Raphidocelis subcapitata strain:NIES-35
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ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| DRR090198_1.fastq.gz | Fastqsanger.gz | |||
| DRR090198_2.fastq.gz | Fastqsanger.gz | |||
| DRR090199_1.fastq.gz | Fastqsanger.gz | |||
| DRR090199_2.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Analysis of single nucleotide polymorphisms (SNPs) in Raphidocelis subcapitata
| PRJDB10240 | ENA
Project description:Microalgae play important ecological roles and serve as useful models for assessing impacts of environmental contaminants on lower trophic aquatic organisms. Sertraline, a commonly prescribed selective serotonin reuptake inhibitor (SSRI) found in urban waters, has been observed to induce chlorosis in Raphidocelis subcapitata close to environmentally relevant concentrations. This study estimated potentially hazardous concentrations of sertraline hydrochloride by deriving transcriptomic and metabolomic points of departure (tPODs and mPODs) below which chronic adverse effects would not be expected. Additionally, an Adverse Outcome Pathway describing the mechanism by which sertraline hydrochloride impacted R. subcapitata was proposed using a multi-omics approach. The mPOD derived from nontargeted metabolomics was comparable to the tPOD (455 µg/L vs 690 µg/L) and annotated dysregulated metabolites along with reduced photosynthetic capability indicated that uncoupling of the cyclic electron flow required for photosynthesis led to a reactive oxygen species (ROS) burst. This probable ROS burst altered cell membrane composition and downregulated genes associated with protoporphyrinogen IX and heme biosynthesis pathways. This research highlights the molecular mechanisms underlying pharmaceutical-induced chlorosis in a model microalgae species and demonstrates the utility of integrating metabolomics and transcriptomics for assessing the potential ecological risks of SSRIs.
2025-08-18 | GSE305568 | GEO
Project description:Nanoscale zero valent iron (nZVI) is used to remediate aquifers polluted by organochlorines or heavy metals and was also suggested to eliminate harmful algal blooms. nZVI can therefore affect microorganisms in the vicinity of the application area, including microalgae. However, studies on early transcriptomic effects of microalgae after exposure to nZVI are rare. Here, we described the early physiological and transcriptomic response of the freshwater ecological indicator green microalga, Raphidocelis subcapitata ATCC 22662, to 100 mg/L of reactive nZVI and non-reactive nano-magnetite (nFe3O4). The combined effect of shading and the release of total iron from nZVI posed a short-term inhibition effect leading to 15 % of deformed cells and cytosol leakage, while cells viability increased after 24 h. nZVI triggered a more pronounced transcriptomic response with (7380 differentially expressed genes [DEGs]) compared to nFe3O4 (4601 DEGs) after 1 h. nZVI, but not nFe3O4 increased the expression of genes function in DNA repair and replication, while deactivated carbohydrate-energy metabolisms, mitochondria signaling, and transmembrane ion transport. This study highlights an early fate assessment of algal cells under nZVI and nFe3O4 exposure using next-generation risk assessment methods and will serve as valuable information for safe and sustainable application of nZVI in water remediation.
2023-06-06 | GSE234088 | GEO
Project description:Due to their environmental prevalence, persistence, and potential toxicity, per- and polyfluoroalkyl substances (PFAS) are contaminants of concern. However, except for a few well studied PFAS, hazard data required to evaluate their risk to aquatic ecosystems are limited. The present study used a 24-hour, high throughput assay to screen 22 PFAS with varying chain lengths and functional groups for effects on the transcriptome of a green algal species, Raphidocelis subcapitata. The tested PFAS included perfluoroalkyl carboxylic acids, perfluoroalkyl carboxylic acid ethers, alcohols, sulfonic acids, and sulfonamides. Algae were exposed in a 96-well microplate format to 8 concentrations (nominally, 100 to 0.03 uM) of each PFAS, in a 1/2 log dilution series. Analytical measurements of PFAS concentration were made at the initiation of exposure and after 24 hours. In addition to traditional endpoints (i.e., biomass, viability, and chlorophyll), RNA was extracted for sequencing of the transcriptome. Concentration response curves were fit to the resulting transcriptomic data to calculate gene-specific benchmark concentrations. The distribution of benchmark concentrations was subsequently used to calculate a transcriptomic point of departure (tPOD) which represents a concentration below which no concerted molecular change is detected in response to PFAS exposure. The resulting tPODs were compared with traditional endpoints and environmentally detected concentrations of specific PFAS.
2025-06-06 | GSE269539 | GEO
Project description:Transcriptomic analysis and cellular responses to nanoscale zero-valent iron in green microalga Raphidocelis subcapitata
| PRJNA980090 | ENA
Project description:Sertraline Hydrochloride Exposure Leads to Reactive Oxygen Species Burst in Model Microalgae Species (Raphidocelis subcapitata)
| PRJNA1306547 | ENA
Project description:The microalga Raphidocelis subcapitata was isolated from the Nitelva River (Norway) and subsequently deposited in the collection of the Norwegian Institute of Water Research as "Selenastrum capricornutum Printz". This freshwater microalga, also known as Pseudokirchneriella subcapitata, acquired much of its notoriety due to its high sensitivity to different chemical species, which makes it recommended by different international organizations for the assessment of ecotoxicity. However, outside this scope, R. subcapitata continues to be little explored. This review aims to shed light on a microalga that, despite its popularity, continues to be an "illustrious" unknown in many ways. Therefore, R. subcapitata taxonomy, phylogeny, shape, size/biovolume, cell ultra-structure, and reproduction are reviewed. The nutritional and cultural conditions, chronological aging, and maintenance and preservation of the alga are summarized and critically discussed. Applications of R. subcapitata, such as its use in aquatic toxicology (ecotoxicity assessment and elucidation of adverse toxic outcome pathways) are presented. Furthermore, the latest advances in the use of this alga in biotechnology, namely in the bioremediation of effluents and the production of value-added biomolecules and biofuels, are highlighted. To end, a perspective regarding the future exploitation of R. subcapitata potentialities, in a modern concept of biorefinery, is outlined. KEY POINTS: • An overview of alga phylogeny and physiology is critically reviewed. • Advances in alga nutrition, cultural conditions, and chronological aging are presented. • Its use in aquatic toxicology and biotechnology is highlighted.
| S-EPMC10876740 | biostudies-literature
Project description:To investigate gene expression in different cells of Chara braunii we performed RNA sequencing of whole thali with rhizoids and thalli without rhizoids in strains NIES 1604 and S276.
2025-09-30 | GSE275253 | GEO
Project description:The Sphaeropleales are a dominant group of green algae, which contain species important to freshwater ecosystems and those that have potential applied usages. In particular, Raphidocelis subcapitata is widely used worldwide for bioassays in toxicological risk assessments. However, there are few comparative genome analyses of the Sphaeropleales. To reveal genome evolution in the Sphaeropleales based on well-resolved phylogenetic relationships, nuclear, mitochondrial, and plastid genomes were sequenced in this study. The plastid genome provides insights into the phylogenetic relationships of R. subcapitata, which is located in the most basal lineage of the four species in the family Selenastraceae. The mitochondrial genome shows dynamic evolutionary histories with intron expansion in the Selenastraceae. The 51.2 Mbp nuclear genome of R. subcapitata, encoding 13,383 protein-coding genes, is more compact than the genome of its closely related oil-rich species, Monoraphidium neglectum (Selenastraceae), Tetradesmus obliquus (Scenedesmaceae), and Chromochloris zofingiensis (Chromochloridaceae); however, the four species share most of their genes. The Sphaeropleales possess a large number of genes for glycerolipid metabolism and sugar assimilation, which suggests that this order is capable of both heterotrophic and mixotrophic lifestyles in nature. Comparison of transporter genes suggests that the Sphaeropleales can adapt to different natural environmental conditions, such as salinity and low metal concentrations.
| S-EPMC5966456 | biostudies-literature