Anwar Saiful, Shidiq Fajrin, Noor Ronny Rachman, Semiadi Gono, Dharmayanthi Anik Budhi, Furqon Ahmad, Khaerunnisa Isyana, Sutikno Sutikno, Margawati Endang Tri, Jakaria Jakaria
Graduate 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.
Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Bogor 16911, West Java, Indonesia.
Gene. 2025 Sep 20;966:149706. doi: 10.1016/j.gene.2025.149706. Epub 2025 Jul 31.
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.
巴厘牛由野生爪哇野牛（Bos javanicus）驯化而来，是印度尼西亚重要的本土遗传资源。构建详细的巴厘牛线粒体基因组（mitogenome）序列对于群体遗传学研究和促进可持续育种至关重要。本研究旨在组装巴厘牛的完整线粒体基因组序列，分析其遗传特征，并探索其在牛属中的系统发育位置。从一头雄性巴厘牛的血液中提取高分子量基因组DNA，并使用牛津纳米孔长读长测序技术进行线粒体基因组测序，结合纳米孔自适应采样（NAS）和基于扩增子的测序方法。NAS和基于扩增子的方法都可以组装巴厘牛的完整线粒体基因组。然而，通过基于扩增子的测序验证NAS组装可以提高准确性和完整性。巴厘牛的完整线粒体基因组跨度为16387 bp，包括13个蛋白质编码基因（PCGs）、22个转移RNA（tRNA）基因、两个核糖体RNA（rRNA）基因和一个非编码控制区（CR），其结构与其他牛种相似。系统发育分析表明，巴厘牛与爪哇野牛聚为一类，与爪哇爪哇野牛（B. j. javanicus）密切相关。有趣的是，仅在包括巴厘牛在内的爪哇爪哇野牛的CR中发现了一个独特的串联重复序列。值得注意的是，目前NCBI上爪哇野牛的参考线粒体基因组（NC_012706.1）与黄牛的关系比与经过验证的爪哇野牛序列的关系更密切，这突出了需要一个可靠的爪哇野牛特异性参考线粒体基因组。本研究为巴厘牛的完整线粒体基因组结构提供了新的见解。此外，独特串联重复基序的发现为巴厘牛的鉴定及其在法医和产品认证中的应用提供了潜在的标记。
