5 research outputs found
Biogeography and Character Evolution of the Ciliate Genus Euplotes (Spirotrichea, Euplotia), with Description of Euplotes curdsi sp. nov.
Ciliates comprise a diverse and ecologically important phylum of unicellular protists. One of
the most specious and best-defined genera is Euplotes, which constitutes more than 70
morphospecies, many of which have never been molecularly tested. The increasing number
of described Euplotes taxa emphasizes the importance for detailed characterizations of
new ones, requiring standardized morphological observations, sequencing of molecular
markers and careful comparison with previous literature. Here we describe Euplotes curdsi
sp. nov., distinguishable by the combination of the following features: 45±65 μm length,
oval or elongated shape with both ends rounded, narrow peristome with 25±34 adoral
membranelles, conspicuous paroral membrane, double-eurystomus dorsal argyrome type,
6±7 dorsolateral kineties and 10 frontoventral cirri. Three populations of the novel species
have been found in brackish and marine samples in the Mediterranean and the White Sea.
We provide the SSU rRNA gene sequences of these populations, and an updated phylogeny
of the genus Euplotes. Using the molecular phylogenetic tree, we inferred aspects of
the biogeographical history of the genus and the evolution of its most important taxonomic
characters in order to provide a frame for future descriptions. Ultimately, these data reveal
recurrent trends of freshwater invasion and highlight the dynamic, yet convergent, morphological
evolution of Euplotes
Pseudofinder: Detection of Pseudogenes in Prokaryotic Genomes
Prokaryotic genomes are usually densely packed with intact and functional genes. However, in certain contexts, such as after recent ecological shifts or extreme population bottlenecks, broken and nonfunctional gene fragments can quickly accumulate and form a substantial fraction of the genome. Identification of these broken genes, called pseudogenes, is a critical step for understanding the evolutionary forces acting upon, and the functional potential encoded within, prokaryotic genomes. Here, we present Pseudofinder, an open-source software dedicated to pseudogene identification and analysis in bacterial and archaeal genomes. We demonstrate that Pseudofinder’s multi-pronged, reference-based approach can detect a wide variety of pseudogenes, including those that are highly degraded and typically missed by gene-calling pipelines, as well newly formed pseudogenes containing only one or a few inactivating mutations. Additionally, Pseudofinder can detect genes that lack inactivating substitutions but experiencing relaxed selection. Implementation of Pseudofinder in annotation pipelines will allow more precise estimations of the functional potential of sequenced microbes, while also generating new hypotheses related to the evolutionary dynamics of bacterial and archaeal genomes
Sampling locations of the three described populations of <i>Euplotes curdsi</i> sp. nov.
<p>The species has been observed in a brackish lagoon in Italy as well as in marine sediments from the Mediterranean and White Sea.</p
Morphological comparisons between <i>Euplotes curdsi</i> sp. nov. and five similar species.
<p>Characters that are unambiguously different are in bold.</p