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. 2023 Jul;23(5):1014-1022.
doi: 10.1111/1755-0998.13765. Epub 2023 Feb 18.

Long amplicon HiFi sequencing for mitochondrial DNA genomes

Zheng-Fei Cai  1   2 , Ji-Yuan Hu  3 , Ting-Ting Yin  2 , Da Wang  3 , Quan-Kuan Shen  2 , Cheng Ma  2   4 , Ding-Qin Ou  5 , Ming-Min Xu  2   4 , Xian Shi  2   4 , Qing-Long Li  1   2 , Ru-Nian Wu  2 , Lameck Ajuma  2   4 , Adeniyi C Adeola  2 , Ya-Ping Zhang  1   2   4 , Min-Sheng Peng  2   4
Affiliations

Long amplicon HiFi sequencing for mitochondrial DNA genomes

Zheng-Fei Cai et al. Mol Ecol Resour. 2023 Jul.

Abstract

Long-read sequencing technology is a powerful approach with application in various genetic and genomic research. Herein, we developed the pipeline for long amplicon high-fidelity (HiFi) sequencing and then applied it for sequencing mitochondrial DNA (mtDNA) genomes from pools of 79 Tibetan Mastiffs. We amplified the mtDNA genome with long-range PCR using two pairs of primers. Two rounds of circular consensus sequencing (CCS) were conducted and their accuracy was evaluated. The results indicate that the second round of CCS can improve the accuracy of HiFi reads. In addition, the analysis of 79 high-quality mtDNA genomes shows the Tibetan Mastiffs from outside of the Tibetan Plateau experienced hybridization with other dogs. The high quality reads generator (HQGR) software is provided to facilitate data analyses, which is publicly accessible on GitHub (https://github.com/Caizf-script/HQGR). Our long amplicon HiFi sequencing pipeline can also be applied in various target enrichment strategies for small genomes and candidate genes.

Keywords: HiFi; PacBio; amplicon; dog; mtDNA; sequencing.

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