Evidence map›Paper›PMID 41063778›Full record

ArticleEcology and evolution2025

Pruning the Tree: Comparing OTUs and ASVs in High-Throughput Sequencing of 5S-IGS Nuclear Ribosomal DNA in Phylogenetic Studies.

Simone Cardoni, Roberta Piredda, Guido W Grimm, Mariangela Santorsola, Ernst-Detlef Schulze, Thomas Denk, Daniele De Luca, Marco Cosimo Simeone

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Ecology and evolution, 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

8 authors.

Simone CardoniWater Research Institute (IRSA), National Research Council Taranto Italy.
Roberta PireddaDepartment of Research Infrastructures for Marine Biological Resources Naples Italy.
Guido W GrimmUnaffiliated Orléans France.ORCID https://orcid.org/0000-0003-0674-3553
Mariangela SantorsolaDepartment of Biology and Biotechnology 'Lazzaro Spallanzani' University of Pavia Pavia Italy.
Ernst-Detlef SchulzeMax-Planck Institute for Biogeochemistry Jena Germany.
Thomas DenkDepartment of Palaeobiology Swedish Museum of Natural History Stockholm Sweden.
Daniele De LucaDepartment of Humanities Università Degli Studi Suor Orsola Benincasa Naples Italy.ORCID https://orcid.org/0000-0002-1639-9138
Marco Cosimo SimeoneDepartment of Agricultural and Forestry Science (DAFNE) Università Degli Studi Della Tuscia Viterbo Italy.ORCID https://orcid.org/0000-0003-3798-9580

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Amplicon sequencing of the nuclear ribosomal 5S RNA gene arrays is highly promising for genotaxonomy, to delineate genetic resources of species and trace their evolution. However, the huge amount of data retrieved with this approach is difficult to manage and prone to redundancy, error, and computational difficulties. Reducing the amount of data per sample without losing molecular-phylogenetic signal is therefore a crucial step for downstream analyses. In this work, we compared operational taxonomic units (OTUs, 100% identity) and amplicon sequence variants (ASVs) from 5S intergenic spacer (5S-IGS) amplicons of seven beech species (

Indexed as

5S nrDNADADA2Fagushigh‐throughput sequencingMOTHURphylogenetic analysis

Identifiers

PMID41063778
PMCPMC12502049

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

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.