Subject	Genomics
Specific subject area	Lepidoptera, Papilionidae, Mitogenomics
Type of data	•Fasta: Mitogenome sequence data •Tables: Sequencing data, gene features, base composition, list of Lepidoptera mitogenomes used for phylogenetic analyses •Figures: Circular mitogenome map, features of the D-loop regions, phylogenetic tree analysis
How the data were acquired	Whole genome shotgun sequencing using Illumina NovaSeq 6000 platform with 150 paired-end mode (PE150)
Data format	Raw and analyzed
Parameters for data collection	Genomic DNA was extracted from fresh tissue sample of Pachliopta aristolochiae using the Qiagen Blood and Tissue Kit (Qiagen, Valencia, CA) and fragmented using a Bioruptor® system. The library was prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®. The sample was then sent for sequencing using the Illumina NovaSeq 6000 platform with 150 paired-end mode (PE150).
Description of data collection	The assembly was done using NOVOPlasty v.4.2 and run through a PALEOMIX BAM pipeline to assess the mitogenome mapping. Annotation was done using the MITOS v2 web server and the predicted protein-coding genes were further verified using the Open Reading Frame (ORF) Finder. The circular mitogenome map was generated using OGDRAW. PhyloSuite v1.2.2 was used to extract, align and concatenate 13 protein-coding genes from 22 Lepidoptera mitogenomes prior to phylogenetic analysis. IQ-Tree and MrBayes v3.2.7 programs were used to build the phylogenetic trees using Maximum-Likelihood (ML) and Bayesian Inference (BI) probability method. PartitionFinder v2.2.1 was used to set the best partitioning schemes for the dataset. The resulting phylogenetic trees were visualized using Figtree v1.4.4.
Data source location	The sample Pachliopta aristolochiae (voucher no: DIB022) was collected from Sungai Semawak Taman Negara Endau-Rompin Johor, Malaysia (5.62 N, 100.46 E) in March 2019.
Data accessibility	Repository name: NCBI BioProject Data identification number: PRJNA753627 Direct URL to data: http://www.ncbi.nlm.nih.gov/bioproject/753627 Repository name: NCBI GenBank Data identification number: MZ781228 Direct URL to data: https://www.ncbi.nlm.nih.gov/nuccore/mz781228 Repository name: Mendeley Data Data identification number: 10.17632/n52pmth7cc.2 Direct URL to data: https://data.mendeley.com/datasets/n52pmth7cc/2