ArticleApplications in plant sciences2018
Algorithms and strategies in short-read shotgun metagenomic reconstruction of plant communities.
Article in Applications in plant sciences, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 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
10 citing papers in PubMed, 20 citations in OpenAlex.
- Ancient DNA sheds light on the historical distribution of the rare and ephemeral plant Coleanthus subtilis in Southern Siberia.BMC genomics · 2025Article
- wholeskim: Utilising Genome Skims for Taxonomically Annotating Ancient DNA Metagenomes.Molecular ecology resources · 2025Article
- New prospects of environmental RNA metabarcoding research in biological diversity, ecotoxicological monitoring, and detection of COVID-19: a critical review.Environmental science and pollution research international · 2024Review
- Shotgun metagenomics of soil invertebrate communities reflects taxonomy, biomass, and reference genome properties.Ecology and evolution · 2022Article
- Strategies for molecular authentication of herbal products: from experimental design to data analysis.Chinese medicine · 2022Review
- Article
- Shotgun sequencing of honey DNA can describe honey bee derived environmental signatures and the honey bee hologenome complexity.Scientific reports · 2020Article
- Paleo-metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA.Ecology and evolution · 2020Article
- Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard.Genes · 2018Article
- Algorithms and strategies in short-read shotgun metagenomic reconstruction of plant communities.Applications in plant sciences · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
premise of the studyDNA may be preserved for thousands of years in very cold or dry environments, and plant tissue fragments and pollen trapped in soils and shallow aquatic sediments are well suited for the molecular characterization of past floras. However, one obstacle in this area of study is the limiting bias in the bioinformatic classification of short fragments of degraded DNA from the large, complex genomes of plants.
methodsTo establish one possible baseline protocol for the rapid classification of short-read shotgun metagenomic data for reconstructing plant communities, the read classification programs Kraken, Centrifuge, and MegaBLAST were tested on simulated and ancient data with classification against a reference database targeting plants.
resultsPerformance tests on simulated data suggest that Kraken and Centrifuge outperform MegaBLAST. Kraken tends to be the most conservative approach with high precision, whereas Centrifuge has higher sensitivity. Reanalysis of 13,000 years of ancient sedimentary DNA from North America characterizes potential post-glacial vegetation succession. DISCUSSION: Classification method choice has an impact on performance and any downstream interpretation of results. The reanalysis of ancient DNA from glacial lake sediments yielded vegetation histories that varied depending on method, potentially changing paleoecological conclusions drawn from molecular evidence.
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.