Ion Torrent data for the genome assembly and phylogenomic placement of mitochondrial genomes with a focus on houndsharks (Chondrichthyes: Triakidae)
Authors/Creators
- 1. Stellenbosch University
- 2. Norwegian Institute of Bioeconomy Research
Description
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.
Notes
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
Funding provided by: National Research Foundation
Crossref Funder Registry ID: https://ror.org/05s0g1g46
Award Number: MND210614611484
Methods
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 mustelus mitogenome (NC_039629.1) using the Geneious read mapper with medium sensitivity settings and five iterations in Geneious Prime (version 2019.1.3). The reads that mapped to the reference mitogenome were then saved in BAM format as filtered Ion Torrent reads to use for mitogenome assembly in SPAdes v.3.15 with the input set for unpaired Ion Torrent reads with 8 threads, kmers 21,33,55,77,99,127, the careful option to reduce the number of mismatches and short indels and all other parameters left as default.
Files
1_IonTorrent_NGS_Filtered_RawData.zip
Files
(4.3 MB)
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Additional details
Related works
- Is cited by
- 10.1016/j.ygeno.2023.110771 (DOI)