ArticleMycoKeys2019
PacBio amplicon sequencing for metabarcoding of mixed DNA samples from lichen herbarium specimens.
Article in MycoKeys, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Whole genome sequencing of historical specimens from the world's largest fungal collection yields high-quality assemblies.The New phytologist · 2026Article
- Global dataset of soil eukaryotic communities created with a uniform protocol and long read sequencing.Scientific data · 2026Article
- The First Whole Genome Sequencing of Historical Lichen Specimens Enables Genome-Wide Analysis of Fungal and Algal Symbionts.Ecology and evolution · 2025Article
- Survey of Lichenized Fungi DNA Barcodes on King George Island (Antarctica): An Aid to Species Discovery.Journal of fungi (Basel, Switzerland) · 2023Article
- Article
- A long-read amplicon approach to scaling up the metabarcoding of lichen herbarium specimens.MycoKeys · 2022Article
- Perspectives and Benefits of High-Throughput Long-Read Sequencing in Microbial Ecology.Applied and environmental microbiology · 2021Review
- Probiotics: their action against pathogens can be turned around.Scientific reports · 2021Article
- Symbiotic microalgal diversity within lichenicolous lichens and crustose hosts on Iberian Peninsula gypsum biocrusts.Scientific reports · 2020Article
- RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory Mechanism.International journal of molecular sciences · 2019Review
- Applying a modified metabarcoding approach for the sequencing of macrofungal specimens from fungarium collections.Applications in plant sciencesArticle
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6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The detection and identification of species of fungi in the environment using molecular methods heavily depends on reliable reference sequence databases. However, these databases are largely incomplete in terms of taxon coverage, and a significant effort is required from herbaria and living fungal collections for the mass-barcoding of well-identified and well-curated fungal specimens or strains. Here, a PacBio amplicon sequencing approach is applied to recent lichen herbarium specimens for the sequencing of the fungal ITS barcode, allowing a higher throughput sample processing than Sanger sequencing, which often required the use of cloning. Out of 96 multiplexed samples, a full-length ITS sequence of the target lichenised fungal species was recovered for 85 specimens. In addition, sequences obtained for co-amplified fungi gave an interesting insight into the diversity of endolichenic fungi. Challenges encountered at both the laboratory and bioinformatic stages are discussed, and cost and quality are compared with Sanger sequencing. With increasing data output and reducing sequencing cost, PacBio amplicon sequencing is seen as a promising approach for the generation of reference sequences for lichenised fungi as well as the characterisation of lichen-associated fungal communities.
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