Evidence map›Paper›PMID 40985414›Full record

ArticleJournal of fungi (Basel, Switzerland)2025

Methodology for Extracting High-Molecular-Weight DNA from Field Collections of Macrofungi.

Leigh A Burgoyne, Andy R Nilsen, Teresa Lebel, Pamela S Catcheside, Tom W May, David Orlovich, Alan Kuo, Anna Lipzen, Kurt Labutti, Robert Riley and 6 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of fungi (Basel, Switzerland), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

16 authors.

Leigh A BurgoyneBiological Sciences, College of Science and Engineering, Flinders University, Adelaide 5001, Australia.
Andy R NilsenDepartment of Botany, University of Otago, Dunedin 9016, New Zealand.ORCID 0000-0003-4724-6289
Teresa LebelBiological Sciences, College of Science and Engineering, Flinders University, Adelaide 5001, Australia.
Pamela S CatchesideBiological Sciences, College of Science and Engineering, Flinders University, Adelaide 5001, Australia.
Tom W MayRoyal Botanic Gardens Victoria, Melbourne 3004, Australia.ORCID 0000-0003-2214-4972
David OrlovichDepartment of Botany, University of Otago, Dunedin 9016, New Zealand.ORCID 0000-0002-9266-2188
Alan KuoU.S Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.ORCID 0000-0003-3514-3530
Anna LipzenU.S Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.ORCID 0000-0003-2293-9329
Kurt LabuttiU.S Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.ORCID 0000-0002-5838-1972
Robert RileyU.S Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.ORCID 0000-0003-0224-0975
William AndreopoulosU.S Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Maxim KoriabineU.S Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Mi YanU.S Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Vivian NgU.S Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.ORCID 0000-0001-8941-6931
Igor V GrigorievU.S Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.ORCID 0000-0002-3136-8903
David E A CatchesideBiological Sciences, College of Science and Engineering, Flinders University, Adelaide 5001, Australia.ORCID 0000-0002-7101-6849

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Many macrofungi are impractical or impossible to culture. Consequently, DNA for long-read sequencing required for the assembly of high-quality genomes must be isolated from samples taken from the environment. Collection is often in remote locations, limiting the options for stabilising samples to methods that do not require refrigeration. Fungi contain species-specific arrays of metabolites that may complicate purification techniques and call for judgement to be made to apply appropriate modifications to the DNA extraction protocol in specific cases. The protocols and commentary we describe are informed by the preparation of DNA from a range of Australasian ectomycorrhizal and saprotrophic macrofungi. We collect samples into isopropanol at ambient temperature and employ a strategy of chromatin isolation followed by the sequential removal of unwanted molecular components to purify DNA.

Indexed as

chromatinDNA extractionfungigenomeslong-read sequencingpurificationremote sampling

Identifiers

PMID40985414
PMCPMC12296062

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.