retinal domains can adapt to radically different visual environments.
2025-11-18 | GSE306228 | GEO
Project description:Evolutionary remodeling of the ventral retina enables aerial vision in the four-eyed fish Anableps anableps [Spatial Transcriptomics]
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Project description:Toxic compounds such as organochlorine pesticides (OCs), polychlorinated biphenyls (PCBs), and polybrominated diphenyl ether flame retardants (PBDEs) have been detected in fish, birds, and aquatic mammals that live in the Columbia River or use the river as a food source. We developed a custom microarray for largescale suckers (Catostomus macrocheilus) and used it to investigate the molecular effects of contaminant exposure on wild fish in the Columbia River. Using Significance Analysis of Microarrays (SAM) we identified 72 probes representing 69 unique genes with expression patterns that correlated with hepatic tissue levels of OCs, PCBs, or PBDEs. These genes were involved in many biological processes previously shown to respond to contaminant exposure, including drug and lipid metabolism, apoptosis, cellular transport, oxidative stress, and cellular chaperone function. The relation between gene expression and contaminant burden suggests that these genes may respond to environmental contaminant exposure and are promising candidates for further field and laboratory studies to develop biomarkers for monitoring exposure of wild fish to contaminant mixtures found in the Columbia River Basin Correlation between contaminant exposure and gene expression profiles of wild largescale suckers collected from three different sites in the Columbia River. At each site, liver samples of six to eight different fish were analyzed using microarrays.
2013-12-04 | E-GEOD-41016 | biostudies-arrayexpress
Project description:During early stages of development, juvenile fish must rely on their innate immune system to defend against pathogens. At these early stages, the immune system is immature and is unlikely to express the full repertoire of genes that control defences. Although vulnerable, these larval fish can still fight of infections, indicating there are active defence mechanisms. Using rainbow trout as a model, we have taken a transcriptomics approach to determine the antibacterial (Aeromonas salmonicida) and antiviral (VHSV) responses to infection at four early life history stages, eyed egg, post-hatch, first feeding and three weeks post-first feeding. We performed microarray analysis using an Agilent 4x44K custom designed array, using a common RNA reference hybridization design. We show that all stages of the developing fish respond to the disease challenge at 3 days post-challenge, but the number and complexity of the response increases with developmental stage. Specifically, the response to virus at eyed egg and hatch stages does not show the full interferon response as is found at first feeding and 3 weeks post-first feeding. The experiments were carried out with a custom-designed Agilent (Agilent design ID: 028918) oligonucleotide microarray (A-MEXP-2315) named Trout_imm_v1. In total, 46 hybridisations were performed on individual animals, with 4 biological replicates per sampling point (apart from Bacteria infected eyed eggs for which two hybridizations were not used). This work was funded by the European Community’s seventh framework programme (FP7/2007-2013), under grant agreement no. 222719 (LIFECYCLE).
2016-03-03 | E-MTAB-3401 | biostudies-arrayexpress
Project description:Anableps anableps isolate:Para Raw sequence reads
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