Animal Bioscience

Asian Australasian Association of Animal Production Societies (아세아태평양축산학회)
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Revealing the complete mtDNA genome sequence of Cemani chicken (Gallus gallus) by using Nanopore sequencing analysis

  • Sutopo Sutopo (Department of Animal Science, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro) ;
  • Dela Ayu Lestari (Department of Animal Science, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro) ;
  • Asep Setiaji (Department of Animal Science, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro) ;
  • Sri Rachma Aprilita Bugiwati (Department of Animal Production, Faculty of Animal Science, Universitas Hasanuddin) ;
  • Muhammad Ihsan Andi Dagong (Department of Animal Production, Faculty of Animal Science, Universitas Hasanuddin) ;
  • Nena Hilmia (Department of Animal Production, Faculty of Animal Husbandry, Universitas Padjajaran) ;
  • Dani Garnida (Department of Animal Production, Faculty of Animal Husbandry, Universitas Padjajaran) ;
  • Indrawati Yudha Asmara (Department of Animal Production, Faculty of Animal Husbandry, Universitas Padjajaran) ;
  • Edy Kurnianto (Department of Animal Science, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro)
  • Received : 2023.12.11
  • Accepted : 2024.05.24
  • Published : 2024.10.01
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Abstract

Objective: This study aimed to identify, discover and explore the characteristics of the mtDNA genomes of Cemani chicken (Gallus gallus). Methods: This study used gDNA of Cemani chicken isolated from liver tissue. mtDNA sequencing was performed using WGS mtDNA analysis with nanopore technology by Oxford Nanopore Technologies GridION. Bioinformatics and data analysis were then performed. Results: This study showed that the length of the mtDNA genome is 16,789 bp, consisting of two ribosomal RNA (12S rRNA, 16S rRNA), 22 transfer RNA genes (trnR, trnG, trnK, trnD, trnS, trnY, trnC, trnN, trnA, trnW, trnM, trnQ, trnl, trnL, trnV, trnF, trnP, trnT, trnE, trnL, trnS, trnH), 13 protein-coding genes (PCGs) (ND4l, ND3, COX3, ATP6, ATP8, COX2, COX1, ND2, ND1, CYTB, ND6, ND5, ND4), and a noncoding control region (Dloop). Furthermore, analysis showed there were polymorphic sites and amino acid alterations when mtDNA Cemani chicken was aligned with references from GenBank. Conclusion: Site (988T>*) in Dloop genes and (328A>G) in ND3 genes which alter glycine to stop codon, were specific markers found only in Cemani chicken.

Keywords

Acknowledgement

All authors thank Lembaga Penelitian dan Pengabdian Masyarakat, Universitas Diponegoro for providing financial support for this research through Riset Kolaborasi Indonesia with contract number 391-08/UN7. D2/PP/V/2023.

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