Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of the complete mitogenome of the estuarine benthic ribbon worm Yininemertes pratensis (Sun and Lu 1998) (Nemertea: Lineidae).

ABSTRACT: The complete mitogenome of the estuarine ribbon worm Yininemertes pratensis (Sun and Lu 1998) (Nemertea: Lineidae) was sequenced for the first time in the present study. The total length of the newly sequenced mitogenome is 15,616 bp, and it includes 13 protein-coding, 2 rRNA, and 24 tRNA genes, in addition to a noncoding region of 571 bp. The phylogenetic position of Y. pratensis was examined through maximum-likelihood analysis using a concatenated dataset of 13 protein-coding genes from seven selected nemertean species. Yininemertes pratensis is placed within the pilidiophoran group and is closely related to Lineus alborostratus among the selected nemerteans. The newly determined mitogenome sequence will further our knowledge for future phylogenetic and ecological studies of this species.

SUBMITTER: Lee SH

PROVIDER: S-EPMC8451698 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Characterization of the complete mitogenome of the estuarine benthic ribbon worm Yininemertes pratensis (Sun and Lu 1998) (Nemertea: Lineidae).

Lee Sang-Hwa SH Seul Yi Y Kim Kwang-Soo KS Park Taeseo T

Mitochondrial DNA. Part B, Resources 20210915 10

The complete mitogenome of the estuarine ribbon worm Yininemertes pratensis (Sun and Lu 1998) (Nemertea: Lineidae) was sequenced for the first time in the present study. The total length of the newly sequenced mitogenome is 15,616 bp, and it includes 13 protein-coding, 2 rRNA, and 24 tRNA genes, in addition to a noncoding region of 571 bp. The phylogenetic position of Y. pratensis was examined through maximum-likelihood analysis using a concatenated dataset of 13 protein-coding gen ...[more]

PMID: 34553053

Similar Datasets

Tetrodotoxins Secretion and Voltage-Gated Sodium Channel Adaptation in the Ribbon Worm Kulikovia alborostrata (Takakura, 1898) (Nemertea).

Project description:Nemertea is a phylum of marine worms whose members bear various toxins, including tetrodotoxin (TTX) and its analogues. Despite the more than 30 years of studying TTXs in nemerteans, many questions regarding their functions and the mechanisms ensuring their accumulation and usage remain unclear. In the nemertean Kulikovia alborostrata, we studied TTX and 5,6,11-trideoxyTTX concentrations in body extracts and in released mucus, as well as various aspects of the TTX-positive-cell excretion system and voltage-gated sodium (Nav1) channel subtype 1 mutations contributing to the toxins' accumulation. For TTX detection, an immunohistological study with an anti-TTX antibody and HPLC-MS/MS were conducted. For Nav1 mutation searching, PCR amplification with specific primers, followed by Sanger sequencing, was used. The investigation revealed that, in response to an external stimulus, subepidermal TTX-positive cells released secretions actively to the body surface. The post-release toxin recovery in these cells was low for TTX and high for 5,6,11-trideoxyTTX in captivity. According to the data obtained, there is low probability of the targeted usage of TTX as a repellent, and targeted 5,6,11-trideoxyTTX secretion by TTX-bearing nemerteans was suggested as a possibility. The Sanger sequencing revealed identical sequences of the P-loop regions of Nav1 domains I-IV in all 17 studied individuals. Mutations comprising amino acid substitutions, probably contributing to nemertean channel resistance to TTX, were shown.

| S-EPMC8472881 | biostudies-literature

Comparative development of the serotonin- and FMRFamide-immunoreactive components of the nervous system in two distantly related ribbon worm species (Nemertea, Spiralia)

Project description: Not available

| S-EPMC10998470 | biostudies-literature

Genome Size Dynamics in Marine Ribbon Worms (Nemertea, Spiralia).

Project description:Nemertea is a phylum consisting of 1300 mostly marine species. Nemertea is distinguished by an eversible muscular proboscis, and most of the species are venomous. Genomic resources for this phylum are scarce despite their value in understanding biodiversity. Here, we present genome size estimates of Nemertea based on flow cytometry and their relationship to different morphological and developmental traits. Ancestral genome size estimations were done across the nemertean phylogeny. The results increase the available genome size estimates for Nemertea three-fold. Our analyses show that Nemertea has a narrow genome size range (0.43-3.89 pg) compared to other phyla in Lophotrochozoa. A relationship between genome size and evolutionary rate, developmental modes, and habitat was found. Trait analyses show that the highest evolutionary rate of genome size is found in upper intertidal, viviparous species with direct development. Despite previous findings, body size in nemerteans was not correlated with genome size. A relatively small genome (1.18 pg) is assumed for the most recent common ancestor of all extant nemerteans. The results provide an important basis for future studies in nemertean genomics, which will be instrumental to understanding the evolution of this enigmatic and often neglected phylum.

| S-EPMC8468679 | biostudies-literature

Investigation of Peptide Toxin Diversity in Ribbon Worms (Nemertea) Using a Transcriptomic Approach.

Project description:Nemertea is a phylum of nonsegmented worms (supraphylum: Spiralia), also known as ribbon worms. The members of this phylum contain various toxins, including peptide toxins. Here, we provide a transcriptomic analysis of peptide toxins in 14 nemertean species, including Cephalothrix cf. simula, which was sequenced in the current study. The summarized data show that the number of toxin transcripts in the studied nemerteans varied from 12 to 82. The most represented groups of toxins were enzymes and ion channel inhibitors, which, in total, reached a proportion of 72% in some species, and the least represented were pore-forming toxins and neurotoxins, the total proportion of which did not exceed 18%. The study revealed that nemerteans possess a much greater variety of toxins than previously thought and showed that these animals are a promising object for the investigation of venom diversity and evolution, and in the search for new peptide toxins.

| S-EPMC9415933 | biostudies-literature

Mutation and selection cause codon usage and bias in mitochondrial genomes of ribbon worms (Nemertea).

Project description:The phenomenon of codon usage bias is known to exist in many genomes and it is mainly determined by mutation and selection. To understand the patterns of codon usage in nemertean mitochondrial genomes, we use bioinformatic approaches to analyze the protein-coding sequences of eight nemertean species. Neutrality analysis did not find a significant correlation between GC12 and GC3. ENc-plot showed a few genes on or close to the expected curve, but the majority of points with low-ENc values are below it. ENc-plot suggested that mutational bias plays a major role in shaping codon usage. The Parity Rule 2 plot (PR2) analysis showed that GC and AT were not used proportionally and we propose that codons containing A or U at third position are used preferentially in nemertean species, regardless of whether corresponding tRNAs are encoded in the mitochondrial DNA. Context-dependent analysis indicated that the nucleotide at the second codon position slightly affects synonymous codon choices. These results suggested that mutational and selection forces are probably acting to codon usage bias in nemertean mitochondrial genomes.

| S-EPMC3893253 | biostudies-literature

Evaluating the Utility of Single-Locus DNA Barcoding for the Identification of Ribbon Worms (Phylum Nemertea).

Project description:Whereas many nemerteans (ribbon worms; phylum Nemertea) can be identified from external characters if observed alive, many are still problematic. When it comes to preserved specimens (as in e.g. marine inventories), there is a particular need for specimen identifier alternatives. Here, we evaluate the utility of COI (cytochrome c oxidase subunit I) as a single-locus barcoding gene. We sequenced, data mined, and compared gene fragments of COI for 915 individuals representing 161 unique taxonomic labels for 71 genera, and subjected different constellations of these to both distance-based and character-based DNA barcoding approaches, as well as species delimitation analyses. We searched for the presence or absence of a barcoding gap at different taxonomic levels (phylum, subclass, family and genus) in an attempt to understand at what level a putative barcoding gap presents itself. This was performed both using the taxonomic labels as species predictors and using objectively inferred species boundaries recovered from our species delimitation analyses. Our data suggest that COI works as a species identifier for most groups within the phylum, but also that COI data are obscured by misidentifications in sequence databases. Further, our results suggest that the number of predicted species within the dataset is (in some cases substantially) higher than the number of unique taxonomic labels-this highlights the presence of several cryptic lineages within well-established taxa and underscores the urgency of an updated taxonomic backbone for the phylum.

| S-EPMC4865114 | biostudies-literature

A shore-based preliminary survey of marine ribbon worms (Nemertea) from the Caribbean coast of Colombia.

Project description:A checklist of benthic ribbon worm species from the Caribbean coast of Colombia is presented, including synonyms, distributions, a photographic record, and the main morphologic characters of each species for a rapid identification. This is the first research focused broadly on nemerteans in Colombia. 54 specimens of nemerteans were hand-collected from the rocky littoral of two different localities, and identified according to personal experience and specialist literature. 13 species were found; of which 11 represent new records for the country. These species belong to eight different traditionally used families: Tubulanidae, Valenciniidae, Lineidae, Amphiporidae, Cratenemertidae, Emplectonematidae, Drepanophoridae and Ototyphlonemertidae. The most common and abundant species was Dushia atra. The biodiversity of nemerteans in Colombia seems to overlap with the nemertean fauna from Florida and Brazil, explained by the convergence of the North Brazil Current, Guiana Current, Caribbean Currents and the Panama-Colombia Contracurrent in the sampled region. The results of this work suggest that the Caribbean coast of Colombia is a region with a high diversity of nemerteans, and provide important taxonomic data for environmental assessments and future biological research.

| S-EPMC4195936 | biostudies-literature

Intrabody Tetrodotoxin Distribution and Possible Hypothesis for Its Migration in Ribbon Worms Cephalothrix cf. simula (Palaeonemertea, Nemertea).

Project description:Tetrodotoxin (TTX) is a potent neurotoxin found in many marine and terrestrial animals, but only a few species, such as the ribbon worms of the genus Cephalothrix, accumulate it in extremely high concentrations. The intrabody distribution of TTX in highly toxic organisms is of great interest because it helps researchers to understand the pathways by which the toxin migrates, accumulates, and functions in tissues. Using immunohistochemistry with anti-TTX antibodies, the authors of this study investigated the toxin's distribution inside the organs, tissues, and cells of Cephalothrix cf. simula. The cell types of TTX-positive tissues were identified by light microscopy. The main sites of TTX accumulation occurred in the secretory cells of the integuments, the microvilli of the epidermal ciliary cells, cephalic glands, the glandular epithelia of the proboscises, the enterocytes of the digestive systems, and nephridia. Obtained data suggest the toxin migrates from the digestive system through blood vessels to target organs. TTX is excreted from the body through the nephridia and mucus of epidermal cells.

| S-EPMC8465930 | biostudies-literature

Geochemical and Dietary Drivers of Mercury Bioaccumulation in Estuarine Benthic Invertebrates.

Project description:Sediments represent the main reservoir of mercury (Hg) in aquatic environments and may act as a source of Hg to aquatic food webs. Yet, accumulation routes of Hg from the sediment to benthic organisms are poorly constrained. We studied the bioaccumulation of inorganic and methylmercury (HgII and MeHg, respectively) from different geochemical pools of Hg into four groups of benthic invertebrates (amphipods, polychaetes, chironomids, and bivalves). The study was conducted using mesocosm experiments entailing the use of multiple isotopically enriched Hg tracers and simulation of estuarine systems with brackish water and sediment. We applied different loading regimes of nutrients and terrestrial organic matter and showed that the vertical localization and the chemical speciation of HgII and MeHg in the sediment, in combination with the diet composition of the invertebrates, consistently controlled the bioaccumulation of HgII and MeHg into the benthic organisms. Our results suggest a direct link between the concentration of MeHg in the pelagic planktonic food web and the concentration of MeHg in benthic amphipods and, to some extent, in bivalves. In contrast, the quantity of MeHg in benthic chironomids and polychaetes seems to be driven by MeHg accumulation via the benthic food web. Accounting for these geochemical and dietary drivers of Hg bioaccumulation in benthic invertebrates will be important to understand and predict Hg transfer between the benthic and the pelagic food web, under current and future environmental scenarios.

| S-EPMC9301910 | biostudies-literature

The Microbial Community of Tetrodotoxin-Bearing and Non-Tetrodotoxin-Bearing Ribbon Worms (Nemertea) from the Sea of Japan.

Project description:A potent marine toxin, tetrodotoxin (TTX), found in a great variety of marine and some terrestrial species, leaves intriguing questions about its origin and distribution in marine ecosystems. TTX-producing bacteria were found in the cultivable microflora of many TTX-bearing hosts, thereby providing strong support for the hypothesis that the toxin is of bacterial origin in these species. However, metagenomic studies of TTX-bearing animals addressing the whole microbial composition and estimating the contribution of TTX-producing bacteria to the overall toxicity of the host were not conducted. The present study is the first to characterize and compare the 16S rRNA gene data obtained from four TTX-bearing and four non-TTX-bearing species of marine ribbon worms. The statistical analysis showed that different nemertean species harbor distinct bacterial communities, while members of the same species mostly share more similar microbiomes. The bacterial species historically associated with TTX production were found in all studied samples but predominated in TTX-bearing nemertean species. This suggests that deeper knowledge of the microbiome of TTX-bearing animals is a key to understanding the origin of TTX in marine ecosystems.

| S-EPMC7143766 | biostudies-literature