Mesophilic non-seaweed red algae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA376227 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5278930_1.fastq.gz | Fastqsanger.gz | |||
| SRR5278930_2.fastq.gz | Fastqsanger.gz | |||
| SRR5278931_1.fastq.gz | Fastqsanger.gz | |||
| SRR5278931_2.fastq.gz | Fastqsanger.gz | |||
| SRR5278932_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 13 |
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Project description:The study of macroalgae capacity to acclimate and recover in environments contaminated with Cu and Cd could prove a promising way to understand the tolerance mechanisms of these seaweeds against different pollutants. This study used as a model organism Gracilaria tenuistipitata (Rhodophyta), a macroalga with economic and ecological importance. The partial transcriptome of G. tenuistipitata was profiled using cDNA microarrays in the sixth day of exposition to EC50 metals. Genes involved in Cu and Cd chronic stress belonging to various functional categories suffered shallow modifications. This possibly indicates that G. tenuistipitata would be in the acclimatization process. In addition, the expression of nine stress genes accompanied by analysis of the photosynthetic rate of seaweed to both metals in three different time frames was analyzed. Genetic variation linked to the mechanism of resistance of the algae, determined from EC50 culture conditions established for two metals, occurred in the early hours of treatment. It was found that G. tenuistipitata was able to accumulate these two metals and to resist and acclimate to the negative effects produced by these elements. The temporal analysis from the nine specific genes showed some specific transcriptional responses of the G. tenuistipitata, exposed to Cu and Cd. Three-condition experiment, control cells cultivated in seawater enriched with von Stosch solution vs. copper and cadmium (indepedent) treated cells. Biological replicates: 4 control, 2 copper treated, 2 cadmium treated. All independently grown and harvested. Four replicates per array.
2013-06-01 | E-GEOD-42988 | biostudies-arrayexpress
Project description:The study of macroalgae capacity to acclimate and recover in environments contaminated with Cu and Cd could prove a promising way to understand the tolerance mechanisms of these seaweeds against different pollutants. This study used as a model organism Gracilaria tenuistipitata (Rhodophyta), a macroalga with economic and ecological importance. The partial transcriptome of G. tenuistipitata was profiled using cDNA microarrays in the sixth day of exposition to EC50 metals. Genes involved in Cu and Cd chronic stress belonging to various functional categories suffered shallow modifications. This possibly indicates that G. tenuistipitata would be in the acclimatization process. In addition, the expression of nine stress genes accompanied by analysis of the photosynthetic rate of seaweed to both metals in three different time frames was analyzed. Genetic variation linked to the mechanism of resistance of the algae, determined from EC50 culture conditions established for two metals, occurred in the early hours of treatment. It was found that G. tenuistipitata was able to accumulate these two metals and to resist and acclimate to the negative effects produced by these elements. The temporal analysis from the nine specific genes showed some specific transcriptional responses of the G. tenuistipitata, exposed to Cu and Cd.
2013-06-01 | GSE42988 | GEO
Project description:Light is one of the main environmental cues that affects the physiology and behavior of many organisms. The effect of light on genome-wide transcriptional regulation has been well-studied in green algae and plants, but not in red algae. Cyanidioschyzon merolae is used as a model red algae, and is suitable for studies on transcriptomics because of its compact genome with a relatively small number of genes. In addition, complete genome sequences of the nucleus, mitochondrion, and chloroplast of this organism have been determined. Together, these attributes make C. merolae an ideal model organism to study the response to light stimuli at the transcriptional and the systems biology levels. Previous studies have shown that light significantly affects cell signaling in this organism, but there are no reports on its blue light- and red light-mediated transcriptional responses. We investigated the direct effects of blue and red light at the transcriptional level using RNA-seq. Blue and red light were found to regulate 35% of the total genes in C. merolae. Blue light affected the transcription of genes involved protein synthesis while red light specifically regulated the transcription of genes involved in photosynthesis and DNA repair. Blue or red light regulated genes involved in carbon metabolism and pigment biosynthesis. Overall, our data showed that red and blue light regulate the majority of the cellular, cell division, and repair processes in C. merolae.
2016-09-10 | GSE83828 | GEO
Project description:Light is one of the main environmental cues that affects the physiology and behavior of many organisms. The effect of light on genome-wide transcriptional regulation has been well-studied in green algae and plants, but not in red algae. Cyanidioschyzon merolae is used as a model red algae, and is suitable for studies on transcriptomics because of its compact genome with a relatively small number of genes. In addition, complete genome sequences of the nucleus, mitochondrion, and chloroplast of this organism have been determined. Together, these attributes make C. merolae an ideal model organism to study the response to light stimuli at the transcriptional and the systems biology levels. Previous studies have shown that light significantly affects cell signaling in this organism, but there are no reports on its blue light- and red light-mediated transcriptional responses. We investigated the direct effects of blue and red light at the transcriptional level using RNA-seq. Blue and red light were found to regulate 35% of the total genes in C. merolae. Blue light affected the transcription of genes involved protein synthesis while red light specifically regulated the transcription of genes involved in photosynthesis and DNA repair. Blue or red light regulated genes involved in carbon metabolism and pigment biosynthesis. Overall, our data showed that red and blue light regulate the majority of the cellular, cell division, and repair processes in C. merolae.
2016-09-01 | GSE67303 | GEO
Project description:The common ancestor of red algae (Rhodophyta) has undergone massive genome reduction, whereby 25% of the gene inventory has been lost, followed by its split into the species-poor extremophilic Cyanidiophytina and the broadly distributed mesophilic red algae. Success of the mesophile radiation is surprising given their highly reduced gene inventory. To address this latter issue, we combine an improved genome assembly from the unicellular red alga Porphyridium purpureum with a diverse collection of other algal genomes to reconstruct ancient endosymbiotic gene transfers (EGTs) and gene duplications. We find EGTs associated with the core photosynthetic machinery that may have played important roles in plastid establishment. More significant are the extensive duplications and diversification of nuclear gene families encoding phycobilisome linker proteins that stabilize light-harvesting functions. We speculate that the origin of these complex families in mesophilic red algae may have contributed to their adaptation to a diversity of light environments.
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Project description:Light is one of the main environmental cues that affects the physiology and behavior of many organisms. The effect of light on genome-wide transcriptional regulation has been well-studied in green algae and plants, but not in red algae. Cyanidioschyzon merolae is used as a model red algae, and is suitable for studies on transcriptomics because of its compact genome with a relatively small number of genes. In addition, complete genome sequences of the nucleus, mitochondrion, and chloroplast of this organism have been determined. Together, these attributes make C. merolae an ideal model organism to study the response to light stimuli at the transcriptional and the systems biology levels. Previous studies have shown that light significantly affects cell signaling in this organism, but there are no reports on its blue light- and red light-mediated transcriptional responses. We investigated the direct effects of blue and red light at the transcriptional level using RNA-seq. Blue and red light were found to regulate 35% of the total genes in C. merolae. Blue light affected the transcription of genes involved protein synthesis while red light specifically regulated the transcription of genes involved in photosynthesis and DNA repair. Blue or red light regulated genes involved in carbon metabolism and pigment biosynthesis. Overall, our data showed that red and blue light regulate the majority of the cellular, cell division, and repair processes in C. merolae. Identification of blue light and red light regulated genes by deep sequencing in biological duplicates. qRT-PCR was performed to verify the RNA-seq results.
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Project description:The red seaweed, Asparagopsis taxiformis, is a promising ruminant feed-additive with significant anti-methanogenic properties, which could provide a global solution to climate-change. Emerging genomics in this species has provided a strong foundation for in-depth molecular investigations, including proteomics. Here, we investigated the A. taxiformis (L6) proteome of sporophyte and gametophyte (male and female), using soluble and insoluble extraction methods followed by mass spectrometry. A combined total of 741 and 2007 unique non-redundant proteins were identified using genome-derived and transcriptome-derived databases, respectively. Genome-derived proteins were used for further analysis including a relatively large proportion of proteins that were annotated as ion binding proteins (i.e. iron, zinc, manganese, potassium and copper), which may play a role in heavy metal bioremediation. In addition, we identified 44 photosynthesis-related proteins (e.g. phycobilisomes, photosystem I, photosystem II and ATPase) and 58 stress-related proteins (e.g. heat shock proteins and vanadium-dependent haloperoxidases). Forty proteins were predicted to be secreted, supporting a role for them in extracellular activities such as mucilage development and defence. Two Gal-2,6-Sulfurylases II proteins are likely necessary for carrageenan biosynthesis, as well as development of reproductive-associated structures. These findings provide a comprehensive overview of expressed proteins in A. taxiformis (L6) at two different life stages, highlighting the potential of proteomic approaches and warrant further studies for understanding protein functions.
2023-01-26 | PXD035669 | Pride