Multi-omics analysis reveals the molecular response to heat stress in a “red tide” dinoflagellate

Genome biology, Journal Year: 2023, Volume and Issue: 24(1)

Published: Nov. 23, 2023

Abstract Background “Red tides” are harmful algal blooms caused by dinoflagellate microalgae that accumulate toxins lethal to other organisms, including humans via consumption of contaminated seafood. These driven a combination environmental factors nutrient enrichment, particularly in warm waters, and increasingly frequent. The molecular, regulatory, evolutionary mechanisms underlie the heat stress response these bloom-forming species remain little understood, due part limited genomic resources from dinoflagellates, complicated large sizes genomes, exhibiting features atypical eukaryotes. Results We present de novo assembled genome (~ 4.75 Gbp with 85,849 protein-coding genes), transcriptome, proteome, metabolome Prorocentrum cordatum , globally abundant, dinoflagellate. Using axenic cultures, we study molecular underpin stress, which is relevant current ocean warming trends. first evidence complementary interplay between RNA editing exon usage regulates expression functional diversity biomolecules, reflected reduction photosynthesis, central metabolism, protein synthesis. results reveal signatures post-transcriptional regulation for time pelagic Conclusions Our multi-omics analyses uncover an important species, complex gene structures large, high-G+C genome, combined multi-level transcriptional regulation. dynamics regulatory may explain how dinoflagellates diversified become some most ecologically successful organisms on Earth.

Language: Английский

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Developing model systems for dinoflagellates in the post‐genomic era

Journal of Phycology, Journal Year: 2023, Volume and Issue: 59(5), P. 799 - 808

Published: Sept. 1, 2023

Dinoflagellates are a diverse group of eukaryotic microbes that ubiquitous in aquatic environments. Largely photosynthetic, they encompass symbiotic, parasitic, and free-living lineages with broad spectrum trophism. Many taxa can produce bioactive secondary metabolites such as biotoxins, some which cause harmful algal blooms. In contrast, most symbiotic species crucial for sustaining coral reef health. The year 2023 marked decade since the first genome data dinoflagellates became available. growing genome-scale resources these highlighting their remarkable evolutionary genomic complexities. Here, we discuss prospect developing dinoflagellate models using criteria accessibility, tractability, resources, research support, promise. Moving forward post-genomic era, argue development fit-to-purpose tailor to specific biological contexts, one-size-fits-all model is inadequate encapsulating complex biology, ecology, history dinoflagellates.

Language: Английский

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Massive genome reduction predates the divergence of Symbiodiniaceae dinoflagellates

The ISME Journal, Journal Year: 2024, Volume and Issue: 18(1)

Published: Jan. 1, 2024

Dinoflagellates in the family Symbiodiniaceae are taxonomically diverse, predominantly symbiotic lineages that well-known for their association with corals. The ancestor of these taxa is believed to have been free-living. establishment symbiosis (i.e. symbiogenesis) hypothesized occurred multiple times during evolution, but its impact on genome evolution largely unknown. Among Symbiodiniaceae, genus Effrenium a free-living lineage phylogenetically positioned between two robustly supported groups genera within which emerged. apparent lack symbiogenesis suggests ancestral features may retained this lineage. Here, we present de novo assembled genomes (1.2-1.9 Gbp size) and transcriptome data from three isolates voratum conduct comparative analysis includes 16 other dinoflagellates. Surprisingly, find reduction, often associated lifestyle, predates origin Symbiodiniaceae. lifestyle distinguishes vis-à-vis longer introns, more-extensive mRNA editing, fewer (~30%) lineage-specific gene sets, lower (~10%) level pseudogenization. These results demonstrate how reduction adaptation distinct lifestyles intersect drive diversification

Language: Английский

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Facultative lifestyle drives diversity of coral algal symbionts

Trends in Ecology & Evolution, Journal Year: 2023, Volume and Issue: 39(3), P. 239 - 247

Published: Nov. 10, 2023

The photosynthetic symbionts of corals sustain biodiverse reefs in nutrient-poor, tropical waters. Recent genomic data illuminate the evolution coral under genome size constraints and suggest that retention facultative lifestyle, widespread among these algae, confers a selective advantage when compared with strict symbiotic existence. We posit symbiosis is analogous to 'bioreactor' selects winner genotypes allows them rise high numbers sheltered habitat prior release by host. Our observations lead novel hypothesis, 'stepping-stone model', which predicts local adaptation both free-living stages, stepwise fashion, accelerates alga diversity origin endemic strains species.

Language: Английский

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Gene duplication is the primary driver of intraspecific genomic divergence in coral algal symbionts

Open Biology, Journal Year: 2023, Volume and Issue: 13(9)

Published: Sept. 1, 2023

Dinoflagellates in the order Suessiales include family Symbiodiniaceae, which have essential roles as photosymbionts corals, and their cold-adapted sister group, Polarella glacialis. These diverse taxa exhibit extensive genomic divergence, although genomes are relatively small (haploid size < 3 Gbp) when compared with most other free-living dinoflagellates. Different strains of Symbiodiniaceae form symbiosis distinct hosts different regimes gene expression, but intraspecific whole-genome divergence is poorly understood. Focusing on three species (the Effrenium voratum symbiotic Symbiodinium microadriaticum Durusdinium trenchii) outgroup P. glacialis, for data from multiple isolates available, we assessed respect to sequence structure. Our analysis, based alignment alignment-free methods, revealed a greater extent than results underscore role duplication generating functional innovation, prevalence tandemly duplicated single-exon genes observed symbionts. demonstrate remarkable dinoflagellates under constraint reduced genome sizes, shaped by genetic duplications symbiogenesis events during diversification Symbiodiniaceae.

Language: Английский

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Contaminant or goldmine? In silico assessment of Symbiodiniaceae community using coral hologenomes

Frontiers in Protistology, Journal Year: 2024, Volume and Issue: 2

Published: April 2, 2024

Endosymbiotic dinoflagellates of the family Symbiodiniaceae are symbionts essential to corals and other marine organisms. A coral holobiont consists host, Symbiodiniaceae, microbes that together sustain overall productivity health. Coral hologenome data, generated from all interacting components a holobiont, key for elucidating molecular mechanisms underpin resilience changing environments. Although data often dominated by host genomic sequences, they provide an avenue recovering sequences in hospite . Here, we review recent advances approaches assessing community diversity data. Using case study based on existing datasets Acropora kenti coral, highlight how large numbers can useful analysis platform their function holobionts.

Language: Английский

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Nuclear genomes of dinoflagellates reveal evolutionarily conserved pattern of RNA editing relative to stress response

Frontiers in Protistology, Journal Year: 2024, Volume and Issue: 2

Published: May 10, 2024

Dinoflagellates are a group of diverse protists with complex genomes whose gene expression regulation mechanisms remain little known. RNA editing is post-transcriptional regulatory mechanism utilized by species, and has been described primarily in the plastid mitochondrial dinoflagellates. Its role nuclear dinoflagellates remains largely unexplored. Here, integrating genome transcriptome data from two dinoflagellate taxa comparative analysis, we identified 10,486 69,953 putative sites coral symbiont, Durusdinium trenchii CCMP2556 free-living bloom-forming taxon, Prorocentrum cordatum CCMP1329. We recovered all 12 possible types edits, more edits representing transitions than transversions. In contrast to other eukaryotes, found dominance A-to-T transversion non-coding regions, many which were condition-specific. Overall, implicate 7.5% D. genes 13.2% P. genes. Some (1.5% more-substantially 62.3% ) edited at significantly different frequencies distinct growth conditions. The distribution locations exhibited conserved patterns between phylogenetically distant species. Interestingly, within untranslated regions appear be associated upregulation response heat stress. These results lend support hypothesis that key molecular underpins

Language: Английский

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Gene Duplication and Speciation

Elsevier eBooks, Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 1, 2024

Language: Английский

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