Analysis of whole mitogenomes from ancient samples

TL;DR

This paper presents an improved protocol for extracting and enriching ancient mitochondrial genomes using high-throughput sequencing, enabling more efficient recovery from degraded samples for archaeological and palaeontological research.

Contribution

The authors introduce a cost-effective, improved protocol for building sequencing libraries and enriching ancient mitogenomes, adaptable for whole-genome sequencing and other genomic regions.

Findings

Enhanced recovery of short DNA fragments from ancient samples.

Protocol increases efficiency and reduces costs of ancient mitogenome sequencing.

Applicable to degraded samples for broader genomic studies.

Abstract

Ancient mitochondrial DNA has been used in a wide variety of palaeontological and archaeological studies, ranging from population dynamics of extinct species to patterns of domestication. Most of these studies have traditionally been based on the analysis of short fragments from the mitochondrial control region, analysed using PCR coupled with Sanger sequencing. With the introduction of high-throughput sequencing, as well as new enrichment technologies, the recovery of full mitochondrial genomes (mitogenomes) from ancient specimens has become significantly less complicated. Here we present a protocol to build ancient extracts into Illumina high-throughput sequencing libraries, and subsequent Agilent array-based capture to enrich for the desired mitogenome. Both are based on previously published protocols, with the introduction of several improvements aimed to increase the recovery of short DNA fragments, while keeping the cost and effort requirements low. This protocol was designed for enrichment of mitochondrial DNA in ancient or degraded samples. However, the protocols can be easily adapted for using for building libraries for shotgun-sequencing of whole genomes, or enrichment of other genomic regions.