ArticleDatabase : the journal of biological databases and curation2020
PLANiTS: a curated sequence reference dataset for plant ITS DNA metabarcoding.
Article in Database : the journal of biological databases and curation, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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.
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.
Who cites it
56 citing papers in PubMed.
- Distinct Environmental DNA States Reveal Biodiversity and Transport Patterns Across Alpine Watersheds.Molecular ecology resources · 2026Article
- When herbal supplements cause heart problems: Clinical case report and forensic toxicological analysis.Toxicology reports · 2026Article
- Real-time PCR to targetFood chemistry. Molecular sciences · 2026Article
- Advancing plant DNA barcoding: integrating chloroplast genome sequencing, cryptic diversity discovery and machine learning.Molecular biology reports · 2026Review
- Proteogenomic investigation of plant constituents in herbal beverages.NPJ science of food · 2026Article
- Inferring plant-bee-microbe associations: Foragers, hive workers, and honey tell complementary stories.PloS one · 2026Article
- The Appalbees menu: a multiyear, multilocus metagenetic assessment of pollen foraging by AppalachianPeerJ · 2026Article
- Non-Native Plants Alter Bird-Plant Frugivory Network Structure in a Human-Modified Tropical Landscape.Ecology and evolution · 2025Article
- Pollen Foraging by Bumble Bee Queens During a Critical Nesting Period Revealed by DNA Metabarcoding.Ecology and evolution · 2025Article
- A Pilot Investigation of the Hidden Communities Associated With Dryas octopetala L. (Rosaceae) in Svalbard Using DNA Metabarcoding.Environmental microbiology reports · 2025Article
- Seasonal and Landscape-Driven Variations in Forage Resources ofEcology and evolution · 2025Article
- First national survey of terrestrial biodiversity using airborne eDNA.Scientific reports · 2025Article
- Teknonaturalist: A Snakemake Pipeline for Assessing Fungal Diversity From Plant Genome Bycatch.Molecular ecology resources · 2025Article
- The Latitudinal Biotic Interaction Hypothesis revisited: contrasting latitudinal richness gradients in actively vs. passively accumulated interaction partners of honey bees.BMC ecology and evolution · 2025Article
- DNA in honey could describe the changes in flower visits and microbe encounters of honey bees over decades.Scientific reports · 2025Article
- Integrating DNA Barcoding Within an Orthogonal Approach for Herbal Product Authentication: A Narrative Review.Phytochemical analysis : PCA · 2025Review
- Exploring winter diet, gut microbiota and parasitism in caribou using multi-marker metabarcoding of fecal DNA.Scientific reports · 2024Article
- Foraging of Honeybees from Different Ecological Areas Determined through Melissopalynological Analysis and DNA Metabarcoding.Insects · 2024Article
- A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses.Molecular ecology resources · 2024Review
- The diet-intestinal microbiota dynamics and adaptation in an elevational migration bird, the Himalayan bluetail (Ecology and evolution · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA metabarcoding combines DNA barcoding with high-throughput sequencing to identify different taxa within environmental communities. The ITS has already been proposed and widely used as universal barcode marker for plants, but a comprehensive, updated and accurate reference dataset of plant ITS sequences has not been available so far. Here, we constructed reference datasets of Viridiplantae ITS1, ITS2 and entire ITS sequences including both Chlorophyta and Streptophyta. The sequences were retrieved from NCBI, and the ITS region was extracted. The sequences underwent identity check to remove misidentified records and were clustered at 99% identity to reduce redundancy and computational effort. For this step, we developed a script called 'better clustering for QIIME' (bc4q) to ensure that the representative sequences are chosen according to the composition of the cluster at a different taxonomic level. The three datasets obtained with the bc4q script are PLANiTS1 (100 224 sequences), PLANiTS2 (96 771 sequences) and PLANiTS (97 550 sequences), and all are pre-formatted for QIIME, being this the most used bioinformatic pipeline for metabarcoding analysis. Being curated and updated reference databases, PLANiTS1, PLANiTS2 and PLANiTS are proposed as a reliable, pivotal first step for a general standardization of plant DNA metabarcoding studies. The bc4q script is presented as a new tool useful in each research dealing with sequences clustering. Database URL: https://github.com/apallavicini/bc4q; https://github.com/apallavicini/PLANiTS.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.