Breviolum minutum
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA247417 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| DRR003834.fastq.gz | Fastqsanger.gz | |||
| DRR003835.fastq.gz | Fastqsanger.gz | |||
| DRR003836.fastq.gz | Fastqsanger.gz | |||
| DRR003837.fastq.gz | Fastqsanger.gz |
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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.
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Project description:The whole genome sequence of a dinoflagellate, Symbiodinium minutum
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Project description:Emergence of the symbiotic lifestyle fostered the immense diversity of all ecosystems on Earth, but symbiosis plays a particularly remarkable role in marine ecosystems. Photosynthetic dinoflagellate endosymbionts power reef ecosystems by transferring vital nutrients to their coral hosts. The mechanisms driving this symbiosis, specifically those which allow hosts to discriminate between beneficial symbionts and pathogens, are not well understood. Here, we uncover that host immune suppression is key for dinoflagellate endosymbionts to avoid elimination by the host using a comparative, model systems approach. Unexpectedly, we find that the clearance of non-symbiotic microalgae occurs by non-lytic expulsion (vomocytosis) and not intracellular digestion, the canonical mechanism used by professional immune cells to destroy foreign invaders. We provide evidence that suppression of TLR signalling by targeting the conserved MyD88 adapter protein has been co-opted for this endosymbiotic lifestyle, suggesting that this is an evolutionarily ancient mechanism exploited to facilitate symbiotic associations ranging from coral endosymbiosis to the microbiome of vertebrate guts.
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Project description:Symbiodinium minutum transcriptome assembly
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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.
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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 tandem gene arrays, with minimal transcriptional regulation. We analyze the three-dimensional genome of Breviolum minutum, and find large topological domains (dinoflagellate topologically associating domains, which we term 'dinoTADs') without chromatin loops, which are demarcated by convergent gene array boundaries. Transcriptional inhibition disrupts dinoTADs, implicating transcription-induced supercoiling as the primary topological force in dinoflagellates.
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Project description:The algal cell wall is an important cellular component that functions in defense, nutrient utilization, signaling, adhesion, and cell-cell recognition-processes important in the cnidarian-dinoflagellate symbiosis. The cell wall of symbiodiniacean dinoflagellates is not well characterized. Here, we present a method to isolate cell walls of Symbiodiniaceae and prepare cell-wall-enriched samples for proteomic analysis. Label-free liquid chromatography-electrospray ionization tandem mass spectrometry was used to explore the surface proteome of two Symbiodiniaceae species from the Great Barrier Reef: Breviolum minutum and Cladocopium goreaui. Transporters, hydrolases, translocases, and proteins involved in cell-adhesion and protein-protein interactions were identified, but the majority of cell wall proteins had no homologues in public databases. We propose roles for some of these proteins in the cnidarian-dinoflagellate symbiosis. This work provides the first proteomics investigation of cell wall proteins in the Symbiodiniaceae and represents a basis for future explorations of the roles of cell wall proteins in Symbiodiniaceae and other dinoflagellates.
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