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

Isolation, Library Preparation, and Bioinformatic Analysis of Historical and Ancient Plant DNA 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. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Current Protocols in Plant Biology Wiley

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

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Publisher
Wiley
Copyright
© 2020 Wiley Periodicals LLC
ISSN
2379-8068
eISSN
2379-8068
DOI
10.1002/cppb.20121
Publisher site
See Article on Publisher Site

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.

Journal

Current Protocols in Plant BiologyWiley

Published: Dec 1, 2020

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