Hayward, D. C. | Search bioRxiv

bioRxiv2025

Major transitions in early coral development: novel insights enabled by visualisation of a comprehensive transcriptomic dataset for Acropora millepora

BackgroundGiven the ecological importance of reef-building corals (Scleractinia), it is perhaps surprising that the molecular mechanisms underlying many of the morphological and metabolic changes during their development remain unclear. In part, this is due to the lack of a comprehensive transcriptomic dataset for any coral. A second challenge in the analysis of such non-model developmental datasets is that the volume of data often complicates its interpretation. ResultsTo overcome these limitations, we profiled gene expression in Acropora millepora across 26 life stages from unfertilised eggs to juvenile polyps and developed an interactive online tool based on the R-application Shiny to simultaneously visualise changes in the expression of large numbers of genes. As expected, major transcriptomic changes (transitions) occurred during gastrulation and the acquisition of competence. Surprisingly, however, settlement triggered by using the natural inducer CCA did not immediately lead to major changes in gene expression, but a major transition involving many genes was observed 3 - 6 hours after settlement induction. ConclusionsWe hope that providing access to this extensive developmental transcriptome dataset and software to facilitate its analysis will expedite a better understanding of the changes that occur during coral development. The online tool is available at https://amil-deview.mmb.group.

developmental biology↗

bioRxiv2020

Cryptic diversity masks ecologically distinct coral species on tropical reefs

Coral reefs are the epitome of species diversity, yet the number of described scleractinian coral species, the framework-builders of coral reefs, remains moderate by comparison. DNA sequencing studies are rapidly challenging this notion by exposing a wealth of undescribed diversity, but the evolutionary and ecological significance of this diversity remains largely unclear. Here, we present an annotated genome for one of the most ubiquitous corals in the Indo-Pacific (Pachyseris speciosa), and uncover through a comprehensive genomic and phenotypic assessment that it comprises morphologically indistinguishable, but ecologically divergent cryptic lineages. Demographic modelling based on whole-genome resequencing disproved that morphological crypsis was due to recent divergence, and instead indicated ancient morphological stasis. Although the lineages occur sympatrically across shallow and mesophotic habitats, extensive genotyping using a rapid diagnostic assay revealed differentiation of their ecological distributions. Leveraging "common garden" conditions facilitated by the overlapping distributions, we assessed physiological and quantitative skeletal traits and demonstrated concurrent phenotypic differentiation. Lastly, spawning observations of genotyped colonies highlighted the potential role of temporal reproductive isolation in the limited admixture, with consistent genomic signatures in genes related to morphogenesis and reproduction. Overall, our findings demonstrate how ecologically and phenotypically divergent coral species can evolve despite morphological stasis, and provide new leads into the potential mechanisms facilitating such divergence in sympatry. More broadly, they indicate that our current taxonomic framework for reef-building corals may be scratching the surface of the ecologically relevant diversity on coral reefs, consequently limiting our ability to protect or restore this diversity effectively.

evolutionary biology↗