ArticleNucleic acids research2000
Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA.
Article in Nucleic acids research, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed.
- The evolution of gene functional repertoire in Amorphea: divergent strategies across Amoebozoa, Fungi, and Metazoa.Molecular biology and evolution · 2026Article
- Comparison of Deep-Sea Picoeukaryotic Composition Estimated from the V4 and V9 Regions of 18S rRNA Gene with a Focus on the Hadal Zone of the Mariana Trench.Microbial ecology · 2022Article
- 18S rRNA variability maps reveal three highly divergent, conserved motifs within Rotifera.BMC ecology and evolution · 2021Article
- Taxonomy on three novel species of Sphaeromyxa Thélohan 1892 (Myxozoa, Bivalvulida, Sphaeromyxidae) with insight into the evolution of the genus.Parasitology research · 2020Article
- Insight into picophytoplankton diversity of the subarctic White Sea-The first recording of Pedinophyceae in environmental DNA.MicrobiologyOpen · 2019Article
- An algebraic language for RNA pseudoknots comparison.BMC bioinformatics · 2019Article
- Rhizarian 'Novel Clade 10' Revealed as Abundant and Diverse Planktonic and Terrestrial Flagellates, including Aquavolon n. gen.The Journal of eukaryotic microbiology · 2018Article
- Protists Within Corals: The Hidden Diversity.Frontiers in microbiology · 2018Article
- Cryptic infection of a broad taxonomic and geographic diversity of tadpoles by Perkinsea protists.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- New Comparative Analysis Based on the Secondary Structure of SSU-rRNA Gene Reveals the Evolutionary Trend and the Family-Genus Characters of Mobilida (Ciliophora, Peritrichia).Current microbiology · 2015Article
- Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods.Ecology and evolution · 2015Article
- Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities?Ecology and evolution · 2015Article
- Deep sequencing uncovers protistan plankton diversity in the Portuguese Ria Formosa solar saltern ponds.Extremophiles : life under extreme conditions · 2015Article
- Article
- Bioinformatic Amplicon Read Processing Strategies Strongly Affect Eukaryotic Diversity and the Taxonomic Composition of Communities.PloS one · 2015Article
- A Multi Size-Level Assessment of Benthic Marine Communities in a Coastal Environment: Are They Different Sides of the Same Coin?PloS one · 2015Article
- New insights into the molecular phylogeny of Balantidium (Ciliophora, Vetibuliferida) based on the analysis of new sequences of species from fish hosts.Parasitology research · 2014Article
- Diverse molecular signatures for ribosomally 'active' Perkinsea in marine sediments.BMC microbiology · 2014Article
- The complete mitochondrial genomes of six species of Tetranychus provide insights into the phylogeny and evolution of spider mites.PloS one · 2014Article
- Lineage-specific molecular probing reveals novel diversity and ecological partitioning of haplosporidians.The ISME journal · 2014Article
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6 authors.
Funding
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Abstract
The secondary structure of V4, the largest variable area of eukaryotic small subunit ribosomal RNA, was re-examined by comparative analysis of 3253 nucleotide sequences distributed over the animal, plant and fungal kingdoms and a diverse set of protist taxa. An extensive search for compensating base pair substitutions and for base covariation revealed that in most eukaryotes the secondary structure of the area consists of 11 helices and includes two pseudoknots. In one of the pseudoknots, exchange of base pairs between the two stems seems to occur, and covariation analysis points to the presence of a base triple. The area also contains three potential insertion points where additional hairpins or branched structures are present in a number of taxa scattered throughout the eukaryotic domain.
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