Species delimitation for the molecular taxonomy and ecology of the widely distributed microbial eukaryote genus
            <i>Euplotes</i>
            (Alveolata, Ciliophora)

Zhao, Yan; Yi, Zhenzhen; Warren, Alan; Song, Weibo

doi:10.1098/rspb.2017.2159

Cited by 52 publications

(68 citation statements)

References 52 publications

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“…In the present study, we analyze the germline (MIC) and somatic (MAC) genomes of euplotid ciliates to reveal mechanisms of how single celled organisms survive in diverse environments. Euplotids, one of the most common families of free‐living ciliates, play important roles as both predators of microalgae and preys of multicellular eukaryotes in global waters (Dhanker, Kumar, Tseng, & Hwang, ; Sheng, He, Zhao, Shao, & Miao, ; Zhao, Yi, Warren, & Song, ). They have been widely used for decades as model organisms in studies of predator/prey relationships (Kusch, ; Wiąckowski & Szkarłat, ), cell signalling (Hadjivasiliou, Iwasa, & Pomiankowski, ; Jerka‐Dziadosz, Dosche, Kuhlmann, & Heckmann, ), toxicology of marine pollutants (Trielli et al, ) and experimental ecology (Day, Gong, & Hu, ; Walton, Gates, Kloos, & Fisher, ; Xu, Song, & Warren, ).…”

Section: Introductionmentioning

confidence: 99%

Genome analyses of the new model protist Euplotes vannus focusing on genome rearrangement and resistance to environmental stressors

Chen

Jiang

Gao

et al. 2019

Molecular Ecology Resources

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As a model organism for studies of cell and environmental biology, the free‐living and cosmopolitan ciliate Euplotes vannus shows intriguing features like dual genome architecture (i.e., separate germline and somatic nuclei in each cell/organism), “gene‐sized” chromosomes, stop codon reassignment, programmed ribosomal frameshifting (PRF) and strong resistance to environmental stressors. However, the molecular mechanisms that account for these remarkable traits remain largely unknown. Here we report a combined analysis of de novo assembled high‐quality macronuclear (MAC; i.e., somatic) and partial micronuclear (MIC; i.e., germline) genome sequences for E. vannus, and transcriptome profiling data under varying conditions. The results demonstrate that: (a) the MAC genome contains more than 25,000 complete “gene‐sized” nanochromosomes (~85 Mb haploid genome size) with the N50 ~2.7 kb; (b) although there is a high frequency of frameshifting at stop codons UAA and UAG, we did not observe impaired transcript abundance as a result of PRF in this species as has been reported for other euplotids; (c) the sequence motif 5′‐TA‐3′ is conserved at nearly all internally‐eliminated sequence (IES) boundaries in the MIC genome, and chromosome breakage sites (CBSs) are duplicated and retained in the MAC genome; (d) by profiling the weighted correlation network of genes in the MAC under different environmental stressors, including nutrient scarcity, extreme temperature, salinity and the presence of ammonia, we identified gene clusters that respond to these external physical or chemical stimulations, and (e) we observed a dramatic increase in HSP70 gene transcription under salinity and chemical stresses but surprisingly, not under temperature changes; we link this temperature‐resistance to the evolved loss of temperature stress‐sensitive elements in regulatory regions. Together with the genome resources generated in this study, which are available online at Euplotes vannus Genome Database (http://evan.ciliate.org), these data provide molecular evidence for understanding the unique biology of highly adaptable microorganisms.

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Section: Introductionmentioning

confidence: 99%

Genome analyses of the new model protist Euplotes vannus focusing on genome rearrangement and resistance to environmental stressors

Chen

Jiang

Gao

et al. 2019

Molecular Ecology Resources

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“…2017; Wang, Chen, Sheng, Liu, & Gao, 2017;Wang, Zhang, et al, 2017;Xiong et al, 2016;Yan et al, 2018;Yan, Rogers, Gao, & Katz, 2017;Zhang, Wang, Katz, & Gao, 2018;Zhao, Wang, Wang, Liu, & Gao, 2017;Zhao, Yi, Warren, & Song, 2018). Although these topics have been studied for hundreds of years, there are still many unresolved issues, such as the considerable discordance between morphologies and molecules, which can be caused by convergent morphologies, cryptic species, plastic phenotypes or life-cycle stage variation (reviewed in Lahr, Laughinghouse, Oliverio, Gao, & Katz, 2014).…”

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confidence: 99%

Further analyses on the evolutionary “key‐protist” Halteria (Protista, Ciliophora) based on transcriptomic data

et al. 2019

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Considerable discordance between morphologies and molecules, which can be caused by convergent morphologies, cryptic species or plastic phenotypes, has been frequently detected, especially in microbes. One of the best examples could be the well‐known halteriid ciliates, whose systematic position remains highly unresolved, because it resembles oligotrichs in terms of morphology while associates with hypotrichs in phylogeny based on maker genes. In the present work, we report the deep sequencing and analyses of RNA‐seq data from the representative halteriid, Halteria grandinella. The results indicate that: 1) the transcriptome includes 92,114 genes (aa ≥ 50) with the N50 of 957 bp, which is much better than the single‐cell transcriptome; 2) H. grandinella shares more homologous genes in higher sequence identity with hypotrichous oxytrichids than with oligotrichs; 3) the codon usage bias of H. grandinella is much more similar with that of oligotrich Strombidium sulcatum, and UAA and UAG are reassigned to encode glutamine, which is a common feature of oligotrichs and hypotrichs; and 4) phylogenomic analyses based on 132 orthologs and 47,263 amino acid sites place H. grandinella as a sister to hypotrichs while other oligotrichs cluster together. Based on all the information so far available, we thus suggest that H. grandinella could be an extremely specialized “oligotrich‐like” hypotrich. The similar morphology between halteriids and oligotrichs results from convergent evolution to adapt to the planktonic lifestyle. We hypothesize the evolutionary relationship of the core spirotrichs that halteriids and oxytrichids share the most common ancestor, followed successively by other hypotrichs, oligotrichs/choreotrichs, and euplotids.

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“…The early works on ciliate´s taxonomy solely based on living morphology (Kahl;Müller, 1786), then silver staining (Curds, 1975). However, with the advent of the molecular taxonomy era, there is a clearly increasing number of works that use molecular information to define species (Alekperov et al, 2006;Chen et al, 2013;Syberg-Olsen et al, 2016;Zhao et al, 2018). Yet, still the classification of microbial eukaryotes using DNA barcoding and molecular phylogenies is hindered by the difficulty of isolating specific species, and it kept almost restricted to those that are easily cultured in the laboratory.…”

Section: Introductionmentioning

confidence: 99%

Application of DNA barcoding for identifying potential biotechnological candidate organisms from the River Nile, Egypt.

Mohammed-Geba¹,

Galal²,

Osman³

et al. 2019

Egypt. J. of Aquatic Biolo. and Fish.

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Ciliated protozoa play many fundamental roles in the aquatic environments where they thrive. They mediate the microbial loop of the universal food web, control the surrounding organisms, and act as biomarkers for water quality, beside some capability for the production of bioactive compounds. Identification of different ciliate species is chiefly based on morphological taxonomy. In order to develop molecular tools that facilitate the exploration of freshwater Nile ciliates, a direct, 18srDNAbased PCR assay was tuned up. This assay was tested for DNA-barcoding of some species that prevail the Nile in Mansoura City in the North of Egypt. The resulting sequences were applied to design new species-specific PCR assays for detection of density of these ciliates in River Nile. Using both newly-designed primers and assays, the top identified species were Euplotes woodurffi, Halteria grandinella, and Coleps hirtus. The species-specific primers produced variable-sized PCR amplicons, with densities that were at least correlated by 95 % with the real species count in the riverine water. The newly designed molecular tools are expected to facilitate the exploration and quantification of those species in different aquatic habitats where they exist, adding a major contribution to future efforts for exploiting them as resources for blue biotechnology.

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Species delimitation for the molecular taxonomy and ecology of the widely distributed microbial eukaryote genus Euplotes (Alveolata, Ciliophora)

Cited by 52 publications

References 52 publications

Genome analyses of the new model protist Euplotes vannus focusing on genome rearrangement and resistance to environmental stressors

Genome analyses of the new model protist Euplotes vannus focusing on genome rearrangement and resistance to environmental stressors

Further analyses on the evolutionary “key‐protist” Halteria (Protista, Ciliophora) based on transcriptomic data

Application of DNA barcoding for identifying potential biotechnological candidate organisms from the River Nile, Egypt.

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