Identification of DNA Viruses in Ancient DNA from Herbarium Samples.

Autor:	Grasso G; Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi of Turin, Turin, Italy.; Muséum National d'Histoire Naturelle, Institut Systématique Evolution, Biodiversité, (ISYEB: UMR7205 CNRS-MNHN-Sorbonne Université-EPHE-UA), Paris, France.; Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), Turin, Italy., Rotunno S; Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), Turin, Italy., Debruyne R; Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE: UMR 7209 CNRS-MNHN), Paris, France., Bittner L; Muséum National d'Histoire Naturelle, Institut Systématique Evolution, Biodiversité, (ISYEB: UMR7205 CNRS-MNHN-Sorbonne Université-EPHE-UA), Paris, France.; Institut Universitaire de France, Paris, France., Miozzi L; Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), Turin, Italy., Marmeisse R; Muséum National d'Histoire Naturelle, Institut Systématique Evolution, Biodiversité, (ISYEB: UMR7205 CNRS-MNHN-Sorbonne Université-EPHE-UA), Paris, France. roland.marmeisse@mnhn.fr.; Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), Turin, Italy. roland.marmeisse@mnhn.fr., Bianciotto V; Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), Turin, Italy. valeria.bianciotto@ipsp.cnr.it.
Jazyk:	angličtina
Zdroj:	Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2024; Vol. 2732, pp. 221-234.
DOI:	10.1007/978-1-0716-3515-5_15
Abstrakt:	Herbaria encompass millions of plant specimens, mostly collected in the nineteenth and twentieth centuries that can represent a key resource for investigating the history and evolution of phytopathogens. In the last years, the application of high-throughput sequencing technologies for the analysis of ancient nucleic acids has revolutionized the study of ancient pathogens including viruses, allowing the reconstruction of historical genomic viral sequences, improving phylogenetic based molecular dating, and providing essential insight into plant virus ecology. In this chapter, we describe a protocol to reconstruct ancient plant and soil viral sequences starting from highly fragmented ancient DNA extracted from herbarium plants and their associated rhizospheric soil. Following Illumina high-throughput sequencing, sequence data are de novo assembled, and DNA viral sequences are selected, according to their similarity with known viruses. (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)
Databáze:	MEDLINE
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