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: jessica.winn16@gmail.com
   ORCiD: https://orcid.org/0000-0003-1070-1276

   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: simo.maduna@nibio.no
   ORCiD: https://orcid.org/0000-0002-9372-4360

   C. Co-investogator 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
   ORCiD: 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).
   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.

4. Date of data collection (range): Finclip 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.

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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). Annotated bioinformatic pipelines for the genome assembly and phylogenomic placement of mitochondrial genomes with a focus on houndsharks (Chondrichthyes: Triakidae). Current Protocols. In Preparation.
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.

1. 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/ON075076; https://www.ncbi.nlm.nih.gov/nuccore/ON075077; https://www.ncbi.nlm.nih.gov/nuccore/ON652873; 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/biosample/36680060; https://www.ncbi.nlm.nih.gov/biosample/36680061; https://www.ncbi.nlm.nih.gov/biosample/36680062; https://www.ncbi.nlm.nih.gov/biosample/36680063; 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.

1. Links/relationships to ancillary data sets: None

2. Was data derived from another source? No

3. Recommended citation for this dataset:

Winn, Jessica; Bester-Van der Merwe, Aletta; Maduna, Simo (Forthcoming 2024). 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

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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

1. Relationship between files, if important:

The GenBank files for the Triakidae species assembled in this study are the output files created during assembly of the raw Ion Torrent sequences (under 1_IonTorrent_NGS_Filtered_RawData).

1. Additional related data collected that was not included in the current data package: None

2. 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

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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.

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 (version 2019.1.3).
The reads that mapped to the reference mitogenome were then saved in BAM format as filtered Ion Torrent reads.

1. Specialized formats or other abbreviations used: NA

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BIOINFORMATICS PIPELINE

The full bioinformatics pipeline and code describing how to process the data will be available as a Current Protocols manuscript: Winn, J. C., Bester-van der Merwe, A. E., Maduna, S. N. (2024). Annotated bioinformatic pipelines for the genome assembly and phylogenomic placement of mitochondrial genomes with a focus on houndsharks (Chondrichthyes: Triakidae).