Revealing the complete mtDNA genome sequence of Cemani chicken (Gallus gallus) by using Nanopore sequencing analysis

Author:

Sutopo SutopoORCID,Lestari Dela AyuORCID,Setiaji AsepORCID,Bugiwati Sri Rachma AprilitaORCID,Dagong Muhammad Ihsan AndiORCID,Hilmia NenaORCID,Garnida DaniORCID,Asmara Indrawati YudhaORCID,Kurnianto EdyORCID

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.

Funder

Riset Kolaborasi Indonesia

Lembaga Penelitian dan Pengabdian Masyarakat

Universitas Diponegoro

Publisher

Asian Australasian Association of Animal Production Societies

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