Developing model systems for dinoflagellates in the post‐genomic era

Ishida, Hisatake; John, Uwe; Murray, Shauna A.; Bhattacharya, Debashish; Chan, Cheong Xin

doi:10.1111/jpy.13386

Cited by 14 publications

(6 citation statements)

References 86 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Our results are consistent with (but do not prove) the appealing idea that symbiosis offered an “escape” from reduced functional capacity due to genome reduction during the early stages of Symbiodiniaceae evolution; see [ 72 ] for a perspective. Regardless, the mixture of obligate free-living to facultative lifestyles among extant Symbiodiniaceae has resulted in divergent paths of genome evolution [ 53 ].…”

Section: Discussioncontrasting

confidence: 44%

Massive genome reduction predates the divergence of Symbiodiniaceae dinoflagellates

Shah,

Dougan,

Chen

et al. 2024

The ISME Journal

Self Cite

View full text Add to dashboard Cite

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

show abstract

Section: Discussioncontrasting

confidence: 44%

Massive genome reduction predates the divergence of Symbiodiniaceae dinoflagellates

Shah,

Dougan,

Chen

et al. 2024

The ISME Journal

Self Cite

View full text Add to dashboard Cite

show abstract

“…Additional markers such as psbA ncr (LaJeunesse & Thornhill, 2011) may reveal a more complete picture of Symbiodiniaceae communities in these colonies, while genome-wide studies of adaptive variation (Ishida et al, 2023; Reich et al, 2021) may reveal insight into functional differences among closely related Symbiodiniaceae taxa and their effect on heat tolerance.…”

Section: Discussionmentioning

confidence: 99%

Environmental, host, and symbiont drivers of heat tolerance in a species complex of reef-building corals

Naugle,

Denis,

Mocellin

et al. 2024

Preprint

View full text Add to dashboard Cite

Reef-building coral populations are under unprecedented threat from climate warming. Yet, variation in coral heat tolerance exists whereby some colonies can cope with higher sea temperatures than others and thus may hold unique value for conservation and restoration. Here, we quantify variation in heat tolerance of an ecologically important tabular coral species complex across the Great Barrier Reef (GBR) while also measuring genomic variation in the coral host and symbiont partners. Coral bleaching and photochemical traits were measured in 569 colonies within theAcropora hyacinthusspecies complex from 17 reefs following exposure to standardized acute heat stress assays. We detected substantial variation in heat tolerance, where individual colony thermal thresholds differed by up to 7.3°C and 5.7°C among and within reefs, respectively. Sea surface temperature climatology was the strongest predictor of heat tolerance, where colonies from warmer northern and inshore reefs typically exhibited the highest thermal thresholds, while colonies from cooler southern reefs were able to tolerate greater temperature increases relative to their local summer temperatures. Heat tolerance was also positively associated with exposure to thermal stress in the weeks preceding measurements. Assignment of colonies to host genomic clusters revealed four putative species within theA. hyacinthuscomplex that did not vary in their responses to experimental heat stress. Symbiodiniaceae communities within colonies were comprised primarily of Cladocopium ITS2 variants that differed spatially but had minimal effect on heat tolerance. Between 36 - 80% of heat tolerance variation was explained by environmental, host, and symbiont genomic predictors, leaving 20 - 64% to be explained by additional underlying drivers such as functional genomic variation not measured here. These results may be used to inform conservation and restoration actions, including targeting heat tolerant individuals for selective breeding, and will provide a foundation for evaluating the genomic basis of heat tolerance.

show abstract

“…at population scale from more strains and/or locations), and from a broader taxonomic representation. While data generation at such scale remains costly due in part to large genome sizes of dinoflagellates (see [ 37 ] for a perspective), our results suggest a potential linkage of facultative lifestyles to intraspecific genomic variations that discriminate free-living and symbiotic species.…”

Section: Discussionmentioning

confidence: 99%

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

Shah,

Dougan,

Chen

et al. 2023

Open Biol.

Self Cite

View full text Add to dashboard Cite

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

show abstract

Developing model systems for dinoflagellates in the post‐genomic era

Cited by 14 publications

References 86 publications

Massive genome reduction predates the divergence of Symbiodiniaceae dinoflagellates

Massive genome reduction predates the divergence of Symbiodiniaceae dinoflagellates

Environmental, host, and symbiont drivers of heat tolerance in a species complex of reef-building corals

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

Contact Info

Product

Resources

About