Data from: Development and patterning of a highly versatile visual system in spiders
Data files
Jan 20, 2025 version files 19.39 GB
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Drassodes_sp_embryos_Trinity.fasta
167.89 MB
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Marpissa_13_20x.zip
7.16 GB
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Parasteatoda_14_2B.zip
1.63 GB
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Pardosa_13.1-13.2_2.zip
2.19 GB
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Pholcus_13.2-14_20x_4.zip
3.05 GB
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README.md
3 KB
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Segestria_sp_embryos_Trinity.fasta
162.51 MB
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Zygiella_14_20x_5.zip
4.89 GB
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Zygiella_Xnotata_Trinity.fasta
142.19 MB
Abstract
Visual systems provide a key interface between organisms and their surroundings, and have evolved in many forms to perform diverse functions across the animal kingdom. Spiders exhibit a range of visual abilities and ecologies, the diversity of which is underpinned by a highly versatile, modular visual system architecture. This typically includes eight eyes of two developmentally distinct types, but the number, size, location, and function of the eyes can vary dramatically between lineages. Previous studies of visual system development in spiders have confirmed that many components of the retinal determination gene (RDG) network are conserved with other arthropods, but so far, comparative studies among spiders are lacking. We characterised visual system development in seven species of spiders representing a range of morphologies, visual ecologies, and phylogenetic positions, to determine how these diverse configurations are formed, and how they might evolve. Combining synchrotron radiation tomography, transcriptomics, in situ hybridisation, and selection analyses, we characterise the repertoires and expression of key RDGs in relation to adult morphology. We identify key molecular players, timepoints, and developmental events that may contribute to adult diversity, in particular the molecular and developmental underpinnings of eye size, number, position, and identity across spiders
README: Synchrotron scans of developing spider embryos
https://doi.org/10.5061/dryad.fttdz0933
Description of the data and file structure
Morphological and transcriptomic data for a study of visual system development in spiders.
Files and variables
File: Marpissa_13_20x.zip
Description: Synchrotron scan of a stage 13 (after Mittmann and Wolff 2007) Marpissa muscosa embryo. Generated at the TOMCAT beamline of the Swiss Light Source (Paul Scherrer Institute), using 20x magnification. Reconstructed model of CNS in Amira (Thermo Fisher).
File: Pholcus_13.2-14_20x_4.zip
Description: Synchrotron scan of a stage 13.2 (after Mittmann and Wolff 2007) Pholcus phalangioides embryo. Generated at the TOMCAT beamline of the Swiss Light Source (Paul Scherrer Institute), using 20x magnification. Reconstructed model of CNS in Amira (Thermo Fisher).
File: Parasteatoda_14_2B.zip
Description: Synchrotron scan of a stage 14 (after Mittmann and Wolff 2007) Parasteatoda tepidariorum embryo. Generated at the TOMCAT beamline of the Swiss Light Source (Paul Scherrer Institute), using 10x magnification. Reconstructed model of CNS in Amira (Thermo Fisher).
File: Drassodes_sp_embryos_Trinity.fasta
Description: Assembled transcriptome of mixed-stage embryos of Drassodes cupreus. Assembled using the Trinity pipeline with default settings. For full methods, see Baudouin-Gonzalez et al. 2024.
File: Segestria_sp_embryos_Trinity.fasta
Description: Assembled transcriptome of mixed-stage embryos of Segestria senoculata. Assembled using the Trinity pipeline with default settings. For full methods, see Baudouin-Gonzalez et al. 2024.
File: Zygiella_Xnotata_Trinity.fasta
Description: Assembled transcriptome of mixed-stage embryos of Zygiella x-notata. Assembled using the Trinity pipeline with default settings. For full methods, see Baudouin-Gonzalez et al. 2024.
File: Pardosa_13.1-13.2_2.zip
Description: Synchrotron scan of a stage 13.1-13.2 (after Mittmann and Wolff 2007) Pardosa amentata embryo. Generated at the TOMCAT beamline of the Swiss Light Source (Paul Scherrer Institute), using 10x magnification. Reconstructed model of CNS in Amira (Thermo Fisher).
File: Zygiella_14_20x_5.zip
Description: Synchrotron scan of a stage 14 (after Mittmann and Wolff 2007) Zygiella x-notata embryo. Generated at the TOMCAT beamline of the Swiss Light Source (Paul Scherrer Institute), using 20x magnification. Reconstructed model of CNS in Amira (Thermo Fisher).
Code/software
Synchrotron scans contain slices (tiff stacks) and Amira files (.hx network files, and .surf surfaces) for the reconstructed models.
Transcriptomes in fasta format.
Access information
Other publicly accessible locations of the data:
- Transcriptome reads are available on NCBI (BioProject PRJNA707377).
Data was derived from the following sources:
- NA
Methods
Embryos were preserved in 70% ethanol and mounted in pipette tips for scanning at the TOMCAT beamline, Swiss Light Source (Paul Scherrer Institute) (Stampanoni et al. 2006). Scans used a monochromatic beam (16 keV), with propagation distances 10-100 mm and combined magnifications of 4x (effective voxel size 1.65 μm, LuAG:Ce 100 μm scintillator), 10x (0.65 μm, LuAG:Ce 20 μm), or 20x (0.325 μm, LuAG:Ce 20 μm). 2000 projections were recorded across 180° sample rotation, with exposure times of 70 ms (4x), 120 ms (10x), or 200 ms (20x). In-house software reconstructed slices from projections, with Paganin filtering (delta=1e-7, beta=3e-9) (Paganin et al. 2002) and depth reduction to 8-bit tiffs (Marone and Stampanoni 2012). Data were cropped in Fiji (Schindelin et al. 2012) and models were produced in Amira v.2021 (Thermo Fisher), using volume rendering (outer surfaces) and manual segmentation (CNS).