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Molecular Phylogenetics and Evolution Nov 2023Marine planktonic ciliates are largely oligotrichs and choreotrichs, which are two subclasses of the class Spirotrichea. The current phylogenetic assignments of...
Marine planktonic ciliates are largely oligotrichs and choreotrichs, which are two subclasses of the class Spirotrichea. The current phylogenetic assignments of oligotrichs and choreotrichs are inconsistent with previous results based on morphological features, probably hindered by the limited information from a single gene locus. Here we provide 53 new sequences from small subunit ribosomal RNA (SSU rDNA), ITS1-5.8S rDNA-ITS2, and large subunit ribosomal RNA (LSU rDNA) gene loci in 25 oligotrich and choreotrich species. We also predict RNA secondary structures for the ITS2 regions in 55 species, 48 species of which are reported for the first time. Based on these novel data, we make a more comprehensive phylogenetic reconstruction, revealing consistency between morphological taxonomy and an updated phylogenetic system for oligotrichs and choreotrichs. With the addition of data from ciliature patterns and genes, the phylogenetic analysis of the subclass Oligotrichia suggests three evolutionary trajectories, among which: 1) Novistrombidium asserts an ancestral ciliary pattern in Oligotrichia; 2) the subgenera division of Novistrombidium and Parallelostrombidium are fully supported; 3) the three families (Tontoniidae, Pelagostrombidiidae and Cyrtostrombidiidae) all evolved from the most diverse family Strombidiidae, which explains why strombidiids consistently form polyphyletic clades. In the subclass Choreotrichia, Strombidinopsis likely possesses an ancestral position to other choreotrichs, and both phylogenetic analysis and RNA secondary structure prediction support the hypothesis that tintinnids may have evolved from Strombidinopsis. The results presented here offer an updated hypothesis for the evolutionary history of oligotrichs and choreotrichs based on new evidence obtained by expanding sampling of molecular information across multiple gene loci.
Topics: Humans; Phylogeny; Ciliophora; DNA, Ribosomal; RNA; RNA, Ribosomal
PubMed: 37648182
DOI: 10.1016/j.ympev.2023.107911 -
Molecular Phylogenetics and Evolution Sep 2023Peritrichs are one of the largest groups within the class Oligohymenophorea. They have a worldwide distribution and a high degree of species diversity. Using the...
Comparative genomics provides insights into the phylogeny and environmental adaptations of Peritrichia (Protista, Ciliophora) - A potential resource for environmental pollution control and bioremediation.
Peritrichs are one of the largest groups within the class Oligohymenophorea. They have a worldwide distribution and a high degree of species diversity. Using the single-cell genome sequencing technique, we obtained the genomes of five sessilid peritrichs. Combining both genomic and transcriptomic data of other publicly available oligohymenophorean ciliates (including the genomes of three sessilid peritrichs from our team's previous study), we conducted a comparative genomics study. Our phylogenomic analyses using both maximum likelihood and Bayesian inference methods recovered the subclass Peritrichia and each of its two orders (Sessilida and Mobilida) as being monophyletic. The non-monophyly of two families (Vorticellidae and Zoothamniidae) was also well supported in both trees. Molecular clock analysis showed that the origin of the subclass Peritrichia was estimated to be during the late Proterozoic. We also analyzed the stop codon usage of 44 oligohymenophoreans. The results showed that most of these species used TGA as the biased stop codon and reassigned the other two stop codons (TAA and TAG) to code amino acids. In addition, we found that the presence of a typical peritrich lorica is a plesiomorphic character of the family Vaginicolidae. Through GO enrichment analysis for group-specific orthogroups of Vaginicolidae, we successfully identified the biological process and molecular function GO terms that were linked with the typical peritrich lorica, including three glycosaminoglycan-related and two chitin-related GO terms. Finally, our enrichment analyses of significantly expanded gene families in Peritrichia found that sessilids were more tolerant to environmental stress (mainly organic matter) than mobilids, suggesting that peritrich lineages (especially sessilids) may have the potential for application in environmental pollution control and bioremediation. Together, the results presented in this study will facilitate wider genome-scale phylogenetic analyses of Peritrichia and deepen the understanding of their unique advantages for environmental pollution control bioremediation.
Topics: Animals; Phylogeny; Bayes Theorem; Biodegradation, Environmental; Oligohymenophorea; Ciliophora; Genomics; Polyplacophora
PubMed: 37263457
DOI: 10.1016/j.ympev.2023.107835 -
Bioinformatics (Oxford, England) Sep 2023We present an interactive Deep Learning-based software tool for Unsupervised Clustering of DNA Sequences (iDeLUCS), that detects genomic signatures and uses them to...
SUMMARY
We present an interactive Deep Learning-based software tool for Unsupervised Clustering of DNA Sequences (iDeLUCS), that detects genomic signatures and uses them to cluster DNA sequences, without the need for sequence alignment or taxonomic identifiers. iDeLUCS is scalable and user-friendly: its graphical user interface, with support for hardware acceleration, allows the practitioner to fine-tune the different hyper-parameters involved in the training process without requiring extensive knowledge of deep learning. The performance of iDeLUCS was evaluated on a diverse set of datasets: several real genomic datasets from organisms in kingdoms Animalia, Protista, Fungi, Bacteria, and Archaea, three datasets of viral genomes, a dataset of simulated metagenomic reads from microbial genomes, and multiple datasets of synthetic DNA sequences. The performance of iDeLUCS was compared to that of two classical clustering algorithms (k-means++ and GMM) and two clustering algorithms specialized in DNA sequences (MeShClust v3.0 and DeLUCS), using both intrinsic cluster evaluation metrics and external evaluation metrics. In terms of unsupervised clustering accuracy, iDeLUCS outperforms the two classical algorithms by an average of ∼20%, and the two specialized algorithms by an average of ∼12%, on the datasets of real DNA sequences analyzed. Overall, our results indicate that iDeLUCS is a robust clustering method suitable for the clustering of large and diverse datasets of unlabeled DNA sequences.
AVAILABILITY AND IMPLEMENTATION
iDeLUCS is available at https://github.com/Kari-Genomics-Lab/iDeLUCS under the terms of the MIT licence.
Topics: Base Sequence; Deep Learning; Algorithms; Archaea; Cluster Analysis
PubMed: 37589603
DOI: 10.1093/bioinformatics/btad508 -
Nonlinear Dynamics, Psychology, and... Oct 2023In a recent article, we presented evidence demonstrating the existence of hidden y-stories within the genomes of humans and canines. These stories were found not only in...
In a recent article, we presented evidence demonstrating the existence of hidden y-stories within the genomes of humans and canines. These stories were found not only in the non-protein-coding regions but also within the genetic regions and the sequence of exons. Consequently, we are now exploring whether these discoveries are unique to humans and dogs or if they are more widely distributed throughout the cellular world. To approach this question, we embarked on an investigation of the genomes of various species across Whittaker's five kingdoms, namely Animalia, Plantae, Fungi, Protista, and Monera. Through online resources, we obtained and analysed whole-genome sequences of one avian species, one fish species, one reptile species, and one invertebrate species within the Animalia kingdom. Furthermore, we examined the genomes of one plant species, one fungus species, one protozoan species, and two bacterial species. Employing the same methods as in our prior studies, our findings in this study align with our proto knowledge hypothesis, suggesting that all living cells possess a repository of hidden y-information which determines the cellular design, sustains its overall functionality, and governs its performance and behaviour throughout its lifespan until death. We briefly explain life as a bio-linguistic phenomenon and future projects.
Topics: Humans; Animals; Dogs; Eukaryota; Plants; Fungi; Genome; Bacteria
PubMed: 37818598
DOI: No ID Found -
Journal of Chemical Information and... Feb 2024L-tryptophan (l-Trp), a vital amino acid for the survival of various organisms, is synthesized by the enzyme tryptophan synthase (TS) in organisms such as eubacteria,...
L-tryptophan (l-Trp), a vital amino acid for the survival of various organisms, is synthesized by the enzyme tryptophan synthase (TS) in organisms such as eubacteria, archaebacteria, protista, fungi, and plantae. TS, a pyridoxal 5'-phosphate (PLP)-dependent enzyme, comprises α and β subunits that typically form an αβ tetramer. The enzyme's activity is regulated by the conformational switching of its α and β subunits between the open (T state) and closed (R state) conformations. Many microorganisms rely on TS for growth and replication, making the enzyme and the l-Trp biosynthetic pathway potential drug targets. For instance, , bacteria, , , bacteria, and parasitic protozoa depend on l-Trp synthesis. Antibiotic-resistant strains have emerged, underscoring the need for novel drugs targeting the l-Trp biosynthetic pathway, especially for salmonella-related infections. A single amino acid mutation can significantly impact enzyme function, affecting stability, conformational dynamics, and active or allosteric sites. These changes influence interactions, catalytic activity, and protein-ligand/protein-protein interactions. This study focuses on the impact of mutating the βGln114 residue on the catalytic and allosteric sites of TS. Extensive molecular dynamics simulations were conducted on E(PLP), E(AEX), E(A-A), and E(C) forms of TS using the WT, βQ114A, and βQ114N versions. The results show that both the βQ114A and βQ114N mutations increase protein backbone root mean square deviation fluctuations, destabilizing all TS forms. Conformational and hydrogen bond analyses suggest the significance of βGln114 drifting away from cofactor/intermediates and forming hydrogen bonds with water molecules necessary for l-Trp biosynthesis. The βQ114A mutation creates a gap between βAla114 and cofactor/intermediates, hindering hydrogen bond formation due to short side chains and disrupting β-sites. Conversely, the βQ114N mutation positions βAsn114 closer to cofactor/intermediates, forming hydrogen bonds with O3 of cofactors/intermediates and nearby water molecules, potentially disrupting the l-Trp biosynthetic mechanism.
Topics: Humans; Tryptophan Synthase; Catalytic Domain; Molecular Dynamics Simulation; Cryptosporidiosis; Salmonella typhimurium; Cryptosporidium; Protein Conformation; Amino Acids; Mutation; Water; Kinetics
PubMed: 38291608
DOI: 10.1021/acs.jcim.3c01966 -
Scientific Data Oct 2023Calcite shells of planktic foraminifera (Protista, Rhizaria) constitute a large portion of deep-sea sediments. The shells are constructed by sequential addition of...
Calcite shells of planktic foraminifera (Protista, Rhizaria) constitute a large portion of deep-sea sediments. The shells are constructed by sequential addition of partly overlapping chambers with diverse shapes, resulting in complex shell architectures, which are genetically fixed and diagnostic at the species level. The characterisation of the complete architecture requires three-dimensional imaging of the shell, including the partially or entirely covered juvenile chambers. Here we provide reconstructed x-ray micro computed tomography image stacks of 179 specimens of extant planktic foraminifera collected from plankton tows, sediment traps and surface sediments. The specimens have fully resolved and curated taxonomy and represent 43 of the currently recognised 48 holoplanktic species and subspecies. The image stacks form a basis for further applications, such as the characterisation of the architectural morphospace of the extant taxa, allowing studies of species functional ecology, calcification intensity and reconstructions of phylogenetic relationships.
Topics: Ecology; Foraminifera; Phylogeny; X-Ray Microtomography
PubMed: 37798341
DOI: 10.1038/s41597-023-02498-0 -
European Journal of Protistology Oct 2023Erniella Foissner, 1987 is a poorly known genus with its available information limited solely to morphological characteristics. In this study, the type species E....
Morphological, ontogenetic, and phylogenetic research of a poorly known non-dorsomarginalian ciliate: Erniella filiformis Foissner, 1987 (Protista, Ciliophora, Hypotrichia).
Erniella Foissner, 1987 is a poorly known genus with its available information limited solely to morphological characteristics. In this study, the type species E. filiformis, isolated from highly saline water in China, was investigated for morphology, morphogenesis, and phylogeny based on small subunit ribosomal DNA sequences. The main characteristic events during morphogenesis in Erniella filiformis are as follows: (1) in the proter, only the posterior part of the parental adoral zone is renewed and undulating membranes anlage is formed from the dedifferentiation of the old structure; (2) the oral primordium is formed intrakinetally in the opisthe; (3) frontoventral-transverse cirral anlagen II-IV develop in the primary mode, anlage V develops intrakinetally in the proter; and (4) the right frontoventral row is formed by a single anlage. The phylogenetic analyses indicate that Erniella forms a monophyletic group with Bistichella, Keronopsis, Lamtostyla, Orthoamphisiella, Parabistichella, Paraholosticha, and Uroleptoides.
Topics: Phylogeny; DNA, Ribosomal; China; Morphogenesis; Ciliophora; Hypotrichida
PubMed: 37925832
DOI: 10.1016/j.ejop.2023.126031 -
European Journal of Protistology Aug 2023The protist genus Gromia was first described in 1835 by Dujardin and while gromiids are prominent in the marine environment, Gromia oviformis was, for a long time, the...
The protist genus Gromia was first described in 1835 by Dujardin and while gromiids are prominent in the marine environment, Gromia oviformis was, for a long time, the only valid species regularly recorded. To date, 16 species that are morphologically and/or genetically distinct have been described. While recent studies are documenting their diversity and their ecological importance, G. oviformis has been the sole gromiid species identified in the Black Sea, although unnamed Gromia species have also been recorded. We collected sediment samples from the Romanian continental shelf at varying depths (48 - 58 m) to study the morphological and genetic diversity of gromiids in this part of the Black Sea. Three new species, Gromia bugnae sp. nov., Gromia dianae sp. nov. and Gromia fabi sp. nov., were identified based on an integrative taxonomic approach, thus bringing the total described gromiid species to 19. Analysis of partial SSU rRNA gene sequences confirms that these are distinct species. Additionally, an undescribed species is represented by a sequence from the northern part of the Black Sea (Sevastopol, Kazachya Bay). The study provides further evidence of the diversity of gromiids in the Black Sea and underlines the importance of this little-known group in marginal seas.
Topics: Rhizaria; Black Sea; Romania; Eukaryota; Oceans and Seas; Phylogeny
PubMed: 37459806
DOI: 10.1016/j.ejop.2023.126004 -
Molecular Phylogenetics and Evolution Dec 2023The huge variety of species and worldwide distribution of ciliated protists in class Spirotrichea continue to make it one of the most complicated and confused groups in...
Three closely-related subclasses Phacodiniidia Small & Lynn, 1985, Protohypotrichia Shi et al., 1999, and Euplotia Jankowski, 1979 (Protista, Ciliophora): A new contribution to their phylogeny with reconsiderations on the evolutionary hypotheses.
The huge variety of species and worldwide distribution of ciliated protists in class Spirotrichea continue to make it one of the most complicated and confused groups in Ciliophora, despite significant research interest in the unique molecular genetics of these organisms. In this study, the morphological and molecular information were integrated, and it is inferred from a new perspective for the evolutionary relationship among Phacodiniidia, Protohypotrichia, Hypotrichia and Euplotia. Our results indicate that Kiitricha and Caryotricha, two members in Protohypotrichia, may represent two parallel branches of evolution; Euplotidae and Aspidiscidae represent the most recently diverged taxa within Euplotida, followed by Certesiidae, Gastrocirrhidae, and Uronychidae. Further, representative morphological characters (e.g. fronto-ventral-transverse cirral anlagen, undulating membranes, marginal cirri and caudal cirri) were stochastically mapped on phylogenies to speculate evolutionary path and morphological characters of the evolutionary transition node groups were assumed.
Topics: Phylogeny; Ciliophora
PubMed: 37778530
DOI: 10.1016/j.ympev.2023.107936 -
Frontiers in Microbiology 2023Ciliates serve as excellent indicators for water quality monitoring. However, their utilization is hindered by various taxonomic confusions. The ciliate genus Bory de...
Ciliates serve as excellent indicators for water quality monitoring. However, their utilization is hindered by various taxonomic confusions. The ciliate genus Bory de Saint-Vincent, 1824 is commonly found in different aquatic habitats, but its taxonomy has been sparsely investigated using state-of-the-art methods. This study investigated two new species from Nanhui Wetland, Shanghai, China, using living observation, protargol staining, and molecular phylogeny methods. sp. nov. is 180-340 × 20-25 μm in size and possesses 12-16 somatic kineties, 1 terminal contractile vacuole, 2 macronuclear nodules, and 2 types of rod-shaped extrusomes. sp. nov. is distinguished from its congeners by its cell size of 210-400 × 25-35 μm, 14-17 somatic kineties, 1 terminal contractile vacuole, 1 macronucleus, and 2 types of rod-shaped extrusomes. Phylogenetic analyses based on SSU rRNA gene sequences indicate that Lacrymariidae is monophyletic but is not. Additionally, a brief review of the genus is provided in this study. We suggest that Alekperov, 1984, Kahl, 1930, and Burkovsky, 1970 be removed from the genus and propose nov. comb. and nov. comb. for the latter two. ZooBank registration: Present work: urn:lsid:zoobank.org:pub:CDFB1EBD-80BD-4533-B391-CEE89F62EDC4 sp. nov.: urn:lsid:zoobank.org:act:417E7C2D-DAEC-4711-90BB-64AB3CD2F7D5 sp. nov.: urn:lsid:zoobank.org:act:8778D6B0-1F2E-473C-BE19-3F685391A40D.
PubMed: 38029185
DOI: 10.3389/fmicb.2023.1259653