Short communication: Complete mitochondrial genome sequence of Bali cattle (Bos javanicus)

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Published: 2025-04-07
DOI: https://doi.org/10.13057/biodiv/d260406
Keywords:
Bali cattle, mtDNA, phylogenetic analysis, sequencing
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JAKARIA JAKARIA ♥
Department of Animal Production and Technology, Faculty of Animal Science, Institut Pertanian Bogor. Jl. Agatis, Dramaga, Bogor 16680, West Java, Indonesia
ANIK BUDHI DHARMAYANTHI
Research Centre for Biosystematics and Evolution, National Research and Innovation Agency. Jl. Raya Jakarta-Bogor Km 46, Cibinong 16911, West Java, Indonesia
DAIROH
Post Doctoral Program, Department of Animal Production and Technology, Faculty of Animal Science, Institut Pertanian Bogor. Jl. Agatis, Dramaga, Bogor 16680, West Java, Indonesia
MOKHAMAD FAKHRUL ULUM
Division of Reproduction and Obstetrics, School of Veterinary Medicine and Biomedical Sciences, Institut Pertanian Bogor. Jl. Agatis, Dramaga, Bogor 16680, West Java, Indonesia
SAIFUL ANWAR
Doctoral Program, Graduate School of Animal Production and Technology, Faculty of Animal Science, Institut Pertanian Bogor. Jl. Agatis, Dramaga, Bogor 16680, West Java, Indonesia
RONNY RACHMAN NOOR
Department of Animal Production and Technology, Faculty of Animal Science, Institut Pertanian Bogor. Jl. Agatis, Dramaga, Bogor 16680, West Java, Indonesia

Abstract

Abstract. Jakaria J, Dharmawanthi AB, Dairoh, Ulum MF, Anwar S, Noor RR. 2025. Short communication: Complete mitochondrial genome sequence of Bali cattle (Bos javanicus). Biodiversitas 26: 1545-1552. Bali cattle (Bos javanicus), one of the most popular indigenous cattle breeds in Indonesia, was domesticated from the wild Banteng. This study aimed to determine the complete mtDNA sequence and assess its genetic variation utilizing the Illumina NovaSeq6000 platform, marking the first time reporting the complete mitochondrial genome sequence of Bali cattle. Blood samples were collected from BBIB Singosari, Malang, East Java. DNA was extracted using the DNA Extraction Kit protocol (Promega). The total mitochondrial genome was annotated using the MITOS2 software. The result of this study showed that mitochondrial DNA (mtDNA) has a total length of 16,712 bp and comprises 37 genes with a typical structure. These include 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and a D-loop region. The nucleotide composition of the genome is 33.6% Adenine (A), 27.1% Thymine (T)/uracil (U), 25.8% Cytosine (C), and 13.4% Guanine (G). Phylogenetic analysis based on the complete mitochondrial genome sequences distinguished into three clades of cattle breed. Including B. javanicus (GenBank data), B. taurus, B. indicus and Bali cattle groups showed notable genetic variations. The results of this work offer genomic information capable of supporting the next investigations on the genetic structure and evolutionary background of Bali cattle.

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Vol. 26 No. 4 (2025)

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References

Abdul-Muneer PM. 2014. Application of microsatellite markers in conservation genetics and fisheries management: Recent advances in population structure analysis and conservation strategies. Genet Res Intl 2014: 691759. DOI: 10.1155/2014/691759.

Andersson L, Purungganan M. 2022. Molecular genetic variation of animals and plants under domestication. Proc Natl Acad Sci USA 119 (30): e2122150119. DOI: 10.1073/pnas.2122150119.

Arbizu CI, Ferro-Maurico RD, Chávez-Galarza JC, Vásquez HV, Maicelo JL, Poemape C, Gonzales J, Quilcate C, Corredor F-A. 2022. The complete mitochondrial genome of a neglected breed, the Peruvian creole cattle (Bos taurus), and its phylogenetic analysis. Data 7 (6): 76. DOI: 10.3390/data7060076.

Deb GK, Khatun R, Hossain SMJ, Rahaman S, Bhuiyan MAB, Mobassirin S, Afrin S, Islam MS, Sarker NR, Bhuyian MSA, Siddiki AZ. 2021. Complete mitochondrial genome sequence of Bos frontalis (Gayal) of Bangladesh. Res Sq 2021: 1-20. DOI: 10.21203/rs.3.rs-754578/v1.

Di Lorenzo P, Ceccobelli S, Panella F, Attard G, Lasagna E. 2015. The role of mitochondrial DNA to determine the origin of domestic chicken. World’s Poult Sci J 71: 311-318. DOI: 10.1017/S0043933915000318.

Dorji J, Jagt CJV, Chamberlain AJ, Cocks BG, MacLeod IM, Daetwyler HD. 2022. Recovery of mitogenomes from whole genome sequences to infer maternal diversity in 1883 modern taurine and indicine cattle. Sci Rep 12 (1): 5582. DOI: 10.1038/s41598-022-09427-y.

Ferreira T, Rodriguez S. 2024. Mitochondrial DNA: Inherent complexities relevant to genetic analyses. Genes 15 (5): 617. DOI: 10.3390/genes15050617.

Fortuna GM, Zumbach BJ, Johnsson M, Pocrnic I, Gorjanc G. 2024. Accounting for nuclear and mito genome in dairy cattle breeding - A simulation study. JDS Commun 5: 572-576. DOI: 10.3168/jdsc.2023-0522.

Freitas PHF, Wang Y, Yan P, Oliveira HR, Schenkel FS, Zhang Y, Xu Q, Brito LF. 2021. Genetic diversity and signatures of selection for thermal stress in cattle and other two Bos species adapted to divergent climatic conditions. Front Genet 12: 604823. DOI: 10.3389/fgene.2021.604823.

Guo X, Bao P, Xiong L, Zhu Y, Wangdui B, Wu X, Ding X, Pei J, Yan P. 2018. The complete mitochondrial genome of Zhangmu cattle (Bos taurus). Conserv Genet Resour 10: 515-517. DOI: 10.1007/s12686-017-0863-5.

Guo X, Xiong L, Liu J, Qi S, Zhuoma Z, Zengcuo G, Pei J, Bao P, Yan P, Ding X. 2017. Study on the complete mitochondrial genome of Qaidam cattle (Bos taurus). Agric Sci Technol 18 (12): 2461-2462.

Gupta A, Bhardwaj A, Supriya, Sharma P, Pal Y, Mamta, Kumar S. 2015. Mitochondrial DNA- A tool for phylogenetic and biodiversity search in equines. J Biodivers Endanger Species S1: 006. DOI: 10.4172/2167-1206.S1-006.

Hafid H. 2020. Performances body dimensions of Bali cattle of traditional livestock in Southeast Sulawesi. Indones J Agric Res 3: 136-144. DOI: 10.32734/injar.v3i2.3997.

Hoang DT, Vinh LS, Flouri T, Stamatakis A, von Haeseler A, Minh BQ. 2018. MPBoot: Fast phylogenetic maximum parsimony tree inference and bootstrap approximation. BMC Evol Biol 18 (1): 11. DOI: 10.1186/s12862-018-1131-3.

Huang B, Khan MZ, Chai W, Ullah Q, Wang C. 2023. Exploring genetic markers: Mitochondrial DNA and genomic screening for biodiversity and production traits in donkeys. Animals 13 (17): 2725. DOI: 10.3390/ani13172725.

Hunter P. 2018. The genetics of domestication. EMBO Rep 19 (2): 201-205. DOI: 10.15252/embr.201745664.

Jakaria J, Musyaddad T, Rahayu S, Muladno M, Sumantri C. 2019. Diversity of D-loop mitochondrial DNA (mtDNA) sequence in Bali and Sumba Ongole cattle breeds. J Indonesia Trop Anim Agric 44 (4): 335-345. DOI: 10.14710/jitaa.44.4.335-345.

Kamalakkannan R, Bhavana K, Prabhu VR, Sureshgopi D, Singha HS, Nagarajan M. 2020. The complete mitochondrial genome of Indian gaur, Bos taurus and its phylogenetic implications. Sci Rep 10 (1): 11936. DOI: 10.1038/s41598-020-68724-6.

Lee J, Lee K-T, Ahn S, Lee S, Lim D, Kim Y-J, Cho E-S, Kim K-S, Dadi H, Kim T-H. 2012. Genetic characterization of Northeast Asian cattle based on sequence polymorphisms in the complete mitochondrial genome. J Anim Sci 2: 217-223. DOI: 10.4236/ojas.2012.24030.

Liu S-J, Lv J-Z, Tan Z-Y, Ge X-Y. 2020. The complete mitochondrial genome of Uruguayan native cattle (Bos taurus). Mitochondrial DNA B Resour 5 (1): 443-444. DOI: 10.1080/23802359.2019.1704639.

Mannen H, Yonezawa T, Murata K, Noda A, Kawaguchi F, Sasazaki S, Olivieri A, Achilli A, Torroni A. 2020. Cattle mitogenome variation reveals a post?glacial expansion of haplogroup P and an early incorporation into northeast Asian domestic herds. Sci Rep 10 (1): 20842. DOI: 10.1038/s41598-020-78040-8.

Misrianti R, Wijaya SH. Sumantri C, Jakaria J. 2022. Investigating genetic diversity of Indonesian native cattle breeds using mitochondrial DNA 16S rRNA gene. Turkish J Vet Anim Sci 46 (3): 457-464. DOI: 10.55730/1300-0128.4216.

Petretto E, Dettori ML, Pazzola M, Manca F, Amills M, Vacca GM. 2022. Mitochondrial DNA diversity of the Sardinian local cattle stock. Sci Rep 12 (1): 2486. DOI: 10.1038/s41598-022-06420-3.

Prabhu VR, Arjun MS, Bhavana K, Kamalakkannan R, Nagarajan M. 2019. Complete mitochondrial genome of Indian mithun, Bos frontalis and its phylogenetic implications. Mol Biol Rep 46 (2): 2561-2566. DOI: 10.1007/s11033-019-04675-0.

Pribadi LW, Maylinda S, Nasich M, Suyadi S. 2015. Reproductive efficiency of Bali cattle and it’s crosses with Simmental breed in the lowland and highland areas of West Nusa Tenggara Province, Indonesia. Livest Res Rural Dev 27 (2): 28.

Putri AE, Farajallah A, Perwitasari D. 2019. The origin of pesisir cattle based on D-loop mitochondrial DNA. Biodiversitas 20 (9): 2569-2575. DOI: 10.13057/biodiv/d200919.

Ren Q, Liu Y, Xie X, Yan B, Zhang K, Yang Y, Qiu Q. 2018. Complete mitochondrial genome of bovine species Gayal (Bos frontalis). Conserv Genet Resour 10: 889-891. DOI: 10.1007/s12686-017-0889-8.

Rong L, Chunging L, Hesong L, Benjuan Z, Heng X, Shanyuan C. 2018. Mitochondrial diversity and phylogeographic structure of native cattle breeds from Yunnan, Southwestern China. Livest Sci 214: 129-134. DOI: 10.1016/j.livsci.2018.06.003.

Rosli N, Sitam FT, Rovie-Ryan JJ, Gan HM, Lee YP, Ithnin H, Gani M, Abdul Razak MFA, Md-Zain BM, Abdullah MT. 2019. The complete mitochondrial genome of Malayan Gaur (Bos gaurus hubbacki) from Peninsular Malaysia. Mitochondrial DNA B Resour 4 (2): 2535-2536. DOI: 10.1080/23802359.2019.1640085.

Sudrajad P, Subiharta S, Adinata Y, Lathifah A, Lee JH, Lenstra JA, Lee SH. 2020. An insight into the evolutionary history of Indonesian cattle assessed by whole genome data analysis. PLoS One 15: e0241038. DOI: 10.1371/journal.pone.0241038.

Suselowati T, Noor RR, Jakaria J. 2023. Haplotype and phylogenetic diversity using mitochondrial 12S rRNA gene marker in Bali cattle. J Indonesian Trop Anim Agric 48: 169-181. DOI: 10.14710/jitaa.48.3.

Tamura K, Stecher G, Kumar S. 2021. MEGA 11: Molecular Evolutionary Genetics Analysis version 11. Mol Biol Evol 38 (7): 3022-3027. DOI: 10.1093/molbev/msab120.

Vadakedath S, Kandi V, Ca J, Vijayan S, Achyut KC, Uppuluri S, Reddy PKK, Ramesh M, Kumar PP. 2023. Mitochondrial deoxyribonucleic acid (mtDNA), maternal inheritance, and their role in the development of cancers: A scoping review. Cureus 15 (6): e39812. DOI: 10.7759/cureus.39812.

Veira MLC, Santini L, Diniz AL, de Freitas Munhoz C. 2016. Microsatellite markers: What they mean and why they are so useful. Genet Mol Biol 39 (3): 312-328. DOI: 10.1590%2F1678-4685-GMB-2016-0027.

Wang X, Zhang YQ, He DC, Yang XM, Li B, Wang DC, Guang J, Xu F, Li JY, Gao X, Gao HJ, Zhang LP, Zhang XZ. 2016. The complete mitochondrial genome of Bos taurus coreanae (Korean native cattle). Mitochondrial DNA A DNA Mapp Seq Anal 27 (1): 120-121. DOI: 10.3109/19401736.2013.873933.

Widyas N, Widi TSM, Prastowo S, Sumantri I, Hayes BJ, Burrow HM. 2022. Promoting sustainable utilization and genetic improvement of Indonesian local beef cattle breeds: A review. Agriculture 12 (10): 1566. DOI: 10.3390/agriculture12101566.

Xia X, Qu K, Li F, Jia P, Chen Q, Chen N, Zhang J, Chen H, Huang B, Lei C. 2019. Abundant genetic diversity of Yunling cattle based on mitochondrial genome. Animals 9 (9): 641. DOI: 10.3390/ani9090641.

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