Phylogenetic Position of Sorogena stoianovitchae and Relationships within the Class Colpodea (Ciliophora) Based on SSU rDNA Sequences

Two Dexiotricha species (Dexiotricha elliptica nov. comb. and Dexiotricha cf. granulosa), respectively isolated from soil north-west of Riyadh, Saudi Arabia, and freshwater in Shanghai, eastern China, were investigated using standard methods. The species Loxocephalus ellipticus Kahl, 1931 is reclassified here in the genus Dexiotricha and was characterized mainly by constantly showing 16 somatic kineties, three post-oral kineties with the middle one shortened, a contractile vacuole located subcaudally with an excretory pore near the posterior end of somatic kinety 2 and single caudal cilia. A Dexiotricha granulosa-like organism having a subcaudally located contractile vacuole and fewer somatic kineties was designated D. cf. granulosa. The small-subunit rRNA gene (SSU rDNA) sequences of these two species were characterized and their phylogenetic positions based on SSU rDNA sequences were revealed by means of Bayesian inference and maximum-likelihood analysis. Phylogenetic analyses confirmed Dexiotricha as a monophyletic genus and supported its assignment to the order Loxocephalida. However, its family assignment remains unsupported.

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Gastronautidae Deroux, 1994 and Trithigmostoma Jankowski, 1967: Evolutionary Links Among Cyrtophorian Ciliates (Protista, Ciliophora, and Phyllopharyngea)

Frontiers in Marine Science ◽

10.3389/fmars.2021.625644 ◽

2021 ◽

Vol 8 ◽

Author(s):

Zhishuai Qu ◽

Hongbo Pan ◽

Congcong Wang ◽

Honggang Ma ◽

Thorsten Stoeck ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Molecular Data ◽

Ssu Rdna ◽

Phylogenetic Position ◽

Special Position ◽

Morphological Taxonomy ◽

Rdna Sequences ◽

Closed Circle ◽

The Family ◽

Morphological Research

Studies on cyrtophorian ciliates (Cyrtophoria) have accumulated much knowledge on morphological taxonomy and molecular phylogeny, and the general classification and phylogenetic relationships of most families have thereby been revealed. However, the phylogenetic position of the family Gastronautidae Deroux, 1994 remains uncertain. This is due to the presence of specialized characteristics (in particular a circumoral kinety in a closed circle), and most importantly, the lack of molecular data of this family. In addition, TrithigmostomaJankowski, 1967 holds a special position among genera in Chilodonellidae Deroux, 1976 due to its divergent characteristics. In the present work, we studied a new gastronautid, Gastronauta paraloisi sp. n., and three populations of Trithigmostoma cucullulus (Müller, 1786) Jankowski, 1967, using integrative methods. Species identifications were confirmed by morphological research. We also obtained SSU rDNA sequences, which included the first available sequence of Gastronautidae. The following SSU rDNA-inferred phylogenetic analyses showed that the establishment of the family Gastronautidae is necessary, and Gastronautidae and Trithigmostoma may represent intermediate evolutionary links in the order Chlamydodontida.

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Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data

Metabarcoding and Metagenomics ◽

10.3897/mbmg.5.69602 ◽

2021 ◽

Vol 5 ◽

Author(s):

Ľubomír Rajter ◽

Micah Dunthorn

Keyword(s):

Species Richness ◽

Ssu Rdna ◽

Phylogenetic Position ◽

Phylogenetic Placement ◽

Rdna Sequences ◽

Ecological Parameters ◽

Taxonomic Assignments

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 metabarcoding data. Here we fill this gap by providing reference alignments and trees for those ciliates taxa with available SSU-rDNA sequences derived from identified species. Each alignment contains 478 ciliate and six outgroup taxa, and they were made using different masking strategies for alignment positions (unmasked, masked and masked except the hypervariable V4 region). We constrained the monophyly of the major ciliate groups based on the recently updated classification of protists and based on phylogenomic data. Taxa of uncertain phylogenetic position were kept unconstrained, except for Mesodinium species that we constrained to form a clade with the Litostomatea. These ciliate reference alignments and trees can be used to perform taxonomic assignments of metabarcoding data, discover novel ciliate clades, estimate species richness, and overlay measured ecological parameters onto the phylogenetic placements.

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Panagrellus levitatus sp. n. (Rhabditida: Panagrolaimidae), a nematode suppressing Drosophila melanogaster in laboratory cultures

Nematology ◽

10.1163/15685411-00003141 ◽

2018 ◽

Vol 20 (3) ◽

pp. 285-297 ◽

Cited By ~ 2

Author(s):

Elena Ivanova ◽

Ksenia Perfilieva ◽

Sergei Spiridonov

Keyword(s):

Drosophila Melanogaster ◽

New Species ◽

Nematode Species ◽

Laboratory Culture ◽

Ssu Rdna ◽

Lsu Rdna ◽

Red Palm Weevil ◽

Rdna Sequences ◽

Mass Reproduction ◽

First Time

A new nematode species recovered from the laboratory culture ofDrosophila melanogasteris described and illustrated. The mass reproduction ofPanagrellus levitatussp. n. in the fly culture occurred several times and resulted in a significant reduction of the fly population. Nematode outbreaks happened after the introduction ofD. melanogasterto the culture from natural sources. The new species is morphologically similar toP. ulmi. Partial LSU rDNA and SSU rDNA sequences were obtained and subjected to phylogenetic analysis that demonstrated the affinity of the new species withPanagrellussp. ‘MC2014’ from a red palm weevil. For the first time, the dauer juveniles ofPanagrelluswere described.

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Phylogenetic relationships ofSphaerophoraceae (Ascomycetes) inferred from SSU rDNA sequences

Plant Systematics and Evolution ◽

10.1007/bf00991525 ◽

1998 ◽

Vol 209 (1-2) ◽

pp. 75-83 ◽

Cited By ~ 30

Author(s):

Mats Wedin ◽

Anders Tehler ◽

Andrea Gargas

Keyword(s):

Phylogenetic Relationships ◽

Ssu Rdna ◽

Rdna Sequences

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Using Nuclear-encoded LSU and SSU rDNA Sequences to Identify the Eukaryotic Endosymbiont in Amphisolenia bidentata (Dinophyceae)

Protist ◽

10.1016/j.protis.2012.10.001 ◽

2013 ◽

Vol 164 (3) ◽

pp. 411-422 ◽

Cited By ~ 12

Author(s):

Niels Daugbjerg ◽

Maria Hastrup Jensen ◽

Per Juel Hansen

Keyword(s):

Ssu Rdna ◽

Rdna Sequences

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Quantitative Measure of Small-Subunit rRNA Gene Sequences of the Kingdom Korarchaeota

Applied and Environmental Microbiology ◽

10.1128/aem.64.12.5064-5066.1998 ◽

1998 ◽

Vol 64 (12) ◽

pp. 5064-5066 ◽

Cited By ~ 21

Author(s):

Clifford F. Brunk ◽

Nicole Eis

Keyword(s):

Internal Standard ◽

Pcr Amplification ◽

Quantitative Measure ◽

Pcr Primers ◽

Small Subunit ◽

Ssu Rdna ◽

Rdna Sequence ◽

Rrna Gene ◽

Small Subunit Rrna ◽

Rdna Sequences

ABSTRACT Comparative PCR amplification of small-subunit (SSU) rRNA gene (rDNA) sequences indicates substantial preferential PCR amplification of pJP27 sequences with korarchaeote-specific PCR primers. The coamplification of a modified SSU rDNA sequence can be used as an internal standard to determine the amount of a specific SSU rDNA sequence.

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