Pyrodinium bahamense var. compressum
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ABSTRACT:
PROVIDER: PRJNA261863 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Pyrodinium bahamense var. compressum mRNA sequencing
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Project description:Pyrodinium bahamense var. compressum RNASeq Raw sequence reads
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Project description:Pyrodinium bahamense CCFW293-B5 Transcriptome or Gene expression
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Project description:Shotgun proteomics using label-free quantitation analysis of Pyrodinium bahamense from the Philippines.
2022-12-04 | PXD030176 | JPOST Repository
Project description:Characterization of bacterial communities associated With toxic Dinoflagellates: pyrodinium bahamense Var. compressum
| PRJNA299717 | ENA
Project description:The dataset comprises a whole-genome sequence of Ruegeria sp. PBVC088, a symbiotic (Gram-negative) bacterium associated with Pyrodinium bahamense var. compressum, which has been associated with harmful algal blooms in the coastal waters of west Sabah, Malaysia. Harmful algal blooms contribute to economic losses for the aquaculture industry, as well as human illnesses and fatalities due to paralytic shellfish poisoning. Bacteria-algae dynamics have posited that the interaction is potentially responsible for the toxin production during a toxic harmful algal bloom event. Despite the expanding body of literature on the capabilities of these bacteria to metabolize, produce, and modify toxins autonomously, it has yet to be confirmed that these toxin-producing bacteria are capable of autonomous toxin synthesis. Saxitoxin, a paralytic shellfish poisoning toxin, is produced by a unique biosynthetic pathway, where the genetic basis for the saxitoxin production was first reported in the saxitoxin-producing cyanobacteria strain Cylindrospermopsis raciborskii T3 (NCBI accession no. DQ787200). The genes responsible for saxitoxin biosynthesis in dinoflagellates, have yet to be fully elucidated. The identification of cyanobacteria saxitoxin biosynthesis genes (sxt) may eventually lead to the identification of homologous genes within the dinoflagellates. Previous studies on the diversity of the bacterial communities associated with the same toxic P. bahamense harmful alga has been carried out by using both the culture-dependent 16S ribosomal RNA gene sequence analysis and culture-independent 16S metagenomic sequence analysis. This study extends the knowledge pertaining to the genomic aspect of an associated bacterium isolated from P. bahamense alga by adopting a whole genome sequencing approach. Here, we report the genome sequencing, de novo assembly, and annotation data of a bacterium, Ruegeria sp. PBVC088, associated with harmful alga P. bahamense, which can be referenced by researchers to identify the genes and pathways related to toxin biosynthesis from a much larger data set. The genome of Ruegeria sp. PBVC088 was sequenced using the Illumina MiSeq platform with 250 bp paired-end reads. The number of reads generated from the MiSeq sequencer was 1,135,484, with an estimated coverage of 100X. The estimated genome size for the marine bacterium was computed to be 5.78 Mb. Annotation of the genome predicted 5,689 gene sequences, which were assigned putative functions based on homology to existing protein sequences in public databases. In addition, annotation of genes related to saxitoxin biosynthesis pathway was also performed. Raw fastq reads and the final version of the genome assembly have been deposited in the National Center for Biotechnology Information (NCBI) (BioProject: PRJNA324753, WGS: LZNT00000000, SRA: SRR3646181). The genome data provided here are expected to better understand the genetic processes involved in saxitoxin biosynthesis in marine bacteria associated with dinoflagellates.
| S-EPMC8844759 | biostudies-literature
Project description:Proteins, lipids, and carbohydrates from the harmful algal bloom (HAB)-causing organism Pyrodinium bahamense were characterized to obtain insights into the biochemical processes in this environmentally relevant dinoflagellate. Shotgun proteomics using label-free quantitation followed by proteome mapping using the P. bahamense transcriptome and translated protein databases of Marinovum algicola, Alexandrium sp., Cylindrospermopsis raciborskii, and Symbiodinium kawagutii for annotation enabled the characterization of the proteins in P. bahamense. The highest number of annotated hits were obtained from M. algicola and highlighted the contribution of microorganisms associated with P. bahamense. Proteins involved in dimethylsulfoniopropionate (DMSP) degradation such as propionyl CoA synthethase and acryloyl-CoA reductase were identified, suggesting the DMSP cleavage pathway as the preferred route in this dinoflagellate. Most of the annotated proteins were involved in amino acid biosynthesis and carbohydrate degradation and metabolism, indicating the active roles of these molecules in the vegetative stage of P. bahamense. This characterization provides baseline information on the cellular machinery and the molecular basis of the ecophysiology of P. bahamense.
| S-EPMC8706660 | biostudies-literature
Project description:endosymbiont 'TC1' of Trimyema compressum Genome sequencing and assembly
| PRJNA313245 | ENA