ArticlePloS one2015
Taxonomic resolutions based on 18S rRNA genes: a case study of subclass copepoda.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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45 citing papers in PubMed.
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- Integrated morphometric and molecular approaches to screen hybrid from wild Labeo rohita and Labeo catla parent populations.Molecular biology reports · 2024Article
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- Scoliosis and kyphosis in blue-spotted and marbled flathead fish associated with aJournal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc · 2024Article
- Deep-sea meiofaunal communities in the south-eastern Levantine basin and their shaping factors - Morphological-taxonomy-free metabarcoding approach.Ecology and evolution · 2024Article
- Diabetes and gut microbiome.Frontiers in microbiology · 2024Review
- Phylogenetic diversity and functional potential of the microbial communities along the Bay of Bengal coast.Scientific reports · 2023Article
- The Role of Repetitive Sequences in Repatterning of Major Ribosomal DNA Clusters in Lepidoptera.Genome biology and evolution · 2023Article
- Identifying Eukaryotes and Factors Influencing Their Biogeography in Drinking Water Metagenomes.Environmental science & technology · 2023Article
- Habitat type and host grazing regimen influence the soil microbial diversity and communities within potential biting midge larval habitats.Environmental microbiome · 2023Article
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Biodiversity studies are commonly conducted using 18S rRNA genes. In this study, we compared the inter-species divergence of variable regions (V1-9) within the copepod 18S rRNA gene, and tested their taxonomic resolutions at different taxonomic levels. Our results indicate that the 18S rRNA gene is a good molecular marker for the study of copepod biodiversity, and our conclusions are as follows: 1) 18S rRNA genes are highly conserved intra-species (intra-species similarities are close to 100%); and could aid in species-level analyses, but with some limitations; 2) nearly-whole-length sequences and some partial regions (around V2, V4, and V9) of the 18S rRNA gene can be used to discriminate between samples at both the family and order levels (with a success rate of about 80%); 3) compared with other regions, V9 has a higher resolution at the genus level (with an identification success rate of about 80%); and 4) V7 is most divergent in length, and would be a good candidate marker for the phylogenetic study of Acartia species. This study also evaluated the correlation between similarity thresholds and the accuracy of using nuclear 18S rRNA genes for the classification of organisms in the subclass Copepoda. We suggest that sample identification accuracy should be considered when a molecular sequence divergence threshold is used for taxonomic identification, and that the lowest similarity threshold should be determined based on a pre-designated level of acceptable accuracy.
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