Isolation, Library Preparation, and Bioinformatic Analysis of Historical and Ancient Plant DNA

Abstract

The ability to sequence DNA retrieved from ancient and historical material plays a crucial role in reinforcing evolutionary and anthropological inference. While the focus of the field is largely on analyzing DNA from ancient hominids and other animals, we have also learned from plant ancient DNA (aDNA), in particular, about human farming practices, crop domestication, environment management, species invasion, and adaptation to various environmental conditions. In the following protocols, we outline best practices for plant aDNA isolation, preparation for sequencing, bioinformatic processing, and authentication. We describe the process all the way from processing of archaeological or historical plant material to characterizing and authenticating sequencing reads. In alternative protocols, we include modifications to this process that are tailored to strongly degraded DNA. Throughout, we stress the importance of precautionary measures to successfully analyze aDNA. Finally, we discuss the evolution of the archaeogenomics field and the development of new methods, which both shaped this protocol. © 2020 Wiley Periodicals LLC.

Basic Protocol 1: Isolation of aDNA

Alternate Protocol 1: Isolation of ultra-short DNA (Dabney modification)

Support Protocol 1: Preparation of PTB-based mix

Support Protocol 2: Preparation of binding buffer

Basic Protocol 2: Preparation of genomic libraries

Alternate Protocol 2: Preparation of genomic libraries with uracil removal

Basic Protocol 3: Bioinformatic processing and authentication of aDNA