PyBreMinu3.metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB87268 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| pyBreMinu3.metagenome.1.primary.fa.gz | Other | |||
| pyBreMinu3.Phycisphaeraceae_1.1.primary.fa.gz | Other |
Items per page: 5 1 - 3 of 3 |
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Project description:Dinoflagellate chromosomes represent a unique evolutionary experiment, as they exist in a permanently condensed, liquid crystalline state, are not packaged by histones, and contain genes organized into polycistronic arrays, with minimal transcriptional regulation. We analyze the 3D genome of {Breviolum minutum}, and find large topological domains without chromatin loops, demarcated by convergent gene array boundaries (``dinoTADs’’). Transcriptional inhibition degrades dinoTADs, implicating transcription-induced supercoiling as the primary topological force in dinoflagellates.
2020-07-08 | GSE153950 | GEO
Project description:Breviolum psygmophilum dinoflagellate metagenome assembly, pyBrePsyg7.metagenome
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Project description:Breviolum psygmophilum dinoflagellate metagenome assembly, pyBrePsyg23.metagenome
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Project description:Breviolum psygmophilum dinoflagellate metagenome assembly, pyBrePsyg16.metagenome
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Project description:In dinoflagellates, the most unique and divergent nuclear organization among the known diversity of eukaryotes has evolved. The list of highly unusual features of dinoflagellate nuclei and genomes is long -- permanently condensed liquid crystalline chromosomes, in which histones are not the main packaging component, genes organized as very long unidirectional gene arrays, general absence of transcriptional regulation, high abundance of the otherwise very rare DNA modification 5-hydroxymethyluracil (5-hmU), and many others. Most of these fascinating properties were originally identified in the 1970s and 1980s but have received very little attention in recent decades using modern genomic tools. In this work, we address some of the outstanding questions regarding dinoflagellate genome organization by mapping the genome-wide distribution of 5-hmU (using both immunoprecipitation-based and basepair-resolution chemical mapping approaches) and of chromatin accessibility in the genome of the dinoflagellate Breviolum minutum. We find that the 5-hmU modification is preferentially enriched over certain classes of repetitive elements, and also often coincides with the boundaries between gene arrays. It is generally anti-correlated with chromatin accessibility, the levels of which are lower in those regions. We discuss the potential roles of 5-hmU in the functional organization of dinoflagellate genomes and its relationship to the transcriptional landscape of gene arrays.
2023-10-19 | GSE241969 | GEO
Project description:Cellular mechanisms responsible for the regulation of nutrient exchange, immune responses, and symbiont population growth in the cnidarian-dinoflagellate symbiosis are poorly resolved, particularly with respect to the dinoflagellate symbiont. Here, we characterised proteomic changes in the native symbiont Breviolum minutum during colonisation of its host sea anemone Exaiptasia diaphana (‘Aiptasia’). We also compared the proteome of this native symbiont in the established symbiotic state with that of a non-native symbiont, Durusdinium trenchii. The onset of symbiosis between Aiptasia and B. minutum induced increased accumulation of symbiont proteins associated with acquisition of inorganic carbon and photosynthesis, nitrogen metabolism, micro- and macronutrient starvation, suppression of the host immune responses, tolerance to low pH, and management of oxidative stress. Such responses are consistent with a functional, persistent symbiosis. In contrast, D. trenchii predominantly showed elevated levels of immunosuppressive proteins, consistent with the view that this symbiont is an opportunist that forms a less beneficial, less well-integrated symbiosis with this model anemone. By adding this analyses of the symbiont proteins to the already known responses of the host proteome, our results provide a more holistic view of cellular processes that determine host-symbiont specificity and how differences in symbiont partners, native versus non-native symbionts, may impact the fitness of the cnidarian-dinoflagellate symbiosis in response to thermal stress. This PRIDE entry contains the Breviolum minutum data; Durusdinium trenchii data are uploaded in a separate entry with identical parameters.
2024-01-18 | PXD045585 | Pride
Project description:Cellular mechanisms responsible for the regulation of nutrient exchange, immune responses, and symbiont population growth in the cnidarian-dinoflagellate symbiosis are poorly resolved, particularly with respect to the dinoflagellate symbiont. Here, we characterised proteomic changes in the native symbiont Breviolum minutum during colonisation of its host sea anemone Exaiptasia diaphana (‘Aiptasia’). We also compared the proteome of this native symbiont in the established symbiotic state with that of a non-native symbiont, Durusdinium trenchii. The onset of symbiosis between Aiptasia and B. minutum induced increased accumulation of symbiont proteins associated with acquisition of inorganic carbon and photosynthesis, nitrogen metabolism, micro- and macronutrient starvation, suppression of the host immune responses, tolerance to low pH, and management of oxidative stress. Such responses are consistent with a functional, persistent symbiosis. In contrast, D. trenchii predominantly showed elevated levels of immunosuppressive proteins, consistent with the view that this symbiont is an opportunist that forms a less beneficial, less well-integrated symbiosis with this model anemone. By adding this analyses of the symbiont proteins to the already known responses of the host proteome, our results provide a more holistic view of cellular processes that determine host-symbiont specificity and how differences in symbiont partners, native versus non-native symbionts, may impact the fitness of the cnidarian-dinoflagellate symbiosis in response to thermal stress. This PRIDE entry contains the Durusdinium trenchii data; Breviolum minutum data are uploaded in a separate entry with identical parameters.
2024-01-18 | PXD045587 | Pride
Project description:The physiology and cellular mechanisms of the dinoflagellate symbionts of cnidarians, the Symbiodiniaceae, change as a response to symbiosis, nutrient availability, and their surrounding microhabitat, but the underlying processes are poorly understood. Here, we employed liquid chromatography–mass spectrometry-based proteomics to elucidate the changes associated with the symbiotic and nutritional states of Breviolum minutum, a native symbiont of the sea anemone Exaiptasia diaphana. Both symbiosis and nutritional state had significant impacts on the B. minutum proteome. B. minutum in hospite showed increased abundance of proteins that are involved in phosphoinositol manipulation (e.g., glycerophosphoinositol permease 1 and phosphatidylinositol phosphatase), potentially as a means of interpartner signalling to prevent host phagosomal maturation. Proteins involved in carbon concentration and fixation (e.g. carbonic anhydrase, V-type ATPase) and nitrogen assimilation (e.g. glutamine synthase) were upregulated in ex hospite B. minutum, possibly due to nitrogen limitation by host in hospite and a lack of host carbon concentration mechanisms when ex hospite, respectively. Photosystem proteins increased in abundance at high nutrient levels, as were proteins involved in antioxidant mechanisms (e.g. superoxide dismutase, glutathione s-transferase). Proteins involved in iron metabolism was also affected by nutrient state, indicating increased iron demand and uptake in low nutrient treatments. These results provide better insight on the cellular mechanisms of symbiosis and provides potential target pathways for investigating a functional cnidarian-dinoflagellate symbiosis.
2023-01-31 | PXD036981 | Pride