Assembly of Ancient Mitochondrial Genomes Without a Closely Related Reference Sequence

Area of Science:

• Genomics
• Bioinformatics
• Paleontology

Background:

• Methodological advances in ancient DNA (aDNA) analysis necessitate bioinformatics skills for handling large datasets.
• Processing and analyzing aDNA data are crucial for both aDNA studies and broader biomedical research.

Purpose of the Study:

• To provide a practical guide for assembling ancient mitochondrial genomes from next-generation sequencing (NGS) data.
• To demonstrate these methods in the absence of closely related reference genomes.
• To offer a hands-on tutorial for individuals with limited bioinformatics experience.

Main Methods:

• Assembly of ancient mitochondrial genomes directly from genomic DNA-derived NGS data.
• Utilizing key bioinformatics software tools for sequence assembly.
• Implementing strategies for mitogenome assembly without a reference genome.

Main Results:

• Successful reconstruction of a woolly mammoth mitochondrial genome (~45,000 years old).
• Demonstration of effective quality assessment techniques for assembly results lacking a reference genome.

Conclusions:

• The presented methods enable the assembly of ancient mitochondrial genomes from NGS data, even without reference genomes.
• This approach is valuable for researchers with limited bioinformatics experience, facilitating ancient DNA analysis.