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. 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 ..., 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 decr..., 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..., 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: [[e-mail]](mailto:[e-mail])
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 Sv...

本数据集发布了5种皱唇鲨科（Chondrichthyes: Triakidae，软骨鱼纲）的Ion Torrent® 下一代测序（next-generation sequencing, NGS）数据，涵盖物种包括灰三齿鲨（Galeorhinus galeus，线粒体基因组长度17487 bp，GenBank登录号ON652874）、星棘星鲨（Mustelus asterias，16708 bp，ON652873）、摩西星鲨（Mustelus mosis，16755 bp，ON075077）、帕伦布斯坦星鲨（Mustelus palumbes，16708 bp，ON075076）以及大鳍三齿鲨（Triakis megalopterus，16746 bp，ON075075）。所有组装完成的线粒体基因组（mitogenome）均编码13个蛋白质编码基因（protein-coding genes, PCGs）、2个核糖体RNA（ribosomal RNA, rRNA）基因以及22个转运RNA（transfer RNA, tRNA）基因，其中亮氨酸转运RNA（tRNALeu）与丝氨酸转运RNA（tRNASer）存在拷贝重复；仅灰三齿鲨例外，其线粒体基因组包含23个tRNA基因，其中苏氨酸转运RNA（tRNAThr）发生了拷贝重复。

本数据集同时附带用于组装、注释上述线粒体基因组，制备序列比对、划分数据集、指定进化模型，基于传统位点均效串联法、多物种溯祖模型（multispecies coalescent model, MSCM）以及位点异质模型推导系统发育树，并生成用于对比分析的统计数据的代码与配套数据集。

## 数据收集
1. 基因组DNA提取：采用标准CTAB法，或使用NucleoSpin Plant II微型试剂盒（MACHEREY-NAGEL，德国迪伦）的SDS裂解缓冲液（PL2）进行提取；
2. DNA质量管控：使用Qubit 4.0荧光计（赛默飞世尔科技，ThermoFisher Scientific）与LabChip® GXII Touch系统（珀金埃尔默，PerkinElmer，美国马萨诸塞州沃尔瑟姆）完成质检；
3. 文库制备：按照厂商操作手册《Ion Xpress™ Plus gDNA片段文库制备用户指南（MAN0009847 K.0）》，使用Ion Plus Fragment Library Kit（赛默飞世尔科技）完成文库构建；
4. 聚合酶链式反应：以50 ng灰三齿鲨基因组DNA为模板，配置总体系15 μL的反应液，包含1× GoTaq缓冲液、2.5 mM氯化镁（MgCl₂）、200 μM脱氧核糖核苷三磷酸（dNTPs）、每条引物浓度0.3 μM（Cytb CC F：5’-ACTTGAATTGGAGGGCAACC-3’与Dloop Gga R：5’-AGGGTATGTGGGCCATATCA-3’）以及0.625 U GoTaq DNA聚合酶，使用SimpliAmp™ 热循环仪进行扩增。循环参数如下：(i) 94℃初始变性3 min；(ii) 94℃变性30 s，65℃起始退火30 s并逐步降温……

### BAM格式数据：经过筛选的原始Ion Torrent® NGS数据以BAM格式存储，可通过序列分析软件查看，本研究使用Geneious Prime v.2023.2与SPAdes v.3.15进行相关处理。以GenBank格式存储的线粒体基因组组装结果可通过序列分析软件查看，本研究同样采用Geneious Prime v.2023.2，也可通过记事本等标准文本编辑器进行查看与编辑。

### FASTA格式数据：FASTA格式的Sanger测序数据可通过Finch TV v.1.5进行序列修剪，并通过序列分析软件查看；FASTA格式的多序列比对文件可通过序列分析软件查看，本研究使用Geneious Prime v.2023.2，也可选用DAMBE v.7.0.35与MEGA 11作为替代工具，同样可通过记事本等标准文本编辑器进行查看与编辑。

### NEXUS格式数据：NEXUS格式的多序列比对与数据集划分文件可通过序列分析软件查看，本研究使用Geneious Prime v.2023.2，也可选用DAMBE v.7.0.35、PAUP* v.4.0a169与MEGA 11作为替代工具……

本README文件生成于2025年2月25日，作者为Jessica Winn。

## 基本信息
1. 本数据集配套期刊论文标题：《Ion Torrent数据用于皱唇鲨科（软骨鱼纲：Triakidae）线粒体基因组组装与系统发育组学定位》
2. 作者信息：
A. 项目负责人联系方式
姓名：Jessica C. Winn
所属机构：斯泰伦博斯大学（Stellenbosch University）
地址：南非西开普省斯泰伦博斯，斯泰伦博斯大学遗传学系分子育种与生物多样性研究组，邮编7602
邮箱：[e-mail]
ORCiD：https://orcid.org/0000-0003-1070-1276
B. 联合研究者联系方式
姓名：Simo N. Maduna
所属机构：挪威生物经济研究所（Norwegian Institute of Bioeconomy Research）
地址：挪威斯万霍夫德研究站巴伦支斯地区生态系统系，挪威生物经济研究所，邮编9925……