Ion Torrent data for the genome assembly and phylogenomic placement of mitochondrial genomes with a focus on houndsharks (Chondrichthyes: Triakidae)

Here, we present the Ion Torrent® next-generation sequencing (NGS) data for five houndsharks (Chondrichthyes: Triakidae), which include Galeorhinus galeus (17,487 bp; GenBank accession number ON652874), Mustelus asterias (16,708; ON652873), Mustelus mosis (16,755; ON075077), Mustelus palumbes (16,708; ON075076), and Triakis megalopterus (16,746 bp; ON075075). All assembled mitogenomes encode 13 protein-coding genes (PCGs), two ribosomal (r)RNA genes, and 22 transfer (t)RNA genes (tRNALeu and tRNASer are duplicated), except for G. galeus which contains 23 tRNA genes where tRNAThr is duplicated. The data presented in this paper can assist other researchers in further elucidating the diversification of triakid species and the phylogenetic relationships within Carcharhiniformes (groundsharks) as mitogenomes accumulate in public repositories., Data collection
Genomic DNA extraction: Standard CTAB protocol or SDS-based lysis buffer (PL2) from the NucleoSpin Plant II mini kit (MACHEREY-NAGEL, Dueren, Germany); DNA quality control: Qubit 4.0 fluorometer (ThermoFisher Scientific) and LabChip® GXII Touch (PerkinElmer, Waltham, MA, USA); Library preparation: Ion Plus Fragment Library Kit (ThermoFisher Scientific) according to the manufacturer’s protocol, Ion Xpress™ Plus gDNA Fragment Library Preparation User Guide (MAN0009847 K.0); NGS Sequencing: Ion GeneStudio™ S5 Prime System and postprocessing with Torrent Suite version 5.16 under default settings at the Central Analytical Facility (CAF) at Stellenbosch University.
Data processing
For the five houndshark species for which sequencing data was generated, sequence quality was checked in FastQC, adaptors and poor-quality bases (Phred score below 20) were trimmed, and reads shorter than 25 bp were removed in Torrent Suite Version 5.16. Raw reads were aligned to the Mustelus mustelu..., BAM: Raw filtered Ion Torrent® NGS data files in BAM format can be viewed in a sequence analysis software. Here we use Geneious Prime v.2019.1.3 and SPAdes v.3.15, This README file was generated on 2024-01-31 by Jessica Winn

GENERAL INFORMATION

1. Title of the journal article that uses this data set: Ion Torrent data for the genome assembly and phylogenomic placement of mitochondrial genomes with a focus on houndsharks (Chondrichthyes: Triakidae).

2. Author Information:

A. Principle Investigator contact information
Name: Jessica C. Winn
Institution: Stellenbosch University
Address: Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Stellenbosch, Western Cape, 7602, South Africa.
Email:
ORCiD:

B. Co-investogator contact information
Name: Simo N. Maduna
Institution: Norwegian Institute of Bioeconomy Research
Address: Department of Ecosystems in the Barents Region, Svanhovd Research Station, Norwegian Institute of Bioeconomy Research, 9925 Svanvik, Norway.
Email:
ORCiD:

C. Co-investogator contact information
Name: Aletta E. Bester-van der Merw...