Intraspecies genomic divergence of coral algal symbionts shaped by gene duplication DOI Creative Commons
Sarah Shah, Katherine E. Dougan, Yibi Chen

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: March 29, 2023

Abstract Dinoflagellates of Order Suessiales include the diverse Family Symbiodiniaceae known for their role as essential coral reef symbionts, and cold-adapted Polarella glacialis . These taxa inhabit a broad range ecological niches exhibit extensive genomic divergence, although genomes are in smaller size ranges (haploid < 3 Gbp) compared to most other dinoflagellates. Different isolates species form symbiosis with distinct hosts different regimes gene expression, but intraspecies whole-genome divergence remains little known. Focusing on three (the free-living Effrenium voratum , symbiotic Symbiodinium microadriaticum Durusdinium trenchii ) outgroup P. all which data from multiple available, we assessed at sequence structural levels. Our analysis based alignment alignment-free methods revealed greater extent symbiodiniacean than results also reveal implications duplication generating functional innovation diversification Symbiodiniaceae, particularly D. was involved. Interestingly, tandem single-exon genes found be more prevalent those species. combination demonstrate remarkable dinoflagellates under constraint reduced genome sizes, shaped by genetic duplications symbiogenesis events during Symbiodiniaceae.

Language: Английский

Developing model systems for dinoflagellates in the post‐genomic era DOI Creative Commons
H Ishida, Uwe John, Shauna A. Murray

et al.

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

Citations

14
Facultative lifestyle drives diversity of coral algal symbionts DOI Creative Commons
Debashish Bhattacharya, Timothy G. Stephens,

Erin E. Chille

et al.

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

Citations

12
Global Free‐Living Symbiodiniaceae Biodiversity Mirrors Local Environments DOI Creative Commons

S. Bell,

Kate M. Quigley

Journal of Biogeography, Journal Year: 2025, Volume and Issue: unknown

Published: April 7, 2025

ABSTRACT Aim For free‐living Symbiodiniaceae, we aim to synthesise current knowledge, identify gaps in our understanding of biogeography and conduct the first quantitative genetic analysis at a global scale. Location Global. Taxon Free‐living dinoflagellates Family Symbiodiniaceae. Methods Publicly available sequences were used characterise Symbiodiniaceae community environment. Using ITS2 marker combined with DADA2 pipeline, amplicon sequence variants (ASVs) assess diversity, abundance distribution patterns from local scales. Results Relative abundances, composition diversity differed significantly between wider Caribbean Indo‐Pacific, within across three study regions: Great Barrier Reef (GBR), Flower Garden Banks National Marine Sanctuary (FGBNMS) Moorea French Polynesia. assemblage was most different GBR FGBNMS, dominance Cladocopium Breviolum FGBNMS. There also significant variability these regions, as shown through beta dispersion test. The highest indices found GBR, followed by Main Conclusions We locations Importantly, mirrored local‐scale patterns. These biogeographical hospite symbiont With studies highlight need for expanded sampling efforts unexplored regions such Indian Ocean. Given potentially role coral acclimation climate change, identifying protecting taxa should be conservation priority.

Language: Английский

Citations

0
Gene duplication is the primary driver of intraspecific genomic divergence in coral algal symbionts DOI Creative Commons
Sarah Shah, Katherine E. Dougan, Yibi Chen

et al.

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

Citations

8
Contaminant or goldmine? In silico assessment of Symbiodiniaceae community using coral hologenomes DOI Creative Commons
H Ishida, Cynthia Riginos, Cheong Xin Chan

et al.

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

Citations

1
Peeling back the layers of coral holobiont multi-omics data DOI Creative Commons
Amanda Williams, Timothy G. Stephens,

Alexander Shumaker

et al.

iScience, Journal Year: 2023, Volume and Issue: 26(9), P. 107623 - 107623

Published: Aug. 14, 2023

The integration of multiple 'omics' datasets is a promising avenue for answering many important and challenging questions in biology, particularly those relating to complex ecological systems. Although multi-omics was developed using data from model organisms with significant prior knowledge resources, its application non-model organisms, such as coral holobionts, less clear-cut. We explore, the emerging rice Montipora capitata, intersection holobiont transcriptomic, proteomic, metabolomic, microbiome amplicon investigate how well they correlate under high temperature treatment. Using typical thermal stress regime, we show that transcriptomic proteomic broadly capture response coral, whereas metabolome patterns likely reflect stochastic homeostatic processes associated each sample. These results provide framework interpreting generated systems, biotic interactions among microbial partners.

Language: Английский

Citations

3
The exotic thymidine modification 5-hydroxymethyluridine in dinoflagellateAmphidinium carterae DOI Open Access
Chongping Li, Ying Li,

Yuci Wang

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 1, 2023

Abstract Dinoflagellate chromosomes are extraordinary, as their organization is independent of architectural nucleosomes unlike typical eukaryotes and shows a cholesteric liquid crystal state. 5-hydroxymethyluridine (5hmU) present at unusually high levels its function remains an enigma in dinoflagellates chromosomal DNA. Here, we demonstrate that 5hmU exhibits content variations different generated the poly-nucleotide level through hydroxylation thymidine. Importantly, identified enzyme, which putative dinoflagellate TET/JBP homologue, catalyzing production using either vivo or vitro biochemical assay. Based on near-chromosomal genome assembly Amphidinium carterae , depicted comprehensive landscape found most peaks share conserved TG-rich motif, significantly enriched repeat elements, mark partially overlapping regions with 5-methylcytosine (5mC) sites. Moreover, inhibition via dioxygenase inhibitor leads to transcriptional activation 5hmU-marked transposable elements (TEs), implying appears serve epigenetic marks for silencing retrotransposon. Together, our results revealed biogenesis, genome-wide molecular 5hmU, providing mechanic insight into this enigmatic DNA mark.

Language: Английский

Citations

2
Intraspecies genomic divergence of coral algal symbionts shaped by gene duplication DOI Creative Commons
Sarah Shah, Katherine E. Dougan, Yibi Chen

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: March 29, 2023

Abstract Dinoflagellates of Order Suessiales include the diverse Family Symbiodiniaceae known for their role as essential coral reef symbionts, and cold-adapted Polarella glacialis . These taxa inhabit a broad range ecological niches exhibit extensive genomic divergence, although genomes are in smaller size ranges (haploid < 3 Gbp) compared to most other dinoflagellates. Different isolates species form symbiosis with distinct hosts different regimes gene expression, but intraspecies whole-genome divergence remains little known. Focusing on three (the free-living Effrenium voratum , symbiotic Symbiodinium microadriaticum Durusdinium trenchii ) outgroup P. all which data from multiple available, we assessed at sequence structural levels. Our analysis based alignment alignment-free methods revealed greater extent symbiodiniacean than results also reveal implications duplication generating functional innovation diversification Symbiodiniaceae, particularly D. was involved. Interestingly, tandem single-exon genes found be more prevalent those species. combination demonstrate remarkable dinoflagellates under constraint reduced genome sizes, shaped by genetic duplications symbiogenesis events during Symbiodiniaceae.

Language: Английский

Citations

1