Draft Assembly of the Symbiodinium minutum Nuclear Genome Reveals Dinoflagellate Gene Structure

Genome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in the Breviolum minutum genome

BACKGROUND

In dinoflagellates, a unique and extremely divergent genomic and nuclear organization has evolved. The highly unusual features of dinoflagellate nuclei and genomes include permanently condensed liquid crystalline chromosomes, primarily packaged by proteins other than histones, genes organized in very long unidirectional gene arrays, a general absence of transcriptional regulation, high abundance of the otherwise very rare DNA modification 5-hydroxymethyluracil (5-hmU), and many others. While most of these fascinating properties are originally identified in the 1970s and 1980s, they have not yet been investigated using modern genomic tools.

RESULTS

In this work, we address some of the outstanding questions regarding dinoflagellate genome organization by mapping the genome-wide distribution of 5-hmU (using both immunoprecipitation-based and basepair-resolution chemical mapping approaches) and of chromatin accessibility in the genome of the Symbiodiniaceae dinoflagellate Breviolum minutum. We find that the 5-hmU modification is preferentially enriched over certain classes of repetitive elements, often coincides with the boundaries between gene arrays, and is generally correlated with decreased chromatin accessibility, the latter otherwise being largely uniform along the genome. We discuss the potential roles of 5-hmU in the functional organization of dinoflagellate genomes and its relationship to the transcriptional landscape of gene arrays.

CONCLUSIONS

Our results provide the first window into the 5-hmU and chromatin accessibility landscapes in dinoflagellates.

Full-length transcriptome analysis of a bloom-forming dinoflagellate Prorocentrum shikokuense (Dinophyceae)

Prorocentrum shikokuense (formerly P. donghaiense) is a pivotal dinoflagellate species associating with the HABs in the East China Sea. The complexity of its large nuclear genome hindered us from understanding its genomic characteristics. Full-length transcriptome sequencing offers a practical solution to decipher the physiological mechanisms of a species without the reference genome. In this study, we employed single-molecule real-time (SMRT) sequencing technology to sequence the full-length transcriptome of Prorocentrum shikokuense. We successfully generated 41.73 Gb of clean SMRT sequencing reads and isolated 105,249 non-redundant full-length non-chimeric reads. Our trial has led to the identification of 11,917 long non-coding RNA transcripts, 514 alternative splicing events, 437 putative transcription factor genes from 17 TF gene families, and 34,723 simple sequence repeats. Additionally, a total of 78,265 open reading frames were identified, of them 15,501 were the protein coding sequences. This dataset is valuable for annotating P. shikokuense genome, and will contribute significantly to the in-depth studies on the molecular mechanisms underlining the dinoflagellate bloom formation.

Functional analyses of bacterial genomes found in Symbiodiniaceae genome assemblies

Bacterial-algal interactions strongly influence marine ecosystems. Bacterial communities in cultured dinoflagellates of the family Symbiodiniaceae have been characterized by metagenomics. However, little is known about whole-genome analysis of marine bacteria associated with these dinoflagellates. We performed in silico analysis of four bacterial genomes from cultures of four dinoflagellates of the genera Symbiodinium, Breviolum, Cladocopium and Durusdinium. Comparative analysis showed that the former three contain the alphaproteobacterial family Parvibaculaceae and that the Durusdinium culture includes the family Sphingomonadaceae. There were no large genomic reductions in the alphaproteobacteria with genome sizes of 2.9-3.9 Mb, implying they are not obligate intracellular bacteria. Genomic annotations of three Parvibaculaceae detected the gene for diacetylchitobiose deacetylase (Dac), which may be involved in the degradation of dinoflagellate cell surfaces. They also had metabolic genes for dissimilatory nitrate reduction to ammonium (DNRA) in the nitrogen (N) cycle and cobalamin (vitamin B12 ) biosynthetic genes in the salvage pathway. Those three characters were not found in the Sphingomonadaceae genome. Predicted biosynthetic gene clusters for secondary metabolites indicated that the Parvibaculaceae likely produce the same secondary metabolites. Our study suggests that the Parvibaculaceae is a major resident of Symbiodiniaceae cultures with antibiotics.

Transcriptome analysis reveals limited toxic effects of the UV-filter benzophenone-3 (BP-3) on the hermatypic coral Acropora tenuis and its symbiotic dinoflagellates

This study aimed to investigate the toxic and transcriptomic effects of the ultraviolet filter benzophenone-3 (BP-3) on Acropora tenuis and its symbiotic dinoflagellates while using acetone as a solvent. Seven-day exposure to 50 and 500 μg/L, which is higher than most BP-3 records from coastal waters, did not affect coral colour or dinoflagellate photosynthesis. Differentially expressed genes (DEGs) between seawater and solvent controls were <20 in both corals and dinoflagellates. Eleven coral DEGs were detected after treatment with 50 μg/L BP-3. Fourteen coral DEGs, including several fluorescent protein genes, were detected after treatment with 500 μg/L BP-3. In contrast, no dinoflagellate DEGs were detected in the BP-3 treatment group. These results suggest that the effects of 50-500 μg/L BP-3 on adult A. tenuis and its dinoflagellates are limited. Our experimental methods with lower acetone toxicity provide a basis for establishing standard ecotoxicity tests for corals.

Nuclear genome of dinoflagellates: Size variation and insights into evolutionary mechanisms

Recent progress in high-throughput sequencing technologies has dramatically increased availability of genome data for prokaryotes and eukaryotes. Dinoflagellates have distinct chromosomes and a huge genome size, which make their genomic analysis complicated. Here, we reviewed the nuclear genomes of core dinoflagellates, focusing on the genome and cell size. Till now, the genome sizes of several dinoflagellates (more than 25) have been measured by certain methods (e.g., flow cytometry), showing a range of 3-250 pg of genomic DNA per cell. In contrast to their relatively small cell size, their genomes are huge (about 1-80 times the human haploid genome). In the present study, we collected the genome and cell size data of dinoflagellates and compared their relationships. We found that dinoflagellate genome size exhibits a positive correlation with cell size. On the other hand, we recognized that the genome size is not correlated with phylogenetic relatedness. These may be caused by genome duplication, increased gene copy number, repetitive non-coding DNA, transposon expansion, horizontal gene transfer, organelle-to-nucleus gene transfer, and/or mRNA reintegration into the genome. Ultimate verification of these factors as potential causative mechanisms would require sequencing of more dinoflagellate genomes in the future.

Synergistic response to climate stressors in coral is associated with genotypic variation in baseline expression

As environments are rapidly reshaped due to climate change, phenotypic plasticity plays an important role in the ability of organisms to persist and is considered an especially important acclimatization mechanism for long-lived sessile organisms such as reef-building corals. Often, this ability of a single genotype to display multiple phenotypes depending on the environment is modulated by changes in gene expression, which can vary in response to environmental changes via two mechanisms: baseline expression and expression plasticity. We used transcriptome-wide expression profiling of eleven genotypes of common-gardened Acropora cervicornis to explore genotypic variation in the expression response to thermal and acidification stress, both individually and in combination. We show that the combination of these two stressors elicits a synergistic gene expression response, and that both baseline expression and expression plasticity in response to stress show genotypic variation. Additionally, we demonstrate that frontloading of a large module of coexpressed genes is associated with greater retention of algal symbionts under combined stress. These results illustrate that variation in the gene expression response of individuals to climate change stressors can persist even when individuals have shared environmental histories, affecting their performance under future climate change scenarios.

Multi-Chemical Omics Analysis of the Symbiodiniaceae Durusdinium trenchii under Heat Stress

The urgency of responding to climate change for corals necessitates the exploration of innovative methods to swiftly enhance our understanding of crucial processes. In this study, we employ an integrated chemical omics approach, combining elementomics, metabolomics, and volatilomics methodologies to unravel the biochemical pathways associated with the thermal response of the coral symbiont, Symbiodiniaceae Durusdinium trenchii. We outline the complimentary sampling approaches and discuss the standardised data corrections used to allow data integration and comparability. Our findings highlight the efficacy of individual methods in discerning differences in the biochemical response of D. trenchii under both control and stress-inducing temperatures. However, a deeper insight emerges when these methods are integrated, offering a more comprehensive understanding, particularly regarding oxidative stress pathways. Employing correlation network analysis enhanced the interpretation of volatile data, shedding light on the potential metabolic origins of volatiles with undescribed functions and presenting promising candidates for further exploration. Elementomics proves to be less straightforward to integrate, likely due to no net change in elements but rather elements being repurposed across compounds. The independent and integrated data from this study informs future omic profiling studies and recommends candidates for targeted research beyond Symbiodiniaceae biology. This study highlights the pivotal role of omic integration in advancing our knowledge, addressing critical gaps, and guiding future research directions in the context of climate change and coral reef preservation.

Genomic Data Reveal Diverse Biological Characteristics of Scleractinian Corals and Promote Effective Coral Reef Conservation

Reef-building corals (Scleractinia, Anthozoa, Cnidaria) are the keystone organisms of coral reefs, which constitute the most diverse marine ecosystems. Since the first decoded coral genome reported in 2011, about 40 reference genomes are registered as of 2023. Comparative genomic analyses of coral genomes have revealed genomic characters that may underlie unique biological characteristics and coral diversification. These include existence of genes for biosynthesis of mycosporine-like amino acids, loss of an enzyme necessary for cysteine biosynthesis in family Acroporidae, and lineage-specific gene expansions of DMSP lyase-like genes in the genus Acropora. While symbiosis with endosymbiotic photosynthetic dinoflagellates is a common biological feature among reef-building corals, genes associated with the intricate symbiotic relationship encompass not only those shared by many coral species, but also genes that were uniquely duplicated in each coral lineage, suggesting diversified molecular mechanisms of coral-algal symbiosis. Coral genomic data have also enabled detection of hidden, complex population structures of corals, indicating the need for species-specific, local-scale, carefully considered conservation policies for effective maintenance of corals. Consequently, accumulating coral genomic data from a wide range of taxa and from individuals of a species not only promotes deeper understanding of coral reef biodiversity, but also promotes appropriate and effective coral reef conservation. Considering the diverse biological traits of different coral species and accurately understanding population structure and genetic diversity revealed by coral genomic analyses during coral reef restoration planning could enable us to "archive" coral reef environments that are nearly identical to natural coral reefs.

Massive genome reduction predates the divergence of Symbiodiniaceae dinoflagellates

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 hypothesized 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 pseudogenization. These results demonstrate how genome reduction and the adaptation to distinct lifestyles intersect to drive diversification and genome evolution of Symbiodiniaceae.

MarFERReT, an open-source, version-controlled reference library of marine microbial eukaryote functional genes

Metatranscriptomics generates large volumes of sequence data about transcribed genes in natural environments. Taxonomic annotation of these datasets depends on availability of curated reference sequences. For marine microbial eukaryotes, current reference libraries are limited by gaps in sequenced organism diversity and barriers to updating libraries with new sequence data, resulting in taxonomic annotation of about half of eukaryotic environmental transcripts. Here, we introduce Marine Functional EukaRyotic Reference Taxa (MarFERReT), a marine microbial eukaryotic sequence library designed for use with taxonomic annotation of eukaryotic metatranscriptomes. We gathered 902 publicly accessible marine eukaryote genomes and transcriptomes and assessed their sequence quality and cross-contamination issues, selecting 800 validated entries for inclusion in MarFERReT. Version 1.1 of MarFERReT contains reference sequences from 800 marine eukaryotic genomes and transcriptomes, covering 453 species- and strain-level taxa, totaling nearly 28 million protein sequences with associated NCBI and PR2 Taxonomy identifiers and Pfam functional annotations. The MarFERReT project repository hosts containerized build scripts, documentation on installation and use case examples, and information on new versions of MarFERReT.

In Vitro Phagocytosis of Different Dinoflagellate Species by Coral Cells

Coral-dinoflagellate symbiosis is a unique biological phenomenon, in which animal cells engulf single-celled photosynthetic algae and maintain them in their cytoplasm mutualistically. Studies are needed to reveal the complex mechanisms involved in symbiotic processes, but it is difficult to answer these questions using intact corals. To tackle these issues, our previous studies established an in vitro system of symbiosis between cells of the scleractinian coral Acropora tenuis and the dinoflagellate Breviolum minutum, and showed that corals direct phagocytosis, while algae are likely engulfed by coral cells passively. Several genera of the family Symbiodiniaceae can establish symbioses with corals, but the symbiotic ratio differs depending on the dinoflagellate clades involved. To understand possible causes of these differences, this study examined whether cultured coral cells show phagocytotic activity with various dinoflagellate strains similar to those shown by intact A. tenuis. We found that (a) A. tenuis larvae incorporate Symbiodinium and Breviolum, but not Cladocopium, and very few Effrenium, (b) cultured coral cells engulfed all four species but the ratio of engulfment was significantly higher with Symbiodinium and Breviolum than Cladocopium and Effrenium, (c) cultured coral cells also phagocytosed inorganic latex beads differently than they do dinoflagellates . It is likely that cultured coral cells preferentially phagocytose Symbiodinium and Breviolum, suggesting that specific molecular mechanisms involved in initiation of symbiosis should be investigated in the future.

A coral-associated actinobacterium mitigates coral bleaching under heat stress

BACKGROUND

The positive effects of exposing corals to microorganisms have been reported though how the benefits are conferred are poorly understood. Here, we isolated an actinobacterial strain (SCSIO 13291) from Pocillopora damicornis with capabilities to synthesize antioxidants, vitamins, and antibacterial and antiviral compounds supported with phenotypic and/or genomic evidence. Strain SCSIO 13291 was labeled with 5 (and - 6)-carboxytetramethylrhodamine, succinimidyl ester and the labeled cell suspension directly inoculated onto the coral polyp tissues when nubbins were under thermal stress in a mesocosm experiment. We then visualized the labelled bacterial cells and analyzed the coral physiological, transcriptome and microbiome to elucidate the effect this strain conferred on the coral holobiont under thermal stress.

RESULTS

Subsequent microscopic observations confirmed the presence of the bacterium attached to the coral polyps. Addition of the SCSIO 13291 strain reduced signs of bleaching in the corals subjected to heat stress. At the same time, alterations in gene expression, which were involved in reactive oxygen species and light damage mitigation, attenuated apoptosis and exocytosis in addition to metabolite utilization, were observed in the coral host and Symbiodiniaceae populations. In addition, the coral associated bacterial community altered with a more stable ecological network for samples inoculated with the bacterial strain.

CONCLUSIONS

Our results provide insights into the benefits of a putative actinobacterial probiotic strain that mitigate coral bleaching signs. This study suggests that the inoculation of bacteria can potentially directly benefit the coral holobiont through conferring metabolic activities or through indirect mechanisms of suppling additional nutrient sources.

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

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 algal blooms are driven by a combination of environmental factors including nutrient enrichment, particularly in warm waters, and are increasingly frequent. The molecular, regulatory, and evolutionary mechanisms that underlie the heat stress response in these harmful bloom-forming algal species remain little understood, due in part to the limited genomic resources from dinoflagellates, complicated by the large sizes of genomes, exhibiting features atypical of eukaryotes.

RESULTS

We present the de novo assembled genome (~ 4.75 Gbp with 85,849 protein-coding genes), transcriptome, proteome, and metabolome from Prorocentrum cordatum, a globally abundant, bloom-forming dinoflagellate. Using axenic algal cultures, we study the molecular mechanisms that underpin the algal response to heat stress, which is relevant to current ocean warming trends. We present the first evidence of a complementary interplay between RNA editing and exon usage that regulates the expression and functional diversity of biomolecules, reflected by reduction in photosynthesis, central metabolism, and protein synthesis. These results reveal genomic signatures and post-transcriptional regulation for the first time in a pelagic dinoflagellate.

CONCLUSIONS

Our multi-omics analyses uncover the molecular response to heat stress in an important bloom-forming algal species, which is driven by complex gene structures in a large, high-G+C genome, combined with multi-level transcriptional regulation. The dynamics and interplay of molecular regulatory mechanisms may explain in part how dinoflagellates diversified to become some of the most ecologically successful organisms on Earth.

Does depth divide? Variable genetic connectivity patterns among shallow and mesophotic Montastraea cavernosa coral populations across the Gulf of Mexico and western Caribbean

Despite general declines in coral reef ecosystems in the tropical western Atlantic, some reefs, including mesophotic reefs (30-150 m), are hypothesized to function as coral refugia due to their relative isolation from anthropogenic stressors. Understanding the connectivity dynamics among these putative refugia and more degraded reefs is critical to develop effective management strategies that promote coral metapopulation persistence and recovery. This study presents a geographically broad assessment of shallow (<30 m) and mesophotic (>30 m) connectivity dynamics of the depth-generalist coral species Montastraea cavernosa. Over 750 coral genets were collected across the Northwest and Southern Gulf of Mexico, Florida, Cuba, and Belize, and ~5000 SNP loci were generated to quantify high-resolution genetic structure and connectivity among these populations. Generally, shallow and mesophotic populations demonstrated higher connectivity to distant populations within the same depth zone than to adjacent populations across depth zones. However, exceptions to this pattern include the Northwest Gulf of Mexico and the Florida Keys which exhibited relatively high vertical genetic connectivity. Furthermore, estimates of recent gene flow emphasize that mesophotic M. cavernosa populations are not significant sources for their local shallow counterparts, except for the Northwest Gulf of Mexico populations. Location-based differences in vertical connectivity are likely a result of diverse oceanographic and environmental conditions that may drive variation in gene flow and depth-dependent selection. These results highlight the need to evaluate connectivity dynamics and refugia potential of mesophotic coral species on a population-by-population basis and to identify stepping-stone populations that warrant incorporation in future international management approaches.

Genome sizes and repeatome evolution in zoantharians (Cnidaria: Hexacorallia: Zoantharia)

Across eukaryotes, large variations of genome sizes have been observed even between closely related species. Transposable elements as part of the repeated DNA have been proposed and confirmed as one of the most important contributors to genome size variation. However, the evolutionary implications of genome size variation and transposable element dynamics are not well understood. Together with phenotypic traits, they are commonly referred to as the "C-value enigma". The order Zoantharia are benthic cnidarians found from intertidal zones to the deep sea, and some species are particularly abundant in coral reefs. Despite their high ecological relevance, zoantharians have yet to be largely studied from the genomic point of view. This study aims at investigating the role of the repeatome (total content of repeated elements) in genome size variations across the order Zoantharia. To this end, whole-genomes of 32 zoantharian species representing five families were sequenced. Genome sizes were estimated and the abundances of different repeat classes were assessed. In addition, the repeat overlap between species was assessed by a sequence clustering method. The genome sizes in the dataset varied up to 2.4 fold magnitude. Significant correlations between genome size, repeated DNA content and transposable elements, respectively (Pearson's correlation test R2 = 0.47, p = 0.0016; R2 = 0.22, p = 0.05) were found, suggesting their involvement in the dynamics of genome expansion and reduction. In all species, long interspersed nuclear elements and DNA transposons were the most abundant identified elements. These transposable elements also appeared to have had a recent expansion event. This was in contrast to the comparative clustering analysis which revealed species-specific patterns of satellite elements' amplification. In summary, the genome sizes of zoantharians likely result from the complex dynamics of repeated elements. Finally, the majority of repeated elements (up to 70%) could not be annotated to a known repeat class, highlighting the need to further investigate non-model cnidarian genomes. More research is needed to understand how repeated DNA dynamics relate to zoantharian evolution and their biology.

Developing model systems for dinoflagellates in the post-genomic era

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

Genomic signatures of disease resistance in endangered staghorn corals

White band disease (WBD) has caused unprecedented declines in the Caribbean Acropora corals, which are now listed as critically endangered species. Highly disease-resistant Acropora cervicornis genotypes exist, but the genetic underpinnings of disease resistance are not understood. Using transmission experiments, a newly assembled genome, and whole-genome resequencing of 76 A. cervicornis genotypes from Florida and Panama, we identified 10 genomic regions and 73 single-nucleotide polymorphisms that are associated with disease resistance and that include functional protein-coding changes in four genes involved in coral immunity and pathogen detection. Polygenic scores calculated from 10 genomic loci indicate that genetic screens can detect disease resistance in wild and nursery stocks of A. cervicornis across the Caribbean.

Genome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in the Breviolum minutum genome

In dinoflagellates, a unique and extremely divergent genomic and nuclear organization has evolved. The highly unusual features of dinoflagellate nuclei and genomes include permanently condensed liquid crystalline chromosomes, primarily packaged by proteins other than histones, genes organized in very long unidirectional gene arrays, a general absence of transcriptional regulation, high abundance of the otherwise very rare DNA modification 5-hydroxymethyluracil (5-hmU), and many others. While most of these fascinating properties were originally identified in the 1970s and 1980s, they have not yet been investigated using modern genomic tools. In this work, we address some of the outstanding questions regarding dinoflagellate genome organization by mapping the genome-wide distribution of 5-hmU (using both immunoprecipitation-based and basepair-resolution chemical mapping approaches) and of chromatin accessibility in the genome of the Symbiodiniaceae dinoflagellate Breviolum minutum. We find that the 5-hmU modification is preferentially enriched over certain classes of repetitive elements, often coincides with the boundaries between gene arrays, and is generally correlated with decreased chromatin accessibility, the latter otherwise being largely uniform along the genome. We discuss the potential roles of 5-hmU in the functional organization of dinoflagellate genomes and its relationship to the transcriptional landscape of gene arrays.

Environmental pH signals the release of monosaccharides from cell wall in coral symbiotic alga

Reef-building corals thrive in oligotrophic environments due to their possession of endosymbiotic algae. Confined to the low pH interior of the symbiosome within the cell, the algal symbiont provides the coral host with photosynthetically fixed carbon. However, it remains unknown how carbon is released from the algal symbiont for uptake by the host. Here we show, using cultured symbiotic dinoflagellate, Breviolum sp., that decreases in pH directly accelerates the release of monosaccharides, that is, glucose and galactose, into the ambient environment. Under low pH conditions, the cell surface structures were deformed and genes related to cellulase were significantly upregulated in Breviolum. Importantly, the release of monosaccharides was suppressed by the cellulase inhibitor, glucopyranoside, linking the release of carbon to degradation of the agal cell wall. Our results suggest that the low pH signals the cellulase-mediated release of monosaccharides from the algal cell wall as an environmental response in coral reef ecosystems.

Marine heatwaves threaten cryptic coral diversity and erode associations among coevolving partners

Climate change-amplified marine heatwaves can drive extensive mortality in foundation species. However, a paucity of longitudinal genomic datasets has impeded understanding of how these rapid selection events alter cryptic genetic structure. Heatwave impacts may be exacerbated in species that engage in obligate symbioses, where the genetics of multiple coevolving taxa may be affected. Here, we tracked the symbiotic associations of reef-building corals for 6 years through a prolonged heatwave, including known survivorship for 79 of 315 colonies. Coral genetics strongly predicted survival of the ubiquitous coral, Porites (massive growth form), with variable survival (15 to 61%) across three morphologically indistinguishable-but genetically distinct-lineages. The heatwave also disrupted strong associations between these coral lineages and their algal symbionts (family Symbiodiniaceae), with symbiotic turnover in some colonies, resulting in reduced specificity across lineages. These results highlight how heatwaves can threaten cryptic genotypes and decouple otherwise tightly coevolved relationships between hosts and symbionts.

Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes

Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.

The coral microbiome: towards an understanding of the molecular mechanisms of coral-microbiota interactions

Corals live in a complex, multipartite symbiosis with diverse microbes across kingdoms, some of which are implicated in vital functions, such as those related to resilience against climate change. However, knowledge gaps and technical challenges limit our understanding of the nature and functional significance of complex symbiotic relationships within corals. Here, we provide an overview of the complexity of the coral microbiome focusing on taxonomic diversity and functions of well-studied and cryptic microbes. Mining the coral literature indicate that while corals collectively harbour a third of all marine bacterial phyla, known bacterial symbionts and antagonists of corals represent a minute fraction of this diversity and that these taxa cluster into select genera, suggesting selective evolutionary mechanisms enabled these bacteria to gain a niche within the holobiont. Recent advances in coral microbiome research aimed at leveraging microbiome manipulation to increase coral's fitness to help mitigate heat stress-related mortality are discussed. Then, insights into the potential mechanisms through which microbiota can communicate with and modify host responses are examined by describing known recognition patterns, potential microbially derived coral epigenome effector proteins and coral gene regulation. Finally, the power of omics tools used to study corals are highlighted with emphasis on an integrated host-microbiota multiomics framework to understand the underlying mechanisms during symbiosis and climate change-driven dysbiosis.

Oleaginous Heterotrophic Dinoflagellates—Crypthecodiniaceae

The heterotrophic Crypthecodinium cohnii is a major model for dinoflagellate cell biology, and a major industrial producer of docosahexaenoic acid, a key nutraceutical and added pharmaceutical compound. Despite these factors, the family Crypthecodiniaceae is not fully described, which is partly attributable to their degenerative thecal plates, as well as the lack of ribotype-referred morphological description in many taxons. We report here significant genetic distances and phylogenetic cladding that support inter-specific variations within the Crypthecodiniaceae. We describe Crypthecodinium croucheri sp. nov. Kwok, Law and Wong, that have different genome sizes, ribotypes, and amplification fragment length polymorphism profiles when compared to the C. cohnii. The interspecific ribotypes were supported by distinctive truncation-insertion at the ITS regions that were conserved at intraspecific level. The long genetic distances between Crypthecodiniaceae and other dinoflagellate orders support the separation of the group, which includes related taxons with high oil content and degenerative thecal plates, to be ratified to the order level. The current study provides the basis for future specific demarcation-differentiation, which is an important facet in food safety, biosecurity, sustainable agriculture feeds, and biotechnology licensing of new oleaginous models.

Genomic conservation and putative downstream functionality of the phosphatidylinositol signalling pathway in the cnidarian-dinoflagellate symbiosis

The mutualistic cnidarian-dinoflagellate symbiosis underpins the evolutionary success of stony corals and the persistence of coral reefs. However, a molecular understanding of the signalling events that lead to the successful establishment and maintenance of this symbiosis remains unresolved. For example, the phosphatidylinositol (PI) signalling pathway has been implicated during the establishment of multiple mutualistic and parasitic interactions across the kingdoms of life, yet its role within the cnidarian-dinoflagellate symbiosis remains unexplored. Here, we aimed to confirm the presence and assess the specific enzymatic composition of the PI signalling pathway across cnidaria and dinoflagellates by compiling 21 symbiotic anthozoan (corals and sea anemones) and 28 symbiotic dinoflagellate (Symbiodiniaceae) transcriptomic and genomic datasets and querying genes related to this pathway. Presence or absence of PI-kinase and PI-phosphatase orthologs were also compared between a broad sampling of taxonomically related symbiotic and non-symbiotic species. Across the symbiotic anthozoans analysed, there was a complete and highly conserved PI pathway, analogous to the pathway found in model eukaryotes. The Symbiodiniaceae pathway showed similarities to its sister taxon, the Apicomplexa, with the absence of PI 4-phosphatases. However, conversely to Apicomplexa, there was also an expansion of homologs present in the PI5-phosphatase and PI5-kinase groups, with unique Symbiodiniaceae proteins identified that are unknown from non-symbiotic unicellular organisms. Additionally, we aimed to unravel the putative functionalities of the PI signalling pathway in this symbiosis by analysing phosphoinositide (PIP)-binding proteins. Analysis of phosphoinositide (PIP)-binding proteins showed that, on average, 2.23 and 1.29% of the total assemblies of anthozoan and Symbiodiniaceae, respectively, have the potential to bind to PIPs. Enrichment of Gene Ontology (GO) terms associated with predicted PIP-binding proteins within each taxon revealed a broad range of functions, including compelling links to processes putatively involved in symbiosis regulation. This analysis establishes a baseline for current understanding of the PI pathway across anthozoans and Symbiodiniaceae, and thus a framework to target future research.

Intron-rich dinoflagellate genomes driven by Introner transposable elements of unprecedented diversity

Spliceosomal introns, which interrupt nuclear genes, are ubiquitous features of eukaryotic nuclear genes.¹ Spliceosomal intron evolution is complex, with different lineages ranging from virtually zero to thousands of newly created introns.^2,3,4,5 This punctate phylogenetic distribution could be explained if intron creation is driven by specialized transposable elements ("Introners"), with Introner-containing lineages undergoing frequent intron gain.^6,7,8,9,10 Fragmentation of nuclear genes by spliceosomal introns reaches its apex in dinoflagellates, which have some twenty introns per gene^11,12; however, little is known about dinoflagellate intron evolution. We reconstructed intron evolution in five dinoflagellate genomes, revealing a dynamic history of intron gain. We find evidence for historical creation of introns in all five species and identify recently active Introners in 4/5 studied species. In one species, Polarella glacialis, we find an unprecedented diversity of Introners, with recent Introner insertion leading to creation of some 12,253 introns, and with 15 separate families of Introners accounting for at least 100 introns each. These Introner families show diverse mechanisms of moblization and intron creation. Comparison within and between Introner families provides evidence that biases in the so-called intron phase, intron position relative to codon periodicity, could be driven by Introner insertion site requirements.^9,13,14 Finally, we report additional transformations of the spliceosomal system in dinoflagellates, including widespread loss of ancestral introns, and novelties of tolerated and favored donor sequence motifs. These results reveal unappreciated diversity of intron-creating elements and spliceosomal evolutionary capacity and highlight the complex evolutionary dependencies shaping genome structures.

Building consensus around the assessment and interpretation of Symbiodiniaceae diversity

Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians (e.g., corals, octocorals, sea anemones, jellyfish), other marine invertebrates (e.g., sponges, molluscs, flatworms), and protists (e.g., foraminifera), molecular data have been used extensively over the past three decades to describe phenotypes and to make evolutionary and ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack of consensus among researchers with respect to interpreting genetic data has slowed progress in the field and acted as a barrier to reconciling observations. Here, we identify key challenges regarding the assessment and interpretation of Symbiodiniaceae genetic diversity across three levels: species, populations, and communities. We summarize areas of agreement and highlight techniques and approaches that are broadly accepted. In areas where debate remains, we identify unresolved issues and discuss technologies and approaches that can help to fill knowledge gaps related to genetic and phenotypic diversity. We also discuss ways to stimulate progress, in particular by fostering a more inclusive and collaborative research community. We hope that this perspective will inspire and accelerate coral reef science by serving as a resource to those designing experiments, publishing research, and applying for funding related to Symbiodiniaceae and their symbiotic partnerships.

Harnessing the Power of Model Organisms To Unravel Microbial Functions in the Coral Holobiont

Stony corals build the framework of coral reefs, ecosystems of immense ecological and economic importance. The existence of these ecosystems is threatened by climate change and other anthropogenic stressors that manifest in microbial dysbiosis such as coral bleaching and disease, often leading to coral mortality. Despite a significant amount of research, the mechanisms ultimately underlying these destructive phenomena, and what could prevent or mitigate them, remain to be resolved. This is mostly due to practical challenges in experimentation on corals and the highly complex nature of the coral holobiont that also includes bacteria, archaea, protists, and viruses. While the overall importance of these partners is well recognized, their specific contributions to holobiont functioning and their interspecific dynamics remain largely unexplored. Here, we review the potential of adopting model organisms as more tractable systems to address these knowledge gaps. We draw on parallels from the broader biological and biomedical fields to guide the establishment, implementation, and integration of new and emerging model organisms with the aim of addressing the specific needs of coral research. We evaluate the cnidarian models Hydra, Aiptasia, Cassiopea, and Astrangia poculata; review the fast-evolving field of coral tissue and cell cultures; and propose a framework for the establishment of "true" tropical reef-building coral models. Based on this assessment, we also suggest future research to address key aspects limiting our ability to understand and hence improve the response of reef-building corals to future ocean conditions.

Responses of dinoflagellate cells to ultraviolet-C irradiation

Dinoflagellates are important aquatic microbes and major harmful algal bloom (HAB) agents that form invasive species through ship ballast transfer. UV-C installations are recommended for ballast treatments and HAB controls, but there is a lack of knowledge in dinoflagellate responses to UV-C. We report here dose-dependent cell cycle delay and viability loss of dinoflagellate cells irradiated with UV-C, with significant proliferative reduction at 800 Jm^-2 doses or higher, but immediate LD50 was in the range of 2400-3200 Jm^-2 . At higher dosages, some dinoflagellate cells surprisingly survived after days of recovery incubation, and continued viability loss, with samples exhibiting DNA fragmentations per proliferative resumption. Sequential cell cycle postponements, suggesting DNA damages were repaired over one cell cycle, were revealed with flow cytometric analysis and transcriptomic analysis. Over a sustained level of other DNA damage repair pathways, transcript elevation was observed only for several components of base pair repair and mismatch repair. Cumulatively, our findings demonstrated special DNA damage responses in dinoflagellate cells, which we discussed in relation to their unique chromo-genomic characters, as well as indicating resilience of dinoflagellate cells to UV-C.

Genetic association of toxin production in the dinoflagellate Alexandrium minutum

Dinoflagellates of the genus Alexandrium are responsible for harmful algal blooms and produce paralytic shellfish toxins (PSTs). Their very large and complex genomes make it challenging to identify the genes responsible for toxin synthesis. A family-based genomic association study was developed to determine the inheritance of toxin production in Alexandrium minutum and identify genomic regions linked to this production. We show that the ability to produce toxins is inheritable in a Mendelian way, while the heritability of the toxin profile is more complex. We developed the first dinoflagellate genetic linkage map. Using this map, several major results were obtained: 1. A genomic region related to the ability to produce toxins was identified. 2. This region does not contain any polymorphic sxt genes, known to be involved in toxin production in cyanobacteria. 3. The sxt genes, known to be present in a single cluster in cyanobacteria, are scattered on different linkage groups in A. minutum. 4. The expression of two sxt genes not assigned to any linkage group, sxtI and sxtG, may be regulated by the genomic region related to the ability to produce toxins. Our results provide new insights into the organization of toxicity-related genes in A. minutum, suggesting a dissociated genetic mechanism for the production of the different analogues and the ability to produce toxins. However, most of the newly identified genes remain unannotated. This study therefore proposes new candidate genes to be further explored to understand how dinoflagellates synthesize their toxins.

Multiple waves of viral invasions in Symbiodiniaceae algal genomes

Dinoflagellates from the family Symbiodiniaceae are phototrophic marine protists that engage in symbiosis with diverse hosts. Their large and distinct genomes are characterized by pervasive gene duplication and large-scale retroposition events. However, little is known about the role and scale of horizontal gene transfer (HGT) in the evolution of this algal family. In other dinoflagellates, high levels of HGTs have been observed, linked to major genomic transitions, such as the appearance of a viral-acquired nucleoprotein that originated via HGT from a large DNA algal virus. Previous work showed that Symbiodiniaceae from different hosts are actively infected by viral groups, such as giant DNA viruses and ssRNA viruses, that may play an important role in coral health. Latent viral infections may also occur, whereby viruses could persist in the cytoplasm or integrate into the host genome as a provirus. This hypothesis received experimental support; however, the cellular localization of putative latent viruses and their taxonomic affiliation are still unknown. In addition, despite the finding of viral sequences in some genomes of Symbiodiniaceae, viral origin, taxonomic breadth, and metabolic potential have not been explored. To address these questions, we searched for putative viral-derived proteins in thirteen Symbiodiniaceae genomes. We found fifty-nine candidate viral-derived HGTs that gave rise to twelve phylogenies across ten genomes. We also describe the taxonomic affiliation of these virus-related sequences, their structure, and their genomic context. These results lead us to propose a model to explain the origin and fate of Symbiodiniaceae viral acquisitions.

The enigmatic clock of dinoflagellates, is it unique?

Dinoflagellate clocks are unique as they show no resemblance to any known model eukaryotic or prokaryotic clock architecture. Dinoflagellates are unicellular, photosynthetic, primarily marine eukaryotes are known for their unique biology and rhythmic physiology. Their physiological rhythms are driven by an internal oscillator whose molecular underpinnings are yet unknown. One of the primary reasons that slowed the progression of their molecular studies is their extremely large and repetitive genomes. Dinoflagellates are primary contributors to the global carbon cycle and oxygen levels, therefore, comprehending their internal clock architecture and its interaction with their physiology becomes a subject of utmost importance. The advent of high throughput Omics technology provided the momentum to understand the molecular architecture and functioning of the dinoflagellate clocks. We use these extensive databases to perform meta-analysis to reveal the status of clock components in dinoflagellates. In this article, we will delve deep into the various “Omics” studies that catered to various breakthroughs in the field of circadian biology in these organisms that were not possible earlier. The overall inference from these omics studies points toward an uncommon eukaryotic clock model, which can provide promising leads to understand the evolution of molecular clocks.

Full-Length Transcriptome Maps of Reef-Building Coral Illuminate the Molecular Basis of Calcification, Symbiosis, and Circa-Dian Genes

Coral transcriptomic data largely rely on short-read sequencing, which severely limits the understanding of coral molecular mechanisms and leaves many important biological questions unresolved. Here, we sequence the full-length transcriptomes of four common and frequently dominant reef-building corals using the PacBio Sequel II platform. We obtain information on reported gene functions, structures, and expression profiles. Among them, a comparative analysis of biomineralization-related genes provides insights into the molecular basis of coral skeletal density. The gene expression profiles of the symbiont Symbiodiniaceae are also isolated and annotated from the holobiont sequence data. Finally, a phylogenetic analysis of key circadian clock genes among 40 evolutionarily representative species indicates that there are four key members in early metazoans, including cry genes; Clock or Npas2; cyc or Arntl; and tim, while per, as the fifth member, occurs in Bilateria. In summary, this work provides a foundation for further work on the manipulation of skeleton production or symbiosis to promote the survival of these important organisms.

Temporal gene expression patterns in the coral Euphyllia paradivisa reveal the complexity of biological clocks in the cnidarian-algal symbiosis

Studying chronobiology in reef-building corals is challenging due to the tightly coupled symbiosis with their photosynthetic algae, Symbiodiniaceae. Although symbiosis requires metabolic synchronization and coordination of cellular processes in the holobiont, the cross-talk between the host and symbiont's clocks is still puzzling. Here, we use the mesophotic coral Euphyllia paradivisa to examine temporal gene expression patterns in symbiotic and aposymbiotic morphs exposed to natural light/dark cycles and constant darkness. Our comparative transcriptomic analyses revealed circadian and circatidal cycles of gene expression with a predominant diel pattern in both coral morphs. We found a substantial number of transcripts consistently rhythmic under both light conditions, including genes likely involved in the cnidarians' circadian clock, thus indicating that an endogenous clock, which can oscillate independently from the Symbiodiniaceae clock, exists in E. paradivisa. The analysis further manifests the remarkable impacts of symbiosis on transcriptional rhythms and implies that the algae's presence influences the host's biorhythm.

A Functional Genomics View of Gibberellin Metabolism in the Cnidarian Symbiont Breviolum minutum

Dinoflagellate inhabitants of the reef-building corals exchange nutrients and signals with host cells, which often benefit the growth of both partners. Phytohormones serve as central hubs for signal integration between symbiotic microbes and their hosts, allowing appropriate modulation of plant growth and defense in response to various stresses. However, the presence and function of phytohormones in photosynthetic dinoflagellates and their function in the holobionts remain elusive. We hypothesized that endosymbiotic dinoflagellates may produce and employ phytohormones for stress responses. Using the endosymbiont of reef corals Breviolum minutum as model, this study aims to exam whether the alga employ analogous signaling systems by an integrated multiomics approach. We show that key gibberellin (GA) biosynthetic genes are widely present in the genomes of the selected dinoflagellate algae. The non-13-hydroxylation pathway is the predominant route for GA biosynthesis and the multifunctional GA dioxygenase in B. minutum has distinct substrate preference from high plants. GA biosynthesis is modulated by the investigated bleaching-stimulating stresses at both transcriptional and metabolic levels and the exogenously applied GAs improve the thermal tolerance of the dinoflagellate. Our results demonstrate the innate ability of a selected Symbiodiniaceae to produce the important phytohormone and the active involvement of GAs in the coordination and the integration of the stress response.

Response mechanisms to ocean warming exposure in Effrenium voratum (Symbiodiniaceae)

Ocean warming is an extreme environment event that has profound and lasting impacts on Symbiodiniaceae. However, their response mechanisms to elevated temperature exposure are poorly understood. In this study, the physiological and transcriptional responses of Effrenium voratum (Symbiodiniaceae) to ocean warming were examined. After exposure to 30 °C, no significant variations in growth, chlorophyll a, or photosynthetic and respiration rates were observed, while a higher temperature (34 °C) significantly reduced these physiological measurements. Meanwhile, lipid content and fatty acid composition were altered at high temperature (i.e., elevated degree of fatty acid saturation). Such biochemical constituents likely contributed to the mitigation of the negative effects of elevated temperatures. Furthermore, higher expression levels of genes related to the synthesis and elongation of fatty acids were detected at high temperature. The adjustment of lipids and fatty acid composition may be a potential mechanism by which E. voratum may survive under future global warming. ONE SENTENCE SUMMARY: The adjustment of lipids and fatty acid composition may be a potential mechanism by which E. voratum acclimate to future global warming.

Millennia-old coral holobiont DNA provides insight into future adaptive trajectories

Ancient DNA (aDNA) has been applied to evolutionary questions across a wide variety of taxa. Here, for the first time, we leverage aDNA from millennia-old fossil coral fragments to gain new insights into a rapidly declining western Atlantic reef ecosystem. We sampled four Acropora palmata fragments (dated 4215 BCE - 1099 CE) obtained from two Florida Keys reef cores. From these samples, we established that it is possible both to sequence ancient DNA from reef cores and place the data in the context of modern-day genetic variation. We recovered varying amounts of nuclear DNA exhibiting the characteristic signatures of aDNA from the A. palmata fragments. To describe the holobiont sensu lato, which plays a crucial role in reef health, we utilized metagenome-assembled genomes as a reference to identify a large additional proportion of ancient microbial DNA from the samples. The samples shared many common microbes with modern-day coral holobionts from the same region, suggesting remarkable holobiont stability over time. Despite efforts, we were unable to recover ancient Symbiodiniaceae reads from the samples. Comparing the ancient A. palmata data to whole-genome sequencing data from living acroporids, we found that while slightly distinct, ancient samples were most closely related to individuals of their own species. Together, these results provide a proof-of-principle showing that it is possible to carry out direct analysis of coral holobiont change over time, which lays a foundation for studying the impacts of environmental stress and evolutionary constraints.

Coral Holobionts Possess Distinct Lipid Profiles That May Be Shaped by Symbiodiniaceae Taxonomy

Symbiotic relationships are very important for corals. Abiotic stressors cause the acclimatization of cell membranes in symbionts, which possess different membrane acclimatization strategies. Membrane stability is determined by a unique lipid composition and, thus, the profile of thylakoid lipids can depend on coral symbiont species. We have analyzed and compared thylakoid lipidomes (mono- and digalactosyldiacylglycerols (MGDG and DGDG), sulfoquinovosyldiacylglycerols (SQDG), and phosphatidylglycerols (PG)) of crude extracts from symbiotic reef-building coral Acropora sp., the hydrocoral Millepora platyphylla, and the octocoral Sinularia flexibilis. S. flexibilis crude extracts were characterized by a very high SQDG/PG ratio, a DGDG/MGDG ratio < 1, a lower degree of galactolipid unsaturation, a higher content of SQDG with polyunsaturated fatty acids, and a thinner thylakoid membrane which may be explained by the presence of thermosensitive dinoflagellates Cladocopium C3. In contrast, crude extracts of M. platyphylla and Acropora sp. exhibited the lipidome features of thermotolerant Symbiodiniaceae. M. platyphylla and Acropora sp. colonies contained Cladocopium C3u and Cladocopium C71/C71a symbionts, respectively, and their lipidome profiles showed features that indicate thermotolerance. We suggest that an association with symbionts that exhibit the thermotolerant thylakoid lipidome features, combined with a high Symbiodiniaceae diversity, may facilitate further acclimatization/adaptation of M. platyphylla and Acropora sp. holobionts in the South China Sea.

An overview of transcription in dinoflagellates

Dinoflagellates are a vital diverse family of unicellular algae widespread in various aquatic environments. Typically large genomes and permanently condensed chromosomes without histones make these organisms unique among eukaryotes in terms of chromatin structure and gene expression. Genomic and transcriptomic sequencing projects have provided new insight into the genetic foundation of dinoflagellate behaviors. Genes in tandem arrays, trans-splicing of mRNAs and lower levels of transcriptional regulation compared to other eukaryotes all contribute to the differences seen. Here we present a general overview of transcription in dinoflagellates based on previously described work.

Intron losses and gains in the nematodes

Background

The evolution of spliceosomal introns has been widely studied among various eukaryotic groups. Researchers nearly reached the consensuses on the pattern and the mechanisms of intron losses and gains across eukaryotes. However, according to previous studies that analyzed a few genes or genomes, Nematoda seems to be an eccentric group.

Results

Taking advantage of the recent accumulation of sequenced genomes, we extensively analyzed the intron losses and gains using 104 nematode genomes across all the five Clades of the phylum. Nematodes have a wide range of intron density, from less than one to more than nine per kbp coding sequence. The rates of intron losses and gains exhibit significant heterogeneity both across different nematode lineages and across different evolutionary stages of the same lineage. The frequency of intron losses far exceeds that of intron gains. Five pieces of evidence supporting the model of cDNA-mediated intron loss have been observed in ten Caenorhabditis species, the dominance of the precise intron losses, frequent loss of adjacent introns, high-level expression of the intron-lost genes, preferential losses of short introns, and the preferential losses of introns close to 3′-ends of genes. Like studies in most eukaryotic groups, we cannot find the source sequences for the limited number of intron gains detected in the Caenorhabditis genomes.

Conclusions

These results indicate that nematodes are a typical eukaryotic group rather than an outlier in intron evolution.

The role of zinc in the adaptive evolution of polar phytoplankton

Zinc is an essential trace metal for oceanic primary producers with the highest concentrations in polar oceans. However, its role in the biological functioning and adaptive evolution of polar phytoplankton remains enigmatic. Here, we have applied a combination of evolutionary genomics, quantitative proteomics, co-expression analyses and cellular physiology to suggest that model polar phytoplankton species have a higher demand for zinc because of elevated cellular levels of zinc-binding proteins. We propose that adaptive expansion of regulatory zinc-finger protein families, co-expanded and co-expressed zinc-binding proteins families involved in photosynthesis and growth in these microalgal species and their natural communities were identified to be responsible for the higher zinc demand. The expression of their encoding genes in eukaryotic phytoplankton metatranscriptomes from pole-to-pole was identified to correlate not only with dissolved zinc concentrations in the upper ocean but also with temperature, suggesting that environmental conditions of polar oceans are responsible for an increased demand of zinc. These results suggest that zinc plays an important role in supporting photosynthetic growth in eukaryotic polar phytoplankton and that this has been critical for algal colonization of low-temperature polar oceans.

Population connectivity and genetic offset in the spawning coral Acropora digitifera in Western Australia

Anthropogenic climate change has caused widespread loss of species biodiversity and ecosystem productivity across the globe, particularly on tropical coral reefs. Predicting the future vulnerability of reef-building corals, the foundation species of coral reef ecosystems, is crucial for cost-effective conservation planning in the Anthropocene. In this study, we combine regional population genetic connectivity and seascape analyses to explore patterns of genetic offset (the mismatch of gene-environmental associations under future climate conditions) in Acropora digitifera across 12 degrees of latitude in Western Australia. Our data revealed a pattern of restricted gene flow and limited genetic connectivity among geographically distant reef systems. Environmental association analyses identified a suite of loci strongly associated with the regional temperature variation. These loci helped forecast future genetic offset in gradient forest and generalised dissimilarity models. These analyses predicted pronounced differences in the response of different reef systems in Western Australia to rising temperatures. Under the most optimistic future warming scenario (RCP 2.6), we predicted a general pattern of increasing genetic offset with latitude. Under the extreme climate scenario (RCP 8.5 in 2090-2100), coral populations at the Ningaloo World Heritage Area were predicted to experience a higher mismatch between current allele frequencies and those required to cope with local environmental change, compared to populations in the inshore Kimberley region. The study suggests complex and spatially heterogeneous patterns of climate-change vulnerability in coral populations across Western Australia, reinforcing the notion that regionally tailored conservation efforts will be most effective at managing coral reef resilience into the future.

Bioinformatics of Corals: Investigating Heterogeneous Omics Data from Coral Holobionts for Insight into Reef Health and Resilience

Coral reefs are home to over two million species and provide habitat for roughly 25% of all marine animals, but they are being severely threatened by pollution and climate change. A large amount of genomic, transcriptomic, and other omics data is becoming increasingly available from different species of reef-building corals, the unicellular dinoflagellates, and the coral microbiome (bacteria, archaea, viruses, fungi, etc.). Such new data present an opportunity for bioinformatics researchers and computational biologists to contribute to a timely, compelling, and urgent investigation of critical factors that influence reef health and resilience. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 5 is August 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Population genomics for symbiotic anthozoans: can reduced representation approaches be used for taxa without reference genomes?

Population genetic studies of symbiotic anthozoans have been historically challenging because their endosymbioses with dinoflagellates have impeded marker development. Genomic approaches like reduced representation sequencing alleviate marker development issues but produce anonymous loci, and without a reference genome, it is unknown which organism is contributing to the observed patterns. Alternative methods such as bait-capture sequencing targeting Ultra-Conserved Elements are now possible but costly. Thus, RADseq remains attractive, but how useful are these methods for symbiotic anthozoan taxa without a reference genome to separate anthozoan from algal sequences? We explore this through a case-study using a double-digest RADseq dataset for the sea anemone Bartholomea annulata. We assembled a holobiont dataset (3854 loci) for 101 individuals, then used a reference genome to create an aposymbiotic dataset (1402 loci). For both datasets, we investigated population structure and used coalescent simulations to estimate demography and population parameters. We demonstrate complete overlap in the spatial patterns of genetic diversity, demographic histories, and population parameter estimates for holobiont and aposymbiotic datasets. We hypothesize that the unique combination of anthozoan biology, diversity of the endosymbionts, and the manner in which assembly programs identify orthologous loci alleviates the need for reference genomes in some circumstances. We explore this hypothesis by assembling an additional 21 datasets using the assembly programs pyRAD and Stacks. We conclude that RADseq methods are more tractable for symbiotic anthozoans without reference genomes than previously realized.

Alignment-Free Analysis of Whole-Genome Sequences From Symbiodiniaceae Reveals Different Phylogenetic Signals in Distinct Regions

Dinoflagellates of the family Symbiodiniaceae are predominantly essential symbionts of corals and other marine organisms. Recent research reveals extensive genome sequence divergence among Symbiodiniaceae taxa and high phylogenetic diversity hidden behind subtly different cell morphologies. Using an alignment-free phylogenetic approach based on sub-sequences of fixed length k (i.e. k-mers), we assessed the phylogenetic signal among whole-genome sequences from 16 Symbiodiniaceae taxa (including the genera of Symbiodinium, Breviolum, Cladocopium, Durusdinium and Fugacium) and two strains of Polarella glacialis as outgroup. Based on phylogenetic trees inferred from k-mers in distinct genomic regions (i.e. repeat-masked genome sequences, protein-coding sequences, introns and repeats) and in protein sequences, the phylogenetic signal associated with protein-coding DNA and the encoded amino acids is largely consistent with the Symbiodiniaceae phylogeny based on established markers, such as large subunit rRNA. The other genome sequences (introns and repeats) exhibit distinct phylogenetic signals, supporting the expected differential evolutionary pressure acting on these regions. Our analysis of conserved core k-mers revealed the prevalence of conserved k-mers (>95% core 23-mers among all 18 genomes) in annotated repeats and non-genic regions of the genomes. We observed 180 distinct repeat types that are significantly enriched in genomes of the symbiotic versus free-living Symbiodinium taxa, suggesting an enhanced activity of transposable elements linked to the symbiotic lifestyle. We provide evidence that representation of alignment-free phylogenies as dynamic networks enhances the ability to generate new hypotheses about genome evolution in Symbiodiniaceae. These results demonstrate the potential of alignment-free phylogenetic methods as a scalable approach for inferring comprehensive, unbiased whole-genome phylogenies of dinoflagellates and more broadly of microbial eukaryotes.

Metatranscriptomic Analysis of Corals Inoculated With Tolerant and Non-Tolerant Symbiont Exposed to High Temperature and Light Stress

Algal symbionts of corals can influence host stress resistance; for example, in the Pacific Ocean, whereas Cladocopium (C-type) is generally dominant in corals, Durusdinium (D-type) is found in more heat-resistant corals. Thus, the presence of D-type symbiont likely increases coral heat tolerance, and this symbiotic relationship potentially provides a hint to increase the stress tolerance of coral–algal symbioses. In this study, transcriptome profiles of Cladocopium- and Durusdinium-harboring Acropora solitaryensis (C-coral and D-coral, respectively) and algal photosystem functioning (Fv/Fm) under bleaching conditions (high temperature and light stress) were compared. Stress treatment caused algal photoinhibition that the Fv/Fm value of Symbiodiniaceae was immediately reduced. The transcriptome analysis of corals revealed that genes involved in the following processes were detected: endoplasmic reticulum (ER) stress, mitophagy, apoptosis, endocytosis, metabolic processes (acetyl-CoA, chitin metabolic processes, etc.), and the PI3K-AKT pathway were upregulated, while DNA replication and the calcium signaling pathway were downregulated in both C- and D-corals. These results suggest that unrepaired DNA and protein damages were accumulated in corals under high temperature and light stress. Additionally, some differentially expressed genes (DEGs) were specific to C- or D-corals, which includes genes involved in transient receptor potential (TRP) channels and vitamin B metabolic processes. Algal transcriptome analysis showed the increased expression of gene encoding photosystem and molecular chaperone especially in D-type symbiont. The transcriptome data imply a possible difference in the stress reactions on C-type and D-type symbionts. The results reveal the basic process of coral heat/light stress response and symbiont-type-specific coral transcriptional responses, which provides a perspective on the mechanisms that cause differences in coral stress tolerance.

Dinoflagellate Phosphopantetheinyl Transferase (PPTase) and Thiolation Domain Interactions Characterized Using a Modified Indigoidine Synthesizing Reporter

Photosynthetic dinoflagellates synthesize many toxic but also potential therapeutic compounds therapeutics via polyketide/non-ribosomal peptide synthesis, a common means of producing natural products in bacteria and fungi. Although canonical genes are identifiable in dinoflagellate transcriptomes, the biosynthetic pathways are obfuscated by high copy numbers and fractured synteny. This study focuses on the carrier domains that scaffold natural product synthesis (thiolation domains) and the phosphopantetheinyl transferases (PPTases) that thiolate these carriers. We replaced the thiolation domain of the indigoidine producing BpsA gene from Streptomyces lavendulae with those of three multidomain dinoflagellate transcripts and coexpressed these constructs with each of three dinoflagellate PPTases looking for specific pairings that would identify distinct pathways. Surprisingly, all three PPTases were able to activate all the thiolation domains from one transcript, although with differing levels of indigoidine produced, demonstrating an unusual lack of specificity. Unfortunately, constructs with the remaining thiolation domains produced almost no indigoidine and the thiolation domain for lipid synthesis could not be expressed in E. coli. These results combined with inconsistent protein expression for different PPTase/thiolation domain pairings present technical hurdles for future work. Despite these challenges, expression of catalytically active dinoflagellate proteins in E. coli is a novel and useful tool going forward.

Kinetic and Stoichiometric Modeling-Based Analysis of Docosahexaenoic Acid (DHA) Production Potential by C. cohnii from Glycerol, Glucose and Ethanol

Docosahexaenoic acid (DHA) is one of the most important long-chain polyunsaturated fatty acids (LC-PUFAs), with numerous health benefits. Crypthecodinium cohnii, a marine heterotrophic dinoflagellate, is successfully used for the industrial production of DHA because it can accumulate DHA at high concentrations within the cells. Glycerol is an interesting renewable substrate for DHA production since it is a by-product of biodiesel production and other industries, and is globally generated in large quantities. The DHA production potential from glycerol, ethanol and glucose is compared by combining fermentation experiments with the pathway-scale kinetic modeling and constraint-based stoichiometric modeling of C. cohnii metabolism. Glycerol has the slowest biomass growth rate among the tested substrates. This is partially compensated by the highest PUFAs fraction, where DHA is dominant. Mathematical modeling reveals that glycerol has the best experimentally observed carbon transformation rate into biomass, reaching the closest values to the theoretical upper limit. In addition to our observations, the published experimental evidence indicates that crude glycerol is readily consumed by C. cohnii, making glycerol an attractive substrate for DHA production.