DOI: 10.5061/dryad.sj3tx969h
title: Ion Torrent data for the genome assembly and phylogenomic placement of mitochondrial genomes with a focus on houndsharks (Chondrichthyes: Triakidae)

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. We also present our
 code and corresponding datasets used to assemble and annotate their
 mitogenomes, prepare alignments, partition our datasets, assign models of
 evolution, infer phylogenies based on traditional site homogeneous
 concatenation approaches as well as under the multispecies coalescent
 model (MSCM) and site heterogenous models, and generate statistical data
 for comparison of different topological outcomes. The data and code
 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.
description: 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); Polymerase chain reaction: 50 ng template
 DNA (Galeorhinus galeus genomic DNA), 1X GoTaq Buffer, 2.5 mM MgCl2, 200
 µM dNTPs, 0.3 µM of each primer [Cytb CC F (5’- ACTTGAATTGGAGGGCAACC-3’)
 and Dloop Gga R (5’- AGGGTATGTGGGCCATATCA -3’)] and 0.625 U GoTaq DNA
 polymerase in a total reaction volume of 15 µL using the SimpliAmp™ Thermo
 Cycler machine. Cycling parameters: (i) one initial denaturation cycle at
 94°C for 3 min, (ii) denaturation at 94°C for 30 s, annealing for 30 s
 starting at 65°C and decreasing in 1°C increments to 55°C for 11 cycles
 and then maintaining 55°C for a further 24 cycles and elongation at 72°C
 for 1 min, and (iii) a final elongation cycle at 72°C for 10 min; PCR
 quality control : 1.5% agarose gel electrophoresis at 100 Volts for 1 hour
 and visualisation using the Gel Doc™ XR+ documentation system (Bio- Rad);
 NGS Sequencing: Ion GeneStudio S5 Prime System and
 postprocessing with Torrent Suite version 5.16 under default settings to
 generate BAM reads and cycle sequencing with standard Sanger sequencing
 chemistry (BigDye® Terminator v.3.1 cycle sequencing kit) and capillary
 electrophoresis on the ABI3730xl genetic analyser (Applied Biosystems®)
 for FASTA reads. Conducted 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 <em>Mustelus mustelus</em> mitogenome
 (NC_039629.1) using the Geneious read mapper with medium sensitivity
 settings and five iterations in Geneious Prime v.2023.2 (Data 1-5). 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. A
 third assembly approach was conducted by mapping the original raw
 reads <em>de novo </em>in SPAdes using the same
 parameters. Sanger sequence reads were generated for
 the <em>Galeorhinus galeus </em>mitogenome to confirm a
 structural deviation (tandem duplication and random loss mutation) in the
 mitogenome and trimmed using Finch TV v.1.5 (Data  6-7). All three
 assemblies were compared to produce a consensus sequence for each species
 and these were annotated with MitoAnnotator in MitoFish v.3.72. Mitogenome
 sequence files in GenBank format were generated and uploaded onto NCBI
 (ON075075, ON075076, ON075077, ON652873, and ON652874) (Data
 8-12). The five newly assembled mitogenomes were used
 in an extensive statistical workflow to expand the phylogeny of Triakidae.
 First, we downloaded additional representative mitogenomes from each
 family in the order Carcharhiniformes and four representative species each
 from the orders Lamniformes and Orectolobiformes from GenBank to complete
 the Galeomorphii cluster (Data 13) and produced codon-aware multiple
 sequence alignments (MSA) for each of the 13 PCGs in MACSE v.2.07 and the
 2 rRNAs in MAFFT v.7.299. We concatenated the PCG alignments (Data 14-16),
 concatenated the PCG and rRNA alignments (Data 17-19), and translated and
 then concatenated the PCG alignments (Data 20-22). These concatenated
 alignments were used for phylogenetic reconstruction under Maximum
 Likelihood (ML) and Bayesian Inference (BI) approaches in IQTree v.2.1.3
 and MrBayes v.3.2.6 as well as multispecies coalescent modelling in ASTRAL
 v.5.6.3 and SVDQuartets in PAUP* v4.0a 169 (a modified input NEXUS file
 with gene partitions is available as Data 23). Site heterogenous models
 were applied in PHYLOBAYES_MPI v.1.9. We designated eight
 different<em> a priori</em> partitioning schemes with varying
 degrees of complexity to determine the effects of partitioning on
 phylogeny estimation (PS01-PS08) for ML and BI analyses.
description: 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.2023.2 and SPAdes
 v.3.15. GenBank: Mitochdonrial genome assemblies in
 GenBank format can be viewed in a sequence analysis software. We used
 Geneious Prime v.2023.2. They can also be viewed and edited in a standard
 text editor such as Notes. FASTA: Sanger sequence data files in FASTA
 format can be trimmed in Finch TV v.1.5 and viewed in a sequence analysis
 software. Multiple sequence alignments in FASTA format can be viewed in a
 sequence analysis software. We used Geneious Prime v.2023.2 but DAMBE
 v.7.0.35 and MEGA 11 can be used as alternatives. They can also be viewed
 and edited in a standard text editor such as Notes.
 NEXUS: Multiple sequence
 alignments and partition files in NEXUS format can be viewed in a sequence
 analysis software. We used Geneious Prime v.2023.2 but DAMBE v.7.0.35,
 PAUP* v.4.0a169 and MEGA 11 can be used as alternatives. They can also be
 viewed and edited in a standard text editor such as
 Notes. PHYLIP: Multiple sequence alignments in PHYLIP
 format can be viewed in a sequence analysis software. We used Geneious
 Prime v.2023.2 but DAMBE v.7.0.35 and MEGA 11 can be used as alternatives.
 They can also be viewed and edited in a standard text editor such as
 Notes.
description: This README file was generated on 2025-02-25 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: [jessica.winn16@gmail.com](mailto:jessica.winn16@gmail.com)
 ORCiD:
 [https://orcid.org/0000-0003-1070-1276](https://orcid.org/0000-0003-1070-1276) B. Co-investigator 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: [simo.maduna@nibio.no](mailto:simo.maduna@nibio.no) ORCiD: [https://orcid.org/0000-0002-9372-4360](https://orcid.org/0000-0002-9372-4360) C. Co-investigator contact information Name: Aletta E. Bester-van der Merwe Institution: Stellenbosch University Address: Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Stellenbosch, Western Cape, 7602, South Africa. Email: [aeb@sun.ac.za](mailto:aeb@sun.ac.za) ORCiD: [https://orcid.org/0000-0002-0332-7864](https://orcid.org/0000-0002-0332-7864) 3. Data collection: Genomic DNA - 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 manufacturers protocol, Ion Xpress Plus gDNA Fragment Library Preparation User Guide (MAN0009847 K.0). Polymerase chain reaction - 50 ng template DNA (Galeorhinus galeus genomic DNA), 1X GoTaq Buffer, 2.5 mM MgCl2, 200 µM dNTPs, 0.3 µM of each primer [Cytb CC F (5’- ACTTGAATTGGAGGGCAACC-3’) and Dloop Gga R (5’- AGGGTATGTGGGCCATATCA -3’)] and 0.625 U GoTaq DNA polymerase in a total reaction volume of 15 µL using the SimpliAmp™ Thermo Cycler machine. Cycling parameters: (i) one initial denaturation cycle at 94°C for 3 min, (ii) denaturation at 94°C for 30 s, annealing for 30 s starting at 65°C and decreasing in 1°C increments to 55°C for 11 cycles and then maintaining 55°C for a further 24 cycles and elongation at 72°C for 1 min, and (iii) a final elongation cycle at 72°C for 10 min. PCR quality control - 1.5% agarose gel electrophoresis at 100 Volts for 1 hour and visualisation using the Gel Doc™ XR+ documentation system (Bio- Rad). NGS Sequencing - Ion GeneStudio S5 Prime System and postprocessing with Torrent Suite version 5.16 under default settings to generate BAM reads and cycle sequencing with standard Sanger sequencing chemistry (BigDye® Terminator v.3.1 cycle sequencing kit) and capillary electrophoresis on the ABI3730xl genetic analyser (Applied Biosystems®) for FASTA reads. Conducted at the Central Analytical Facility (CAF) at Stellenbosch University. 4. Date of data collection (range): Fin clip sampling (2014-2019), Ion Torrent NGS sequencing (2022), Data analysis (2022-2023) 5. Geographic location of data collection: Fin clip tissue samples of Galeorhinus galeus, Mustelus palumbes, and Triakis megalopterus were collected along the coast of South Africa. Mustelus asterias and Mustelus mosis were sampled off the coasts of Wales and the Sultanate of Oman respectively. 6. Information about funding sources that supported the collection of the data: MND210614611484, National Research Foundation, South Africa. \######################################################################### SHARING/ACCESS INFORMATION 1. Licenses/restrictions placed on the data: CC0 1.0 Universal (CC0 1.0) Public Domain 2. Links to publications that cite or use the data: Winn, J. C., Bester-van der Merwe, A. E., Maduna, S. N. (2024). Ion Torrent data for the genome assembly and phylogenomic placement of mitochondrial genomes with a focus on houndsharks (Chondrichthyes: Triakidae). Data in Brief. In Press. Winn, J. C., Bester-van der Merwe, A. E., Maduna, S. N. (2024). A comprehensive phylogenomic study unveils evolutionary patterns and challenges in the mitochondrial genomes of Carcharhiniformes: A focus on Triakidae. Genomics. 11(1): 110771. doi:10.1016/j.ygeno.2023.110771. Winn, J. C., Bester-van der Merwe, A. E. and Maduna, S. N. (2025). Annotated Bioinformatic Pipelines for Genome Assembly and Annotation of Mitochondrial Genomes. Bio-protocol. 15(5): e5231. doi:10.21769/BioProtoc.5231. Winn, J. C., Bester-van der Merwe, A. E. and Maduna, S. N. (2025). Annotated Bioinformatic Pipelines for Phylogenomic Placement of Mitochondrial Genomes. Bio-protocol. 15(5): e5232. DOI: 10.21769/BioProtoc.5232. 3. Links to other publicly accessible locations of the data: Assembled mitochondrial genomes Repository name: GenBank Data identification number: ON075075, ON075076, ON075077, ON652873, and ON652874 Direct URL to data: [https://www.ncbi.nlm.nih.gov/nuccore/ON075075](https://www.ncbi.nlm.nih.gov/nuccore/ON075075); [https://www.ncbi.nlm.nih.gov/nuccore/ON075076](https://www.ncbi.nlm.nih.gov/nuccore/ON075076); [https://www.ncbi.nlm.nih.gov/nuccore/ON075077](https://www.ncbi.nlm.nih.gov/nuccore/ON075077); [https://www.ncbi.nlm.nih.gov/nuccore/ON652873](https://www.ncbi.nlm.nih.gov/nuccore/ON652873); [https://www.ncbi.nlm.nih.gov/nuccore/ON652874](https://www.ncbi.nlm.nih.gov/nuccore/ON652874). Raw Ion Torrent® next-generation sequencing (NGS) data Repository name: BioProject * Data identification number: PRJNA997468 BioSample accessions: SAMN36680060, SAMN36680061, SAMN36680062, SAMN36680063, SAMN36680064 Direct URL to data: [https://www.ncbi.nlm.nih.gov/bioproject/997468](https://www.ncbi.nlm.nih.gov/bioproject/997468); [https://www.ncbi.nlm.nih.gov/biosample/36680060](https://www.ncbi.nlm.nih.gov/biosample/36680060); [https://www.ncbi.nlm.nih.gov/biosample/36680061](https://www.ncbi.nlm.nih.gov/biosample/36680061); [https://www.ncbi.nlm.nih.gov/biosample/36680062](https://www.ncbi.nlm.nih.gov/biosample/36680062); [https://www.ncbi.nlm.nih.gov/biosample/36680063](https://www.ncbi.nlm.nih.gov/biosample/36680063); [https://www.ncbi.nlm.nih.gov/biosample/36680064](https://www.ncbi.nlm.nih.gov/biosample/36680064). * The data has been uploaded as a BioProject onto the SRA database, but it has been suppressed until the release of a related manuscript. 4. Links/relationships to ancillary data sets: None 5. Was data derived from another source? No 6. Recommended citation for this dataset: Winn, Jessica; Bester-van der Merwe, Aletta; Maduna, Simo (2025). Ion Torrent data for the genome assembly and phylogenomic placement of mitochondrial genomes with a focus on houndsharks (Chondrichthyes: Triakidae) [Dataset]. Dryad. [https://doi.org/10.5061/dryad.sj3tx969h](https://doi.org/10.5061/dryad.sj3tx969h) \######################################################################### DATA & FILE OVERVIEW 1. File List: A) 1_IonTorrent_NGS_Filtered_RawData.zip Data_1_Galeorhinus_galeus_IonTorrent_Filtered_RawData.bam Data_2_Mustelus_asterias_IonTorrent_Filtered_RawData.bam Data_3_Mustelus_mosis_IonTorrent_Filtered_RawData.bam Data_4_Mustelus_palumbes_IonTorrent_Filtered_RawData.bam Data_5_Triakis_megalopterus_IonTorrent_Filtered_RawData.bam Data_6_Galeorhinus_galeus_Sanger_Forward Data_7_Galeorhinus_galeus_Sanger_Reverse B) 2_Galeomorphii_mitogenome_sequences Data_8_ON652873_Mustelus_asterias Data_9_ON652874_Galeorhinus_galeus Data_10_ON075075_Triakis_megalopterus Data_11_ON075076_Mustelus_palumbes Data_12_ON075077_Mustelus_mosis Data_13_Winn2023_Galeomorphii_mitogenome_seqs C) 3_Multiple_sequence_alignments Data_14_Galeomorphii_13PCGs_NT.fasta Data_15_Galeomorphii_13PCGs_NT.phy Data_16_Galeomorphii_13PCGs_NT.nex Data_17_Galeomorphii_13PCGs_2rRNAs_NT.fasta Data_18_Galeomorphii_13PCGs_2rRNAs_NT.phy Data_19_Galeomorphii_13PCGs_2rRNAs_NT.nex Data_20_Galeomorphii_13PCGs_AA.fasta Data_21_Galeomorphii_13PCGs_AA.phy Data_22_Galeomorphii_13PCGs_AA.nex D) 4_Partition_files 0_partition_key 13PCGs_2rRNAs_NT.part PS01.nex PS01AA.nex PS02.nex PS03.nex PS04.nex PS05.nex PS05AA.nex PS06.nex PS07.nex PS08.nex 2. Relationship between files, if important: The GenBank files for the Triakidae species assembled in this study (2_Galeomorphii_mitogenome_sequences) are the output files created during assembly of the raw Ion Torrent sequences (under 1_IonTorrent_NGS_Filtered_RawData). The multiple sequence alignment files (3_Multiple_sequence_alignments) were created using the Triakidae GenBank files (2_Galeomorphii_mitogenome_sequences) and additional Galeomorphii mitogenomes and outgroups saved together as Data_13_Winn2023_Galeomorphii_mitogenome_seqs. The multiple sequence alignment files (3_Multiple_sequence_alignments) and partition files (4_Partition_files) are used together for mitophylogenomic analyses under Maximum Likelihood and Bayesian Inference frameworks. 3. Additional related data collected that was not included in the current data package: None 4. Are there multiple versions of the dataset? No A. If yes, name of file(s) that was updated: NA i. Why was the file updated? NA ii. When was the file updated? NA \######################################################################### DATA-SPECIFIC INFORMATION FOR: 1_Raw_IonTorrent_NGS_data 1. Data type: Raw Mitogenomic Ion Torrent® NGS data files in BAM format for Galeorhinus galeus, Mustelus asterias, Mustelus mosis, Mustelus palumbes and Triakis megalopterus and Sanger sequence reads in FASTA format for the duplicated portion of the Galeorhinus galeus mitogenome. 2. Data processing: Adaptors and poor-quality bases (Phred score below 20) have been trimmed and reads shorter than 25 base pairs (bp) 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 v.2023.2. The reads that mapped to the reference mitogenome were then saved in BAM format as filtered Ion Torrent reads. The first and last 20-30 nucleotides were trimmed from the Sanger sequence reads in Finch TV v.1.5 and saved in FASTA format. 3. Specialized formats or other abbreviations used: NA DATA-SPECIFIC INFORMATION FOR: 2_Galeomorphii_mitogenome_sequences 1. Data type: Mitochondrial genome assemblies in GenBank format for Galeorhinus galeus, Mustelus asterias, Mustelus mosis, Mustelus palumbes and Triakis megalopterus. A combined GenBank file with our new assemblies, additional representative Galeomorphii mitogenomes and outgroups. 2. Data processing: All three assemblies were compared to produce consensus sequences for each species which were annotated with MitoAnnotator in MitoFish v.3.72. Mitogenome sequence files in GenBank format were generated and uploaded onto NCBI (ON075075, ON075076, ON075077, ON652873, and ON652874) (Data 8-12). Additional representative mitogenomes from each family in the order Carcharhiniformes and four representative species each from the orders Lamniformes and Orectolobiformes were downloaded from GenBank to complete the Galeomorphii cluster and merged with our newly assembled mitogenomes to create a single GenBank file (Data 13). 3. Specialized formats or other abbreviations used: NA DATA-SPECIFIC INFORMATION FOR: 3_Multiple_sequence_alignments 1. Data type: Concatenated multiple sequence alignments in FASTA, NEXUS and PHYLIP format. 2. Data processing: Codon-aware multiple sequence alignments (MSA) were produced for each of the 13 PCGs in MACSE v.2.07 and the 2 rRNAs in MAFFT v.7.299 using the Q-INS-i iterative refinement method. Geneious Prime v.2023.2 was used to remove stop codons and check the reading frame of each PCG alignment. Ambiguously aligned regions were cleaned in BMGE v.1.12_1. The 13 PCG alignments were concatenated and saved in FASTA, NEXUS and PHYLIP format to create Data 14-16, the 13 PCG and 2 rRNA alignments were concatenated and saved in FASTA, NEXUS and PHYLIP format to create Data 17-19, and the 13 PCGs were translated and then concatenated and saved in FASTA, NEXUS and PHYLIP format to create Data 20-22. Gene partitions were added to the Data_19_Galeomorphii_13PCGs_2rRNAs_NT.nex file to create an input file (Data 23) for multispecies coalescent modelling with SVDQuartets in PAUP* v.4.0a169. 3. Specialized formats or other abbreviations used: NA DATA-SPECIFIC INFORMATION FOR: 4_Partition_files 1. Data type: Raw Mitogenomic Ion Torrent® NGS data files in BAM format for Galeorhinus galeus, Mustelus asterias, Mustelus mosis, Mustelus palumbes and Triakis megalopterus. 2. Data processing: Gene and codon partition files in NEXUS format. Length summaries were made with the length and alignment locations of each PCG from the alignment information in Geneious Prime v.2023.2 and used to create codon, gene and gene x codon partition files. 3. Specialized formats or other abbreviations used: NA \######################################################################### BIOINFORMATICS PIPELINE The full bioinformatics pipeline and code describing how to process the data is available in two separate Bio-protocol articles: Winn, J. C., Bester-van der Merwe, A. E. and Maduna, S. N. (2025). Annotated Bioinformatic Pipelines for Genome Assembly and Annotation of Mitochondrial Genomes. Bio-protocol. 15(5): e5231. doi:10.21769/BioProtoc.5231. Winn, J. C., Bester-van der Merwe, A. E. and Maduna, S. N. (2025). Annotated Bioinformatic Pipelines for Phylogenomic Placement of Mitochondrial Genomes. Bio-protocol. 15(5): e5232. DOI: 10.21769/BioProtoc.5232.