From historical expedition diaries to whole genome sequencing: a case study of the likely extinct Red Sea Torpedo Ray
DOI: | https://doi.org/10.57756/r4cvtt |
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Creator(s): |
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Publication date: | 02 Sep 2023 |
Publisher: | Naturhistorisches Museum Wien (NHMW) |
Collections: | 1. Zoology , Central Research Laboratories |
Instrument: | Illumina NovaSeq 6000 |
Resource type: | Dataset |
Specimen: | NHMW-FS-88240 |
License: |
CC BY 4.0 International |
Tags: | Genomics Lectotype Red sea Torpedo suessii Type material |
Countries: | Yemen |
Taxa: | Torpediniformes |
Share: |
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Abstract
Torpedo rays (Torpedinidae, Torpediniformes)
are small to moderately large batoids
that produce an electric discharge. In the latest lists of living rays,
13 species are accepted in the genus Torpedo, including three of
doubtful validity and several recently discovered undescribed species.
Among the valid species is the critically endangered, possibly extinct,
Torpedo suessii Steindachner, 1898, the
Red Sea torpedo, of which only four specimens have been recorded in the
literature until now. Here, the extended specimen approach was applied
to re-describe and analyse the lectotype of T. suessii (NMW 88240) at
the Natural history museum in Vienna, that has been added to the fish
collection in December 1897. The approach included research of
historical information and whole genome sequencing with Illumina
technology from liver and muscle tissue followed by genome assembly and
phylogenetic analysies.
Publications
Palandačić, A., Kapun, M., Greve, C., Schell, T., Kirchner, S., Kruckenhauser, L., et al. (2023). From historical expedition diaries to whole genome sequencing: A case study of the likely extinct Red Sea torpedo ray. Zoologica Scripta. https://doi.org/10.1111/zsc.12632
Downloads
File | Description | Size |
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AnalysisPipeline.zip | the analysis pipeline of the project including all shell and python scripts. (The shell script /AnalysisPipeline/shell/main.sh contains an overview of all analyses) | 0.05 MB |
README.txt | a README file with the description of all datasets | 0 MB |
Tsue_mitochondrion.zip | the genome assembly files for the full Mitochondrion (GenBank Accession: OR506611; Tsue_mitochondrion.zip) | 0.02 MB |
Tsue_NuclearGenomeAssembly.zip | the genome assembly files for the draft nuclear genome (NCBI Project Number: PRJNA1008877; Tsue_NuclearGenomeAssembly.zip) | 510.95 MB |