Biology subjects

Miller, D. J.

Publications and source records attributed to Miller, D. J..

At least 19 recordsLinked to original sources

bioRxiv2026

Corallimorpharian genome supports the monophyly of Scleractinia and illuminates the cellular evolution of coral calcification

The production of calcified skeletons by stony corals is the cornerstone of reef ecosystems and the persistence of marine biodiversity. Corallimorpharians, sometimes described as naked corals, resemble stony corals in many respects but lack hardened skeletons. However, whether they are stony corals that secondarily lost their skeletons has been a subject of much debate. Here, we present a chromosome-level genome of the corallimorpharian Ricordea yuma and show that macrosynteny and microsynteny analyses provide strong support for corallimorpharians as the sister group to stony corals. This phylogenetic placement indicates that corallimorpharians were not ancestrally skeletonized and therefore occupy a critical outgroup position for reconstructing the origin of coral calcification. Guided by this phylogenetic context, we sequenced whole-polyp single-cell transcriptomes from R. yuma and the complex coral Galaxea fascicularis and found that the scleractinian skeleton evolved through the emergence of a derived calicoblast cell state in stony corals. A combination of comparative genomics and regeneration experiments in G. fascicularis show that the emergence of the calicoblast cell state was accompanied by the evolution of a biomineralization toolkit assembled from lineage-specific innovations and co-opted ancestral components. Although corallimorpharians retain some ancestral genes later incorporated into coral biomineralization, they lack a detectable calicoblast-like transcriptional state and many core calcification genes. Together, our findings indicate that coral calcification arose through coordinated changes in genome architecture, gene repertoire, and cell identity, highlighting this process as a major evolutionary transition driven by the integration of genomic and cellular innovations.

evolutionary biology↗

bioRxiv2026

microRNA expression during early development in the coral Acropora digitifera

Acropora spp. are the dominant reef-builders of the Indo-Pacific but are also amongst the most stress-sensitive corals. For these reasons, Acropora spp. have become the most studied of corals, two species (A. digitifera and A. millepora) often essentially serving as the basis for understanding molecular responses and processes across the sub-order Refertina and corals in general. The early development of these species has been well-characterised in terms of morphology and gene expression but as yet we have a limited understanding of how transcription is regulated during development. In "higher" animals (bilaterians) microRNAs (miRNAs) are critical regulators of gene expression but until now their involvement in coral development has not been investigated. Building on the existing developmental data for Acropora spp., we catalogued microRNAs (miRNAs) expressed during the early development of Acropora digitifera and profiled their expression in 21 stages from unfertilised eggs to 24h after treatment with a natural settlement cue (CCA chips). 157 miRNAs were recognised, many of which ([~]60%) were novel. These fell into three distinct groups, corresponding to three distinct developmental phases: (1) those present in eggs through to gastrulation (2) a larvally expressed group and (3) those expressed following settlement induction. Exposure of competent larvae to a natural settlement inducer resulted in major changes in the miRNA profile within 10 minutes, indicating that miRNAs may be particularly important in mediating the larva/polyp transition but are also likely to play important regulatory roles throughout early coral development in addition to possible roles in disease resistance.

developmental biology↗

bioRxiv2026

Separable neuronal and glial correlates of visual acuity and lifespan in mammalian primary visual cortex

Visual acuity spans more than a 100-fold range in mammals and yet the neural correlates of this perceptual gradient has not been fully evaluated. Furthermore, even though the known derived features of the human brain include specific changes to the cerebral cortex and the visual system in particular, no evolution of developing life histories approach has been quantitatively applied to metrics of cell composition. In this study, we present stereological estimates of neuron and glia density in V1 and granular layer 4 in a comparative sample of primates. We then integrate these data with the literature to construct a larger comparative dataset to test for phylogenetic relationships in mammalian visual system organization. Our examination revealed a primary relationship between acuity and neuron number along with secondary relationships among cell types tied to metabolic maintenance and support across the lifespan. Retinal metabolics along with phylogenetic position accounts for a large amount of V1 neuron density, which are further related to acuity while glia are related to longevity. These results identify a dissociation in the evolutionary developmental organization and senescence of V1 that map onto first principal parameters to explore the phylogenetic position and ecological pressures acting on the mammalian visual system. In accord with the literature, humans are revealed as outliers in glial support of neuronal metabolism across the lifespan. These findings provide evidence that mammalian visual cortex varies along at least two partially separable cellular dimensions in which visual resolution differs from lifelong maintenance. Summary and SignificanceIf the cellular organization of visual cortex is shaped by a single constraint or multiple independent pressures is debated. We used stereology to test whether V1 neurons and glia make separable contributions to visual performance across the mammal lifespan. V1 neuron density, together with brain size, predicts visual acuity. The glia-to-neuron ratio is alternatively associated with maximum lifespan after controlling for neuron density. Humans and chimpanzees have nearly identical V1 neuron densities, yet humans appear show substantially elevated glial investment across the literature. These findings suggest that mammalian visual cortex evolves under at least two partially separable pressures with neuron density and spatial resolution on one hand and glia investment to sustain function across life on the other.

neuroscience↗

bioRxiv2026

Anatolution, an online platform for consensus morphology

IntroductionSupervised statistical learning for cell-level segmentation and morphometry in optical microscopy is limited less by algorithmic capacity than by the scarcity of reliable, expert-validated ground truth. In comparative neuroscience and quantitative histology, where classical stains such as Nissls method remain the primary means to study cellular morphology, this bottleneck is acute: manual annotation is expensive, subject to individual bias, and rarely performed at the scale or consistency that computational approaches demand. No existing platform integrates a stain-specific bioimage segmentation protocol, a structured multi-annotator workflow, and consensus-based quality control into a single pipeline from image ingestion to machine-readable training data. MethodsWe present Anatolution, an open-source, web-based platform designed to address the gap of quality annotations at https://anatolution.herokuapp.com/public-tool/. Anatolution organizes microscopy images, including 2D arrays or 3D volumes, into project workspaces where multiple annotators independently label cellular structures against a shared computer vision catalogue. This design enables systematic inter-rater and intra-rater reliability assessment, with consensus derived from agreement across annotators rather than from any single experts judgment. The platform enables the export of aggregated labels or annotation datasets for downstream statistical learning methods. We describe the systems architecture, its Nissl-specific segmentation pipeline, the consensus annotation workflow, and validation of inter-rater reliability. ConclusionAcross 20+ histological annotation containers annotated by up to 15 independent raters, consensus boundary agreement increased monotonically with annotator count, reaching a median Dice of 0.79 against the full-rater reference at seven annotators, with top-tier containers achieving leave-one-out ceiling values of 0.621-0.769 for cell-body segmentation. The segmentation pipeline provided effective spatial anchoring, with 88% of consensus-annotated polygons containing at least one algorithmically detected seed. Anatolution provides open-source infrastructure for producing consensus-validated training data from classical histological preparations, addressing the primary bottleneck limiting supervised learning for cell-level morphometry.

neuroscience↗

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↗

bioRxiv2024

Effective and Reliable Metrics to Select Crystal Diffraction Data

X-ray crystal diffraction has provided atomic-level structural information on biological macromolecules. Data quality determines the reliability of structural models. In most cases, multiple data sets are available from different crystals and/or collected with different experimental settings. Reliable metrics are critical to rank and select the data set with the highest quality. Many measures have been created or modified for data quality evaluation. However, some are duplicate in functionality, and some are likely misused due to misunderstanding, which causes confusion or problems, especially at synchrotron beamlines where experiments proceed quickly. In this work, these measures are studied through both theoretical analysis and experimental data with various characteristics, which demonstrated that: 1). {Rmerg, Rmeas, Rpim, CC1/2} all measure the equivalence of reflections, and the low-shell values of these metrics can be used as reliable indicators for correctness (or trueness) of Laue symmetry; 2). High-shell I/{sigma}I is a reliable and better indicator to select resolution cutoff while the overall value measures the overall strength of the data.

biophysics↗

bioRxiv2024

EMhub: a web platform for data management and on-the-fly processing in scientific facilities

Most scientific facilities produce large amounts of heterogeneous data at a rapid pace. Managing users, instruments, reports, and invoices presents additional challenges. To address these challenges, we introduce EMhub, a web platform designed to support the daily operations and record-keeping of a scientific facility. EMhub enables easy management of user information, instruments, bookings, and projects. The application was initially developed to meet the needs of a CryoEM facility, but its functionality and adaptability have proven broad enough to be extended to other data-generating centers. The expansion of EMHub is enabled by the modular nature of its core functionalities. The application allows external processes to be connected via a REST API, automating tasks such as folder creation, user and password generation, and execution of real-time data processing pipelines. EMhub has been used for several years at the Swedish National CryoEM Facility and installed in the CryoEM center at the Structural Biology Department at St. Jude Childrens Research Hospital. A fully automated single-particle pipeline has been implemented for on-the-fly data processing and analysis. At St. Jude, the X-Ray Crystallography Center and the Single-Molecule Imaging Center have already expanded the platform to support their operational and data management workflows.

biophysics↗

bioRxiv2024

Chromosomal inversions harbour excess mutational load in the coral, Acropora kenti, on the Great Barrier Reef

The future survival of coral reefs in the Anthropocene depends on the capacity of corals to adapt as oceans warm and extreme weather events become more frequent. Targeted interventions designed to assist evolutionary processes in corals require a comprehensive understanding of the distribution and structure of standing variation, however, efforts to map genomic variation in corals have so far focussed almost exclusively on SNPs, overlooking structural variants that have been shown to drive adaptive processes in other taxa. Here we show that the reef-building coral, Acropora kenti (syn. tenuis) harbors at least five large, highly polymorphic structural variants, all of which exhibit signatures of strongly suppressed recombination in heterokaryotypes, a feature commonly associated with chromosomal inversions. Based on their high minor allele frequency, uniform distribution across habitats, and elevated genetic load, we propose that these inversions in A. kenti are likely to be under balancing selection. An excess of SNPs with high impact on protein coding genes within these loci elevates their importance both as potential targets for adaptive selection and as contributors to genetic decline if coral populations become fragmented or inbred in future.

evolutionary biology↗

bioRxiv2023

Quantifying myelin density in the feline auditory cortex

The cerebral cortex comprises many distinct regions that differ in structure, function, and patterns of connectivity. Current approaches to parcellating these regions often take advantage of functional neuroimaging approaches that can identify regions involved in a particular process with reasonable spatial resolution. However neuroanatomical biomarkers are also very useful in identifying distinct cortical regions either in addition to, or in place of functional measures. For example, differences in myelin density are thought to relate to functional differences between regions, are sensitive to individual patterns of experience, and have been shown to vary across functional hierarchies in a predictable manner. Accordingly, the current study provides quantitative stereological estimates of myelin density for each of the 13 regions that make up the feline auditory cortex. We demonstrate that significant differences can be observed between auditory cortical regions, with the highest myelin density observed in the regions that comprise the auditory core (i.e., the primary auditory cortex and anterior auditory field). Moreover, our myeloarchitectonic map suggests that myelin density varies in a hierarchical fashion that conforms to the traditional model of spatial organization in auditory cortex. Taken together, these results establish myelin as a useful biomarker for parcellating auditory cortical regions, and provide detailed estimates against which other, less invasive methods of quantifying cortical myelination may be compared.

neuroscience↗

bioRxiv2022

Direct laser writing of 3D electrodes on flexible substrates

This report describes a 3D microelectrode array integrated on a thin-film flexible cable for neural recording in small animals. The micro electrode array fabrication process integrates traditional silicon thin-film processing techniques and direct laser writing of 3D structures at micron resolution via two-photon lithography. While direct laser writing of 3D printed electrodes has been described before, this report is the first to provide a method for high-aspect-ratio laser-written structures integrated with microfabricated electrical traces. One prototype is a 16-channel array composed of 350 m long shanks spaced on a grid with 90 m pitch. Other devices shown here include biomimetic mosquito-needles that penetrate through the dura of birds and porous electrodes designed to promote tissue ingrowth or enhance charge injection capacity for neural stimulation. These devices are just a few examples of a new design space that will enable high-channel-count 3D electrode arrays with features definable at single micrometer resolution. Using a custom laser writer, the 3D printing process is rapid (1 mm3/min). This high-speed printing combined with standard wafer-scale processes will enable efficient device fabrication and new studies examining the relationship between electrode geometry and electrode performance. We anticipate highest impact in small animal models, nerve interfaces, retinal implants, and other applications requiring small, high density 3D electrodes.

bioengineering↗

bioRxiv2022

Evolutionary responses of a reef-building coral to climate change at the end of the last glacial maximum

Climate change threatens the survival of coral reefs on a global scale, primarily through mass bleaching and mortality as a result of marine heatwaves. While these short-term effects are clear, predicting the fate of coral reefs over the coming century is a major challenge. One way to understand the longer-term effects of rapid climate change is to examine the response of coral populations to past climate shifts. Coastal and shallow-water marine ecosystems such as coral reefs have been reshaped many times by sea-level changes during the Pleistocene, yet, few studies have directly linked this with its consequences on population demographics, dispersal, and adaptation. Here we use powerful analytical techniques, afforded by haplotype phased whole-genomes, to establish such links for the reef-building coral, Acropora digitifera. We show that three genetically distinct populations are present in northwestern Australia, and that their rapid divergence since the last glacial maximum (LGM) can be explained by a combination of founder-effects and restricted gene flow. Signatures of selective sweeps, too strong to be explained by demographic history, are present in all three populations and overlap with genes that show different patterns of functional enrichment between inshore and offshore habitats. In contrast to rapid divergence in the host, we find that photosymbiont communities are largely undifferentiated between corals from all three locations, spanning almost 1000 km, indicating that selection on host genes and not acquisition of novel symbionts, has been the primary driver of adaptation for this species in northwestern Australia.

evolutionary biology↗

bioRxiv2020

ampir: an R package for fast genome-wide prediction of antimicrobial peptides

SummaryAntimicrobial peptides (AMPs) are key components of the innate immune system that protect against pathogens, regulate the microbiome, and are promising targets for pharmaceutical research. Computational tools based on machine learning have the potential to aid discovery of genes encoding novel AMPs but existing approaches are not designed for genome-wide scans. To facilitate such genome-wide discovery of AMPs we developed a fast and accurate AMP classification framework, ampir. ampir is designed for high throughput, integrates well with existing bioinformatics pipelines, and has much higher classification accuracy than existing methods when applied to whole genome data. Availability and Implementationampir is implemented primarily in R with core feature calculation methods written in C++. Release versions are available via CRAN and work on all major operating systems. The development version is maintained at https://github.com/legana/ampir Contactlegana.fingerhut@my.jcu.edu.au; ira.cooke@jcu.edu.au Supplementary informationSupplementary data are available at https://github.com/legana/amp_pub

bioinformatics↗

bioRxiv2020

Signatures of selection in the coral holobiont reveal complex adaptations to inshore environments driven by Holocene climate change

Climate change at the Pleistocene/Holocene boundary reshaped many coastal landscapes, and provides an opportunity to study recent adaptive processes in marine species and ecosystems including coral reefs. On the Great Barrier Reef (GBR) sea level rise flooded a vast shelf creating a distinct inshore region which now harbours extensive coral assemblages despite being subject to relatively high turbidity, freshwater input and thermal fluctuations. To investigate how the coral holobiont has adapted to these conditions we first generated a highly contiguous genome assembly for Acropora tenuis based on long-read sequencing, and then used shallow whole-genome resequencing of 148 Acropora tenuis colonies from five inshore locations to model demographic history, identify signatures of selection and profile symbiont communities. We show that corals from Magnetic Island, located in the central inshore region of the GBR, are genetically distinct from those 50-500km further north, reflecting a Pleistocene (250-600Kya) split, whereas photosymbiont genotypes differ between reefs in a pattern more likely to reflect contemporary (Holocene) conditions. We also identified loci in the coral host genome with signatures of positive selection in the northern population and used coalescent simulations to show that these are unlikely to be accounted for by demographic history. Genes at these loci have roles in a diverse range of processes that includes heterotrophic nutrition, osmotic regulation, skeletal development and the establishment and maintenance of symbiosis. Our results show that, in the case of A. tenuis holobionts from the inshore GBR, the genomes of both the coral host and the primary photosymbiont of have been significantly shaped by their environment and illustrate the complexity of adaptations that have occurred in response to past climate change.

genomics↗

bioRxiv2020

An enhanced target-enrichment bait set for Hexacorallia provides phylogenomic resolution of the staghorn corals (Acroporidae) and close relatives.

The phylogenetic utility of targeted enrichment methods has been demonstrated in taxa that often have a history of single gene marker development. These genomic capture methods are now being applied to resolve evolutionary relationships from deep to shallow timescales in clades that were previously deficient in molecular marker development and lacking robust morphological characters that reflect evolutionary relationships. Effectively capturing 1000s of loci, however, in a diverse group across a broad time scale requires a bait set that incorporates multiple baits per locus. We redesigned a custom bait set for the cnidarian class Anthozoa to target 1,436 UCE loci and 1,572 exon regions within the subclass Hexacorallia. We test this redesigned bait set on 99 specimens of hard corals (Scleractinia) spanning both the "complex" (Acroporidae, Agariciidae) and "robust" (Fungiidae) clades. With focused sampling in the staghorn coral genus Acropora we explore the ability of capture data to inform the taxonomy of a clade deficient in molecular resolution. A mean of 1850 ({+/-} 298) loci were captured per taxon (955 UCEs, 894 exons). A 75% complete concatenated alignment included 1792 loci (991 UCE, 801 exons) and [~]1.87 million base pairs. Parsimony informative sites varied from 48% for alignments including all three families, to 1.5% among samples within a single Acropora species. Maximum likelihood and Bayesian analyses recover highly resolved topologies and robust molecular relationships not previously found with traditional markers within the Acroporidae. Species level relationships within the Acropora genus do not support traditional morphological groups or morphological phylogenies. Both UCE and exon datasets delineated six well-supported clades within Acropora. The enhanced bait set for Hexacorallia will allow researchers to survey the evolutionary history of important groups of reef building corals where previous molecular marker development has been unsuccessful.

evolutionary biology↗

bioRxiv2019

Close relationships between coral-associated Chromera strains despite differences within the Symbiodiniaceae

Reef-building corals live in a mutualistic relationship with photosynthetic algae (family Symbiodiniaceae) that usually provide most of the energy required by the coral host. This relationship is sensitive to temperature stress; as little as a 1{degrees}C increase often leading to collapse of the association. This sensitivity has led to interest in the potential of more stress tolerant algae to supplement or substitute for the normal Symbiodiniaceae mutualists. In this respect, the apicomplexan-like microalga Chromera is of particular interest due to its greater temperature tolerance. We generated a de novo transcriptome for a Chromera strain isolated from a GBR coral ("GBR Chromera") and compared to those of the reference strain of Chromera ("Sydney Chromera"), and to those of Symbiodiniaceae (Fugacium, Cladocopium and Breviolum), as well as the apicomplexan parasite, Plasmodium falciparum. By contrast with the Symbiodiniaceae, the two Chromera strains had a high level of sequence similarity evident by very low levels of divergence in orthologous genes. Although KEGG categories provide few criteria by which true coral mutualists might be identified, they do supply a molecular rationalization for the ubiquitous association of Cladocopium strains with Indo-Pacific reef corals. The presence of HSP20 genes may underlie the higher thermal tolerance of Chromera.

genomics↗

bioRxiv2019

Early eukaryotic origins and metazoan elaboration of MAPR family proteins

BackgroundThe membrane-associated progesterone receptor (MAPR) family consists of heme-binding proteins containing a cytochrome b5 (cytb5) domain characterized by the presence of a MAPR-specific interhelical insert region (MIHIR) between helices 3 and 4 of the canonical cytb5-domain fold. Animals possess three MAPR families (PGRMC-like, Neuferricin and Neudesin).\n\nResultsHere we show that all animal MAPR families were already present in the common ancestor of the Opisthokonta (comprising animals and fungi as well as related protistan taxa). All three MAPR genes acquired extensions C-terminal to the cytb5 domain, either before or with the evolution of animals. The archetypical MAPR protein, progesterone receptor membrane component 1 (PGRMC1), contains phosphorylated tyrosines Y139 and Y180. The combination of Y139/Y180 appeared in the common ancestor of Cnidaria and bilaterally symmetrical animals, along with an early embryological organizer and synapsed neurons, and is strongly conserved in all bilateral animals. A predicted protein interaction motif in the PGRMC1 MIHIR is potentially regulated by Y139 phosphorylation. A multilayered model of animal MAPR function acquisition includes some pre-metazoan functions (e.g., heme binding and cytochrome P450 interactions) and some acquired animal-specific functions that involve regulation of strongly conserved protein interaction motifs acquired by early-branching animals.\n\nConclusionsThis study provides a conceptual framework for future studies, against which PGRMC1s multiple functions can perhaps be stratified and functionally dissected. In accompanying papers we show that mutational perturbation of PGRMC1 phosphorylation status of the Y180 motif is associated with dramatic changes cell pasticity assayed by protein abundances, cell morphology, mitochondrial function, genomic stability, and epigenetic status, with pathways analysis associating Y180 mutation with processes related to organizer function. These combined works reveal previously unrecognized involvement of PGRMC1 in foundational animal processes of great relevance to disease.

evolutionary biology↗

bioRxiv2019

A Protein Engineering Approach for Uncovering Cryptic Ubiquitin-binding Sites: from a Ubiquitin-Variant Inhibitor of APC/C to K48 Chain Binding

Ubiquitin-mediated proteolysis is a fundamental mechanism used by eukaryotic cells to maintain homeostasis and protein quality, and to control timing in biological processes. Two essential aspects of ubiquitin regulation are conjugation through E1-E2-E3 enzymatic cascades, and recognition by ubiquitin-binding domains. An emerging theme in the ubiquitin field is that these two properties are often amalgamated in conjugation enzymes. In addition to covalent thioester linkage to ubiquitins C-terminus for ubiquitin transfer reactions, conjugation enzymes often bind non-covalently and weakly to ubiquitin at \"exosites\". However, identification of such sites is typically empirical and particularly challenging in large molecular machines. Here, studying the 1.2 MDa E3 ligase Anaphase-Promoting Complex/Cyclosome (APC/C), which controls cell division and many aspects of neurobiology, we discover a method for identifying unexpected ubiquitin-binding sites. Using a panel of ubiquitin variants (UbVs) we identify a protein-based inhibitor that blocks ubiquitin ligation to APC/C substrates in vitro and ex vivo. Biochemistry, NMR, and cryo EM structurally define the UbV interaction, explain its inhibitory activity through binding the surface on the APC2 subunit that recruits the E2 enzyme UBE2C, and ultimately reveal that this APC2 surface is also a ubiquitin-binding exosite with preference for K48-linked chains. The results provide a new tool for probing APC/C activity, have implications for the coordination of K48-linked Ub chain binding by APC/C with the multistep process of substrate polyubiquitylation, and demonstrate the power of UbV technology for identifying cryptic ubiquitin binding sites within large multiprotein complexes.\n\nSIGNIFICANCE STATEMENTUbiquitin-mediated interactions influence numerous biological processes. These are often transient or a part of multivalent interactions. Therefore, unmasking these interactions remains a significant challenge for large, complicated enzymes such as the Anaphase-Promoting Complex/Cyclosome (APC/C), a multisubunit RING E3 ubiquitin (Ub) ligase. APC/C activity regulates numerous facets of biology by targeting key regulatory proteins for Ub-mediated degradation. Using a series of Ub variants (UbVs), we identified a new Ub-binding site on the APC/C that preferentially binds to K48-linked Ub chains. More broadly, we demonstrate a workflow that can be exploited to uncover Ub-binding sites within ubiquitylation machinery and other associated regulatory proteins to interrogate the complexity of the Ub code in biology.

biochemistry↗

bioRxiv2019

Transcriptomic insights into the establishment of coral-algal symbioses from the symbiont perspective

Despite the ecological significance of the mutualistic relationship between Symbiodiniaceae and reef-building corals, the molecular machinery underpinning the establishment of this relationship is not well understood. This is especially true of the symbiont side, as previous attempts to understand the interaction between coral larvae and Symbiodiniaceae have focused nearly exclusively on the host. In the current study, Acropora tenuis planula larvae were exposed to a compatible strain of Symbiodiniaceae (Cladocopium) and the transcriptomic landscape of the symbiont profiled at 3, 12, 48 and 72 h post-exposure using RNA-Seq. The transcriptomic response of Cladocopium to the symbiotic state was complex, the most obvious feature being an extensive and generalised downregulation of gene expression. Included in this \"symbiosis-derived transcriptional repression\" were a range of stress response and immune-related genes. In contrast, genes implicated in metabolism were upregulated in the symbiotic state. Consistent with previous ecological studies, this transcriptomic response of Cladocopium implied that active translocation of metabolites to the host occurred, and thus that the mutualistic relationship can be established at the larval stage. This study provides novel insights into the transcriptomic remodelling that occurs in Symbiodiniaceae, with important implications for understanding the establishment of symbiosis between corals and their dinoflagellate partners.

genomics↗