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

IF 2.4 2区农林科学 Q1 AGRICULTURE, DAIRY & ANIMAL SCIENCE

Animal Bioscience Pub Date : 2024-10-01 Epub Date: 2024-06-25 DOI:10.5713/ab.23.0513

Sutopo Sutopo, Dela Ayu Lestari, Asep Setiaji, Sri Rachma Aprilita Bugiwati, Muhammad Ihsan Andi Dagong, Nena Hilmia, Dani Garnida, Indrawati Yudha Asmara, Edy Kurnianto

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引用次数: 0

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.

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利用纳米孔测序分析揭示塞马尼鸡（Gallus gallus）的完整 mtDNA 基因组序列。

研究目的本研究旨在鉴定、发现和探索Cemani鸡（Gallus gallus）mtDNA基因组的特征：牛津纳米孔技术公司（Oxford Nanopore Technologies GridION）利用纳米孔技术进行了WGS mtDNA分析，然后进行了生物信息学和数据分析。然后进行了生物信息学和数据分析：trnQ、trnl、trnL、trnV、trnF、trnP、trnT、trnE、trnL、trnS、trnH）、13 个蛋白编码基因（PCGs）（ND4l、ND3、COX3、ATP6、ATP8、COX2、COX1、ND2、ND1、CYTB、ND6、ND5、ND4）和一个非编码控制区（Dloop）。此外，分析表明，与 GenBank 中的参考文献比对后，Cemani 鸡的 mtDNA 存在多态性位点和氨基酸改变：结论：Dloop基因中的(988T>*)位点和ND3基因中的(328A>G)位点将甘氨酸变为终止密码子，是仅在塞马尼鸡中发现的特异性标记。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Animal Bioscience AGRICULTURE, DAIRY & ANIMAL SCIENCE-

CiteScore

5.00

自引率

0.00%

发文量

223

审稿时长

3 months