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Updated: Sep 13, 2025

Ultra-long Read Sequencing for Whole Genomic DNA Analysis
Published on: March 15, 2019
The complete mitochondrial genome assembly of Bali cattle (Bos javanicus) using Oxford nanopore long-read sequencing
Saiful Anwar1, Fajrin Shidiq2, Ronny Rachman Noor3
1Graduate School of Animal Production and Technology, Faculty of Animal Science, IPB University, Jl. Agatis, Campus Dramaga, Bogor 16680, West Java, Indonesia; Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Bogor 16911, West Java, Indonesia.
Abstract:
Bali cattle, domesticated from wild banteng (Bos javanicus), serve as an important indigenous genetic resource in Indonesia. Creating a detailed mitochondrial genome (mitogenome) sequence of Bali cattle is essential for population genetic research and promoting sustainable breeding. This study aimed to assemble the complete mitogenome sequence of Bali cattle, analyze its genetic features, and explore its phylogenetic position within the Bos genus. High-molecular-weight genomic DNA was extracted from the blood of a male Bali cattle, and mitogenome sequencing was performed using Oxford Nanopore long-read sequencing, combining nanopore adaptive sampling (NAS) and amplicon-based sequencing approaches. Both NAS and amplicon-based methods can assemble a complete mitogenome of Bali cattle. However, validating NAS assemblies through amplicon-based sequencing improves accuracy and completeness. The complete mitogenome of Bali cattle spans 16,387 bp, comprising 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a non-coding control region (CR), which showed a structure similar to that observed in other Bos species. Phylogenetic analysis showed that Bali cattle group with B. javanicus, closely related to Javan banteng (B. j. javanicus). Interestingly, a unique tandem repeat sequence was found only in the CR of B. j. javanicus, including Bali cattle. Notably, the current NCBI reference mitogenome for B. javanicus (NC_012706.1) is more closely related to B. taurus than to verified B. javanicus sequences, underscoring the need for a reliable B. javanicus-specific reference mitogenome. This study offers novel insights into the comprehensive mitogenomic architecture of Bali cattle. Furthermore, the discovery of a unique tandem repeat motif offers potential as a marker for Bali cattle identification and its applications in forensic and product authentication.
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