Long amplicon HiFi sequencing for mitochondrial DNA genomes.

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Long-read sequencing offers advanced genetic and genomic research capabilities.
• Mitochondrial DNA (mtDNA) analysis is crucial for understanding population genetics and evolutionary history.

Purpose of the Study:

• To develop and validate a long amplicon high-fidelity (HiFi) sequencing pipeline for mtDNA genomes.
• To investigate the genetic diversity and population structure of Tibetan Mastiffs using this new pipeline.

Main Methods:

• Developed a long amplicon HiFi sequencing pipeline using long-range PCR and circular consensus sequencing (CCS).
• Sequenced mtDNA genomes from pools of 79 Tibetan Mastiffs.
• Utilized two rounds of CCS to assess and improve read accuracy.
• Developed the High-Quality Reads Generator (HQGR) software for data analysis.

Main Results:

• The second round of CCS significantly improved the accuracy of HiFi reads.
• Analysis of 79 high-quality mtDNA genomes revealed evidence of hybridization in Tibetan Mastiffs from outside the Tibetan Plateau.
• The developed pipeline is adaptable for target enrichment strategies in small genomes and candidate genes.

Conclusions:

• The developed long amplicon HiFi sequencing pipeline is effective for high-accuracy mtDNA genome sequencing.
• The study provides insights into the genetic makeup and hybridization events in Tibetan Mastiff populations.
• The HQGR software facilitates accessible data analysis for genomic research.