通过纳米孔测序分析揭示塞马尼鸡（原鸡）的完整线粒体DNA基因组序列。

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

作者信息

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

机构信息

Department of Animal Science, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, 50275, Indonesia.

Department of Animal Production, Faculty of Animal Science, Universitas Hasanuddin, Makassar, 90245, Indonesia.

出版信息

Anim Biosci. 2024 Oct;37(10):1664-1672. doi: 10.5713/ab.23.0513. Epub 2024 Jun 25.

DOI:10.5713/ab.23.0513

PMID:38938041

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11366513/

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.

摘要

目的

本研究旨在鉴定、发现和探索塞曼尼鸡（原鸡）线粒体DNA基因组的特征。

方法

本研究使用从肝脏组织分离的塞曼尼鸡的基因组DNA。采用牛津纳米孔技术公司的GridION通过全基因组测序线粒体DNA分析进行线粒体DNA测序。然后进行生物信息学和数据分析。

结果

本研究表明，线粒体DNA基因组长度为16789 bp，由两个核糖体RNA（12S rRNA、16S rRNA）、22个转移RNA基因（trnR、trnG、trnK、trnD、trnS、trnY、trnC、trnN、trnA、trnW、trnM、trnQ、trnl、trnL、trnV、trnF、trnP、trnT、trnE、trnL、trnS、trnH）、13个蛋白质编码基因（PCGs）（ND4l、ND3、COX3、ATP6、ATP8、COX2、COX1、ND2、ND1、CYTB、ND6、ND5、ND4）和一个非编码控制区（D环）组成。此外，分析表明，当塞曼尼鸡线粒体DNA与GenBank中的参考序列比对时，存在多态性位点和氨基酸改变。