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Isolation, Characterization, and Total DNA Extraction to Identify Endophytic Fungi in Mycoheterotrophic Plants
Published on: May 5, 2023
Metagenomics Approach for Identification of Arbuscular Mycorrhizal Fungal Sequences in Historical Herbarium Specimens
Gianluca Grasso1,2, Roland Marmeisse3,4, Valeria Bianciotto4
1Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE-PSL, Université des Antilles, Paris, France. gianluca.grasso@mnhn.fr.
Abstract:
Metagenomics offers a powerful alternative to amplicon-based approaches for investigating arbuscular mycorrhizal fungi (AMF) in samples characterized by highly degraded DNA, such as historical herbarium specimens. Here, we present a dedicated bioinformatic pipeline for the retrieval and authentication of AMF sequences from shotgun metagenomic datasets generated from herbarium-associated soils. The workflow integrates quality control and reads preprocessing, taxonomic classification using Kraken2, targeted extrafction of AMF reads, and mapping to reference genomes using short-read-optimized alignment strategies. Authentication of historical DNA is achieved through the analysis of post-mortem damage patterns, including fragment length distributions and cytosine deamination profiles, using MapDamage2. This pipeline enables the detection of ancient AMF DNA, and it could provide a framework for studying long-term dynamics of plant-mycorrhizal associations from historical soil archives.
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