Panagrellus redivivus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA188692 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR678893_1.fastq.gz | Fastqsanger.gz | |||
| SRR678893_2.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:The genome and transcriptome of Panagrellus redivivus is shaped by the harsh demands of a free-living lifestyle
| PRJNA186477 | ENA
Project description:Panagrellus redivivus Small RNA-Seq data (the microworm)
| PRJNA186507 | ENA
Project description:Nematodes comprise an abundant and diverse invertebrate phylum with members inhabiting nearly every ecological niche. Panagrellus redivivus (the ’microworm’) is a free-living nematode frequently used to understand the evolution of developmental and behavioral processes given its phylogenetic distance to Caenorhabditis elegans. Here we report the de novo sequencing of the genome, transcriptome, and small RNAs of P. redivivus. Using a combination of automated gene finders and RNA‑seq data, we predict 24249 genes and 32676 transcripts. Small RNA analysis revealed 248 micro RNA hairpins, of which 63 had orthologs in other species. Fourteen miRNA clusters containing 42 miRNA precursors were found. P. redivivus has a full complement of genes for regulation of dauer formation despite the apparent absence of dauer juveniles in this species. The RNAi and programmed cell death pathways are largely conserved. Analysis of protein family domain abundance revealed that P. redivivus has experienced a striking expansion of BTB domain‑containing proteins and an unprecedented expansion of the cullin scaffold family of proteins involved in multi‑subunit ubiquitin ligases, suggesting proteolytic plasticity and/or tighter regulation of protein turnover. The eukaryotic release factor (eRF1) protein family has also been dramatically expanded and suggests an ongoing evolutionary arms race with viruses and transposons. The P. redivivus genome provides a resource to advance our understanding of nematode evolution and biology and to further elucidate the genomic architecture leading to free-living lineages, taking advantage of the many fascinating features of this worm revealed by comparative studies.
2013-02-07 | GSE44020 | GEO
Project description:Nematodes comprise an abundant and diverse invertebrate phylum with members inhabiting nearly every ecological niche. Panagrellus redivivus (the M-bM-^@M-^YmicrowormM-bM-^@M-^Y) is a free-living nematode frequently used to understand the evolution of developmental and behavioral processes given its phylogenetic distance to Caenorhabditis elegans. Here we report the de novo sequencing of the genome, transcriptome, and small RNAs of P. redivivus. Using a combination of automated gene finders and RNAM-bM-^@M-^Qseq data, we predict 24249 genes and 32676 transcripts. Small RNA analysis revealed 248 micro RNA hairpins, of which 63 had orthologs in other species. Fourteen miRNA clusters containing 42 miRNA precursors were found. P. redivivus has a full complement of genes for regulation of dauer formation despite the apparent absence of dauer juveniles in this species. The RNAi and programmed cell death pathways are largely conserved. Analysis of protein family domain abundance revealed that P. redivivus has experienced a striking expansion of BTB domainM-bM-^@M-^Qcontaining proteins and an unprecedented expansion of the cullin scaffold family of proteins involved in multiM-bM-^@M-^Qsubunit ubiquitin ligases, suggesting proteolytic plasticity and/or tighter regulation of protein turnover. The eukaryotic release factor (eRF1) protein family has also been dramatically expanded and suggests an ongoing evolutionary arms race with viruses and transposons. The P. redivivus genome provides a resource to advance our understanding of nematode evolution and biology and to further elucidate the genomic architecture leading to free-living lineages, taking advantage of the many fascinating features of this worm revealed by comparative studies. Mixed-stage poly-A selected RNA
2013-02-07 | E-GEOD-44020 | biostudies-arrayexpress
Project description:Transcriptome characterization of embryogenesis at a single cell resolution [Panagrellus redivivus]
| PRJNA340451 | ENA
Project description:Nematodes use an extensive chemical language based on glycosides of the dideoxysugar ascarylose for developmental regulation (dauer formation), male sex attraction, aggregation, and dispersal. However, no examples of a female- or hermaphrodite-specific sex attractant have been identified to date. In this study, we investigated the pheromone system of the gonochoristic sour paste nematode Panagrellus redivivus, which produces sex-specific attractants of the opposite sex. Activity-guided fractionation of the P. redivivus exometabolome revealed that males are strongly attracted to ascr#1 (also known as daumone), an ascaroside previously identified from Caenorhabditis elegans hermaphrodites. Female P. redivivus are repelled by high concentrations of ascr#1 but are specifically attracted to a previously unknown ascaroside that we named dhas#18, a dihydroxy derivative of the known ascr#18 and an ascaroside that features extensive functionalization of the lipid-derived side chain. Targeted profiling of the P. redivivus exometabolome revealed several additional ascarosides that did not induce strong chemotaxis. We show that P. redivivus females, but not males, produce the male-attracting ascr#1, whereas males, but not females, produce the female-attracting dhas#18. These results show that ascaroside biosynthesis in P. redivivus is highly sex-specific. Furthermore, the extensive side chain functionalization in dhas#18, which is reminiscent of polyketide-derived natural products, indicates unanticipated biosynthetic capabilities in nematodes.
| S-EPMC3529029 | biostudies-literature
Project description:To better understand the nanosize-relevant toxic effects and underlying mechanisms, N-acetylcysteine (NAC), as a mitigation agent, an ionic form of Zn (ZnCl2), and the binary mixture of ZnO with different particle sizes (15 nm and 140 nm), was used in toxicity assays with the nematode Panagrellus redivivus. The ZnCl2 concentrations were applied to show the amount of dissolved Zn ions present in the test system. Reactive oxygen species (ROS) measuring method was developed to fit the used test system. Our studies have shown that NAC can mitigate the toxic effects of both studied particle sizes. In the applied concentrations, ZnCl2 was less toxic than both of the ZnO particles. This finding indicates that not only ions and ROS produced by the dissolution are behind the toxic effects of the ZnO NPs, but also other particle size-dependent toxic effects, like the spontaneous ROS generation, are also relevant. When the two materials were applied in binary mixtures, the toxic effects increased significantly, and the dissolved zinc content and the ROS generation also increased. It is assumed that the chemical and physical properties of the materials have been mutually reinforcing to form a more reactive mixture that is more toxic to the P. redivivus test organism. Our findings demonstrate the importance of using mitigation agent and mixtures to evaluate the size-dependent toxicity of the ZnO.
| S-EPMC8275494 | biostudies-literature
Project description:The fate of the known sterol precursor squalene 2,3-oxide was investigated in the free-living nematode Panagrellus redivivus. The nematodes were cultured axenically in the presence of [4-(3)H]squalene 2,3-oxide. Radioactivity was found in the total lipids of the isolated nematodes. Essentially all of the radioactivity encountered in the total lipids was found in the non-saponifiable fraction. The components present in the non-saponifiable fraction were separated and isolated by t.l.c. Three labelled components were identified by a combination of t.l.c., g.l.c. and mass spectroscopy. It is established that P. redivivus has the capacity for biosynthesis of lanosterol. No labelled C(27) sterols could be detected.
| S-EPMC1166200 | biostudies-other
Project description:By collecting and processing individual embryonic cells from sequentially older embryos we have generated a single cell transcriptome dataset describing embryogenesis from the fertilized zygote and the first cell divisions for all founder cell lines.
2019-08-29 | GSE86175 | GEO