ArticleRoyal Society open science2017
Taxonomy assignment approach determines the efficiency of identification of OTUs in marine nematodes.
Article in Royal Society open science, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Next-Generation Sequencing for Evaluating the Soil Nematode Diversity and Its Role in Composting Processes.International journal of molecular sciences · 2023Article
- Sensitive and accurate DNA metabarcoding of parasitic helminth mock communities using the mitochondrial rRNA genes.Scientific reports · 2022Article
- Effects of Recreational Boating on Microbial and Meiofauna Diversity in Coastal Shallow Ecosystems of the Baltic Sea.mSphere · 2021Article
- Next-generation sequencing of the soil nematode community enables the sustainability of banana plantations to be monitored.Applied soil ecology : a section of Agriculture, Ecosystems & Environment · 2021Article
- Uncovering diversity and metabolic spectrum of animals in dead zone sediments.Communications biology · 2020Article
- Assessing insect biodiversity with automatic light traps in Brazil: Pearls and pitfalls of metabarcoding samples in preservative ethanol.Ecology and evolution · 2020Article
- Comparison of morphological, DNA barcoding, and metabarcoding characterizations of freshwater nematode communities.Ecology and evolution · 2020Article
- Biodiversity between sand grains: Meiofauna composition across southern and western Sweden assessed by metabarcoding.Biodiversity data journal · 2020Article
- A new nematode species,PeerJ · 2020Article
- Article
- Salinity drives meiofaunal community structure dynamics across the Baltic ecosystem.Molecular ecology · 2019Article
- Metabarcoding free-living marine nematodes using curated 18S and CO1 reference sequence databases for species-level taxonomic assignments.Ecology and evolution · 2019Article
- Biodiversity estimates and ecological interpretations of meiofaunal communities are biased by the taxonomic approach.Communications biology · 2018Article
- NGS-based biodiversity and community structure analysis of meiofaunal eukaryotes in shell sand from Hållö island, Smögen, and soft mud from Gullmarn Fjord, Sweden.Biodiversity data journal · 2017Article
- 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
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Precision and reliability of barcode-based biodiversity assessment can be affected at several steps during acquisition and analysis of data. Identification of operational taxonomic units (OTUs) is one of the crucial steps in the process and can be accomplished using several different approaches, namely, alignment-based, probabilistic, tree-based and phylogeny-based. The number of identified sequences in the reference databases affects the precision of identification. This paper compares the identification of marine nematode OTUs using alignment-based, tree-based and phylogeny-based approaches. Because the nematode reference dataset is limited in its taxonomic scope, OTUs can only be assigned to higher taxonomic categories, families. The phylogeny-based approach using the evolutionary placement algorithm provided the largest number of positively assigned OTUs and was least affected by erroneous sequences and limitations of reference data, compared to alignment-based and tree-based approaches.
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