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
Creator(s):
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
CC BY 4.0 International
Tags: Genomics Lectotype Red sea Torpedo suessii Type material
Countries: Yemen
Taxa: Torpediniformes
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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
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