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Applying a modified metabarcoding approach for the sequencing of macrofungal specimens from fungarium collections

https://doi.org/10.1002/aps3.11508
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/aps3.11410openalex-snapshot
High‐throughput methods for efficiently building massive phylogenies from natural history collections
inferredcites →https://doi.org/10.1002/aps3.11508openalex-snapshot
Applying a modified metabarcoding approach for the sequencing of macrofungal specimens from fungarium collections
inferredcites →https://doi.org/10.1007/s00253-010-2585-4openalex-snapshot
Current state and perspectives of fungal DNA barcoding and rapid identification procedures
inferredcites →https://doi.org/10.1007/s13225-011-0095-zopenalex-snapshot
The contribution of tef-1 sequences to species delimitation in the Cantharellus cibarius complex in the southeastern USA
inferredcites →https://doi.org/10.1007/s13225-020-00455-5openalex-snapshot
Resolving the Mortierellaceae phylogeny through synthesis of multi-gene phylogenetics and phylogenomics
inferredcites →https://doi.org/10.1016/0968-0004(90)90252-7openalex-snapshot
PCR protocols — A guide to methods and applications
inferredcites →https://doi.org/10.1016/b978-0-12-372180-8.50042-1openalex-snapshot
AMPLIFICATION AND DIRECT SEQUENCING OF FUNGAL RIBOSOMAL RNA GENES FOR PHYLOGENETICS
inferredcites →https://doi.org/10.1016/j.fgb.2010.09.006openalex-snapshot
Phylogeny and historical biogeography of true morels (Morchella) reveals an early Cretaceous origin and high continental endemism and provincialism in the Holarctic
inferredcites →https://doi.org/10.1016/j.funbio.2021.10.005openalex-snapshot
Caveats of the internal transcribed spacer region as a barcode to resolve species boundaries in Diaporthe
inferredcites →https://doi.org/10.1016/j.funeco.2012.09.003openalex-snapshot
Comparison of ITS1 and ITS2 rDNA in 454 sequencing of hyperdiverse fungal communities
inferredcites →https://doi.org/10.1038/nmeth.3869openalex-snapshot
DADA2: High-resolution sample inference from Illumina amplicon data
inferredcites →https://doi.org/10.1038/s41579-018-0116-yopenalex-snapshot
Mycobiome diversity: high-throughput sequencing and identification of fungi
inferredcites →https://doi.org/10.1038/srep09687openalex-snapshot
Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform
inferredcites →https://doi.org/10.1073/pnas.1117018109openalex-snapshot
Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
inferredcites →https://doi.org/10.1080/00275514.2021.1897377openalex-snapshot
Morphological and genetic diversification ofRussula floriformis, sp. nov., along the Isthmus of Panama
inferredcites →https://doi.org/10.1080/00275514.2021.1947695openalex-snapshot
Systematic analysis ofRussulain the North American Rocky Mountain alpine zone
inferredcites →https://doi.org/10.1089/cmb.2017.0096openalex-snapshot
cutPrimers: A New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing
inferredcites →https://doi.org/10.1093/bioinformatics/btp033openalex-snapshot
Jalview Version 2—a multiple sequence alignment editor and analysis workbench
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/database/bau061openalex-snapshot
Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
inferredcites →https://doi.org/10.1098/rstb.2017.0392openalex-snapshot
Fungarium specimens: a largely untapped source in global change biology and beyond
inferredcites →https://doi.org/10.1109/gce.2010.5676129openalex-snapshot
Creating the CIPRES Science Gateway for inference of large phylogenetic trees
inferredcites →https://doi.org/10.1111/1755-0998.12065openalex-snapshot
ITS 1 versus ITS 2 as DNA metabarcodes for fungi
inferredcites →https://doi.org/10.1111/1755-0998.12236openalex-snapshot
Next‐generation DNA barcoding: using next‐generation sequencing to enhance and accelerate DNA barcode capture from single specimens
inferredcites →https://doi.org/10.1111/1755-0998.13663openalex-snapshot
DNA barcoding of fungal specimens using PacBio long‐read high‐throughput sequencing
inferredcites →https://doi.org/10.1111/j.1365-294x.1993.tb00005.xopenalex-snapshot
ITS primers with enhanced specificity for basidiomycetes ‐ application to the identification of mycorrhizae and rusts
inferredcites →https://doi.org/10.1111/j.1469-8137.2005.01376.xopenalex-snapshot
UNITE: a database providing web‐based methods for the molecular identification of ectomycorrhizal fungi
inferredcites →https://doi.org/10.1111/j.1469-8137.2011.03707.xopenalex-snapshot
Where is the unseen fungal diversity hidden? A study of Mortierella reveals a large contribution of reference collections to the identification of fungal environmental sequences
inferredcites →https://doi.org/10.1111/j.1574-6941.2012.01437.xopenalex-snapshot
New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities
inferredcites →https://doi.org/10.1111/mec.12481openalex-snapshot
Towards a unified paradigm for sequence‐based identification of fungi
inferredcites →https://doi.org/10.1111/nph.12243openalex-snapshot
Fungal community analysis by high‐throughput sequencing of amplified markers – a user's guide
inferredcites →https://doi.org/10.1111/nph.12923openalex-snapshot
Parsing ecological signal from noise in next generation amplicon sequencing
inferredcites →https://doi.org/10.1128/microbiolspec.funk-0052-2016openalex-snapshot
Fungal Diversity Revisited: 2.2 to 3.8 Million Species
inferredcites →https://doi.org/10.1186/1471-2105-5-113openalex-snapshot
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
inferredcites →https://doi.org/10.1186/1742-9994-4-8openalex-snapshot
Does the DNA barcoding gap exist? – a case study in blue butterflies (Lepidoptera: Lycaenidae)
inferredcites →https://doi.org/10.1186/s40168-017-0259-5openalex-snapshot
Novel soil-inhabiting clades fill gaps in the fungal tree of life
inferredcites →https://doi.org/10.1186/s43008-020-00033-zopenalex-snapshot
Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?
inferredcites →https://doi.org/10.1371/journal.pbio.0030422openalex-snapshot
DNA Barcoding: Error Rates Based on Comprehensive Sampling
inferredcites →https://doi.org/10.1371/journal.pone.0062419openalex-snapshot
Filling Gaps in Biodiversity Knowledge for Macrofungi: Contributions and Assessment of an Herbarium Collection DNA Barcode Sequencing Project
inferredcites →https://doi.org/10.1371/journal.pone.0110808openalex-snapshot
Diverse and Widespread Contamination Evident in the Unmapped Depths of High Throughput Sequencing Data
inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot
Cutadapt removes adapter sequences from high-throughput sequencing reads
inferredcites →https://doi.org/10.15468/dl.fdb9rdopenalex-snapshot
Occurrence Download
inferredcites →https://doi.org/10.3389/fevo.2018.00129openalex-snapshot
Next Generation Sequencing of Ancient Fungal Specimens: The Case of the Saccardo Mycological Herbarium
inferredcites →https://doi.org/10.3390/jof8090932openalex-snapshot
Next-Generation Sequencing of Ancient and Recent Fungarium Specimens
inferredcites →https://doi.org/10.3852/10-331openalex-snapshot
Intragenomic variation in the ITS rDNA region obscures phylogenetic relationships and inflates estimates of operational taxonomic units in genus Laetiporus
inferredcites →https://doi.org/10.3852/12-181openalex-snapshot
Molecular phylogeny and morphology reveal three new species of Cantharellus within 20 m of one another in western Wisconsin, USA
inferredcites →https://doi.org/10.3852/15-230openalex-snapshot
Cantharellus chicagoensis sp. nov. is supported by molecular and morphological analysis as a new yellow chanterelle in midwestern United States
inferredcites →https://doi.org/10.3897/mycokeys.15.9587openalex-snapshot
New reports, phylogenetic analysis, and a key to Lactarius Pers. in the Greater Yellowstone Ecosystem informed by molecular data
inferredcites →https://doi.org/10.3897/mycokeys.30.24376openalex-snapshot
New light on names and naming of dark taxa
inferredcites →https://doi.org/10.3897/mycokeys.53.34761openalex-snapshot
PacBio amplicon sequencing for metabarcoding of mixed DNA samples from lichen herbarium specimens
inferredcites →https://doi.org/10.4137/ebo.s653openalex-snapshot
Intraspecific ITS Variability in the Kingdom Fungi as Expressed in the International Sequence Databases and Its Implications for Molecular Species Identification

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.3897/bdj.14.e198617zenodo-depositor-declared
MycorrhizaTracer: A bioinformatic pipeline for fungi and plant classification of Sanger DNA sequences
inferred← citeshttps://doi.org/10.1002/jmv.70791openalex-snapshot
Geographic and Molecular Insights Into Bat Diversity and Virus Distribution in China: Implications for Public Health
inferred← citeshttps://doi.org/10.1080/00275514.2024.2364567openalex-snapshot
Recent fieldwork and fungarium studies double known diversity of Chlorosplenium and improve understanding of species distributions
inferred← citeshttps://doi.org/10.1080/00275514.2026.2672914openalex-snapshot
Cryptoporus densiflorus , sp. nov. (Polyporaceae), from East Asia and a reassessment of species distributions in Cryptoporus
inferred← citeshttps://doi.org/10.3390/d14040284openalex-snapshot
DNA Barcoding of Fresh and Historical Collections of Lichen-Forming Basidiomycetes in the Genera Cora and Corella (Agaricales: Hygrophoraceae): A Success Story?
inferred← citeshttps://doi.org/10.3390/jof11010060openalex-snapshot
Five New Species of Pezizales from Northeastern China
inferred← citeshttps://doi.org/10.3390/jof8090932openalex-snapshot
Next-Generation Sequencing of Ancient and Recent Fungarium Specimens
inferred← citeshttps://doi.org/10.3390/jof9080788openalex-snapshot
Does One Size Fit All? Variations in the DNA Barcode Gaps of Macrofungal Genera
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