Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data [PDF]
Metabarcoding and Metagenomics, 2021 Although ciliates are one of the most dominant microbial eukaryotic groups in many environments, there is a lack of updated global ciliate alignments and reference trees that can be used for phylogenetic placement methods to analyze environmental ...
Ľubomír Rajter, Micah Dunthorn
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Are microbes fundamentally different than macroorganisms? Convergence and a possible case for neutral phenotypic evolution in testate amoeba (Amoebozoa: Arcellinida) [PDF]
Royal Society Open Science, 2015 This study reveals extensive phenotypic convergence based on the non-monophyly of genera and morphospecies of testate (shelled) amoebae. Using two independent markers, small subunit ribosomal DNA (ssu-rDNA) and mitochondrial cytochrome oxidase I (COI ...
Angela M. Oliverio +3 more
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Assessing whether alpha-tubulin sequences are suitable for phylogenetic reconstruction of Ciliophora with insights into its evolution in euplotids. [PDF]
PLoS ONE, 2012 The current understanding of ciliate phylogeny is mainly based on analyses of a single gene, the small subunit ribosomal RNA (SSU-rDNA). However, phylogenetic trees based on single gene sequence are not reliable estimators of species trees, and SSU-rDNA ...
Zhenzhen Yi, Laura A Katz, Weibo Song
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The limits of nuclear-encoded SSU rDNA for resolving the diatom phylogeny [PDF]
European Journal of Phycology, 2009 A recent reclassification of diatoms based on phylogenies recovered using the nuclear-encoded SSU rRNA gene contains three major classes, Coscinodiscophyceae, Mediophyceae and the Bacillariophyceae (the CMB hypothesis). We evaluated this with a sequence alignment of 1336 protist and heterokont algae SSU rRNAs, which includes 673 diatoms. Sequences were
Edward C, Theriot +3 more
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Evolution of a Planktonic Foraminifer during Environmental Changes in the Tropical Oceans. [PDF]
PLoS ONE, 2016 Ecological adaptation to environmental changes is a strong driver of evolution, enabling speciation of pelagic plankton in the open ocean without the presence of effective physical barriers to gene flow.
Yurika Ujiié, Yoshiyuki Ishitani
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Genetic diversity of Entamoeba: Novel ribosomal lineages from cockroaches. [PDF]
PLoS ONE, 2017 Our current taxonomic perspective on Entamoeba is largely based on small-subunit ribosomal RNA genes (SSU rDNA) from Entamoeba species identified in vertebrate hosts with minor exceptions such as E. moshkovskii from sewage water and E. marina from marine
Tetsuro Kawano +5 more
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Bioinformatics and Biology Insights, 2009 The high sequence divergence within the small subunit ribosomal RNA gene (SSU rDNA) of foraminifera makes it difficult to establish the homology of individual nucleotides across taxa.
Ralf Aurahs +6 more
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Disentangling sources of variation in SSU rDNA sequences from single cell analyses of ciliates: impact of copy number variation and experimental error [PDF]
Proceedings of the Royal Society B: Biological Sciences, 2017 Chundi Wang, Yurui Wang, Laura A Katz
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Frontiers in Cellular and Infection Microbiology, 2023 We reported a new microsporidium Neoflabelliforma dubium n. sp. from the adipose tissue of Diaphanosoma dubium in China. The infected daphnids generally appeared opaque due to the presence of numerous spore aggregates located in the adipose tissue.
Meiqi Weng +9 more
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Positions of multiple insertions in SSU rDNA of lichen-forming fungi. [PDF]
Molecular Biology and Evolution, 1995 Lichen-forming fungi, in symbiotic associations with algae, frequently have nuclear small subunit ribosomal DNA (SSU rDNA) longer than the 1,800 nucleotides typical for eukaryotes. The lichen-forming ascomycetous fungus Lecanora dispersa contains insertions at eight distinct positions of its SSU rDNA; the lichen-forming fungi Calicium tricolor and ...
A, Gargas, P T, DePriest, J W, Taylor
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