AI Article Synopsis
- - Herbaria, which are collections of plant specimens mainly from the 19th and 20th centuries, are valuable for studying the history and evolution of plant pathogens.
- - Recent advancements in high-throughput sequencing technologies have transformed how researchers analyze ancient pathogens, particularly viruses, enabling the reconstruction of historical viral genomes and enhancing our understanding of plant virus ecology.
- - The chapter lays out a specific method for isolating and reconstructing ancient viral sequences from degraded DNA found in herbarium plants and their surrounding soil, utilizing Illumina sequencing and de novo assembly to identify relevant viral DNA.
Article Abstract
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.
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| http://dx.doi.org/10.1007/978-1-0716-3515-5_15 | DOI Listing |
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