ArticleJournal of nematology2023
18S-NemaBase: Curated 18S rRNA Database of Nematode Sequences.
Article in Journal of nematology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Nematode Community Profiling in Organic and Conventional Spinach Systems.Plant-environment interactions (Hoboken, N.J.) · 2026Article
- Geographic distribution of nematodes in the Atacama is associated with elevation, climate gradients and parthenogenesis.Nature communications · 2026Article
- Plant species and soil moisture shape rhizosphere microbiota in an unusually productive tundra ecosystem of North Greenland.Environmental microbiome · 2025Article
- Cas9-based enrichment for targeted long-read metabarcoding.Royal Society open science · 2025Article
- High-Throughput Sequencing Enables Rapid Analyses of Nematode Mitochondrial Genomes from an Environmental Sample.Pathogens (Basel, Switzerland) · 2025Article
- Article
- Identification of potential insect ecological interactions using a metabarcoding approach.PeerJ · 2025Article
- In silico assessment of 18S rDNA metabarcoding markers for the characterization of nematode communities.PloS one · 2024Article
- Metagenomics and metatranscriptomics as potential driving forces for the exploration of diversity and functions of micro-eukaryotes in soil.3 Biotech · 2023Review
- Persistent gaps and errors in reference databases impede ecologically meaningful taxonomy assignments in 18S rRNA studies: a case study of terrestrial and marine nematodes.Environmental DNA (Hoboken, N.J.)Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nematodes are the most abundant and diverse animals on the planet but lack representation in biodiversity research. This presents a problem for studying nematode diversity, particularly when molecular tools (i.e., barcoding and metabarcoding) rely on well-populated and curated reference databases, which are absent for nematodes. To improve molecular identification and the assessment of nematode diversity, we created and curated an 18S rRNA database specific to nematodes (18S-NemaBase) using sequences sourced from the most recent publicly available 18S rRNA SILVA v138 database. As part of the curation process, taxonomic strings were standardized to contain a fixed number of taxonomic ranks relevant to nematology and updated for the most recent accepted nematode classifications. In addition, apparent erroneous sequences were removed. To test the efficacy and accuracy of 18S-NemaBase, we compared it to an older but also curated SILVA v111 and the newest SILVA v138 by assigning taxonomies and analyzing the diversity of a nematode dataset from the Western Nebraska Sandhills. We showed that 18S-NemaBase provided more accurate taxonomic assignments and diversity assessments than either version of SILVA, with a much easier workflow and no need for manual corrections. Additionally, observed diversity further improved when 18S-NemaBase was supplemented with reference sequences from nematodes present in the study site. Although the 18S-NemaBase is a step in the right direction, a concerted effort to increase the number of high-quality, accessible, full-length nematode reference sequences is more important now than ever.
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