Sutopo Sutopo, Dela Ayu Lestari, Asep Setiaji, Sri Rachma Aprilita Bugiwati, Muhammad Ihsan Andi Dagong, Nena Hilmia, Dani Garnida, Indrawati Yudha Asmara, Edy Kurnianto
{"title":"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。","authors":"Sutopo Sutopo, Dela Ayu Lestari, Asep Setiaji, Sri Rachma Aprilita Bugiwati, Muhammad Ihsan Andi Dagong, Nena Hilmia, Dani Garnida, Indrawati Yudha Asmara, Edy Kurnianto","doi":"10.5713/ab.23.0513","DOIUrl":null,"url":null,"abstract":"<p><strong>Objective: </strong>This study aimed to identify, discover and explore the characteristics of the mtDNA genomes of Cemani chicken (Gallus gallus).</p><p><strong>Methods: </strong>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.</p><p><strong>Results: </strong>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.</p><p><strong>Conclusion: </strong>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.</p>","PeriodicalId":7825,"journal":{"name":"Animal Bioscience","volume":" ","pages":"1664-1672"},"PeriodicalIF":2.4000,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11366513/pdf/","citationCount":"0","resultStr":"{\"title\":\"Revealing the complete mtDNA genome sequence of Cemani chicken (Gallus gallus) by using Nanopore sequencing analysis.\",\"authors\":\"Sutopo Sutopo, Dela Ayu Lestari, Asep Setiaji, Sri Rachma Aprilita Bugiwati, Muhammad Ihsan Andi Dagong, Nena Hilmia, Dani Garnida, Indrawati Yudha Asmara, Edy Kurnianto\",\"doi\":\"10.5713/ab.23.0513\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Objective: </strong>This study aimed to identify, discover and explore the characteristics of the mtDNA genomes of Cemani chicken (Gallus gallus).</p><p><strong>Methods: </strong>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.</p><p><strong>Results: </strong>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.</p><p><strong>Conclusion: </strong>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.</p>\",\"PeriodicalId\":7825,\"journal\":{\"name\":\"Animal Bioscience\",\"volume\":\" \",\"pages\":\"1664-1672\"},\"PeriodicalIF\":2.4000,\"publicationDate\":\"2024-10-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11366513/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Animal Bioscience\",\"FirstCategoryId\":\"97\",\"ListUrlMain\":\"https://doi.org/10.5713/ab.23.0513\",\"RegionNum\":2,\"RegionCategory\":\"农林科学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/6/25 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q1\",\"JCRName\":\"AGRICULTURE, DAIRY & ANIMAL SCIENCE\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Animal Bioscience","FirstCategoryId":"97","ListUrlMain":"https://doi.org/10.5713/ab.23.0513","RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/6/25 0:00:00","PubModel":"Epub","JCR":"Q1","JCRName":"AGRICULTURE, DAIRY & ANIMAL SCIENCE","Score":null,"Total":0}
Revealing the complete mtDNA genome sequence of Cemani chicken (Gallus gallus) by using Nanopore sequencing analysis.
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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