Biology subjects

Shoguchi, E.

Publications and source records attributed to Shoguchi, E..

6 recordsLinked to original sources

bioRxiv2026

Genomic insights into polyketide toxin synthesis and algal symbiosis using high-quality genome sequences of the early divergent hexacorallian genus Palythoa (Cnidaria, Zoantharia)

Palytoxin, first isolated from Palythoa toxica, is among the most potent marine toxins known. Despite decades of biochemical investigation, genetic bases underlying its potential biosynthesis in Palythoa remain unresolved. Here we present four high-quality genome assemblies of Palythoa species, including Palythoa cf. toxica, and integrate these with a chromosome-scale genome assembly of P. caribaeorum. Performing comparative genomic analyses, we screened for candidate genes potentially involved in palytoxin biosynthesis and examined patterns of genome evolution. Unexpectedly, we identified only two classes of ketosynthase (KS) domain-containing genes in Palythoa: fatty acid synthases (FAS) and bacterial-like polyketide synthases (PKSs). Contrasting other anthozoans, animal FAS-like PKS (AFPK) genes common to all Palythoa species were not detected. We found no evidence for lineage-specific expansion of PKS genes unique to Palythoa, suggesting that if palytoxin/palytoxin-like molecule biosynthesis is host-encoded, it may involve functional modification or co-opting pre-existing FAS and/or bacterial-like PKS pathways. Comparative analyses revealed expansions of gene families associated with transport and binding functions in Palythoa, potentially reflecting molecular adaptations linked to their sand-incorporating body structure. We identified TPT1 and CLEC4A as rapidly evolving genes in multiple Palythoa species, consistent with possible roles in growth regulation and host-microbe interactions. Additionally, comparison between azooxanthellate and zooxanthellate species revealed mutations within conserved protein domains of LePin, which has been implicated in cnidarian endosymbiosis, suggesting lineage-specific modifications associated with symbiotic state. This study establishes a foundation for zoantharian genomic research, provides insights into lineage-specific genomic signatures, and advances molecular and evolutionary biological knowledge of this ecologically important group.

genomics↗

bioRxiv2026

Possible Novel Sulfolipid Utilization Pathway in Giant Clams and Other Aquatic Invertebrates: Implications for Photosymbiosis and Sulfur Cycling

Photosymbiosis with dinoflagellates of the family Symbiodiniaceae enables giant clams to thrive in oligotrophic coral reef environments. However, mechanisms by which clams utilize algal-derived biomolecules remain largely unexplored. Using newly available genome resources for photosymbiotic bivalves (Tridacna and Fragum), we conducted a comparative genomic analysis to identify positively selected genes from these photosymbiotic bivalve lineages, that are potentially involved in symbiotic adaptations. Among candidate genes, we focused on sulfoquinovosidase (SQase), an enzyme that hydrolyzes sulfoquinovose (SQ) from sulfoquinovosyl diacylglycerol (SQDG), a sulfur-containing sulfolipid abundant in photosynthetic membranes. Although SQDG degradation has been characterized in bacteria, the distribution and role of SQase in animals have not been systematically examined. We found that possibly functional SQase homologs are widely distributed among aquatic invertebrates, but are largely absent in terrestrial taxa. In silico predictions showed that most animal SQases possess signal peptides and enter the secretory pathway, with lineage-specific gains and losses of membrane association, suggesting functional diversification. Transcriptomic analyses further demonstrated that SQase is predominantly expressed in digestive organs in diverse taxa, whereas in giant clams, it is also highly expressed in the outer mantle, the tissue primarily involved in harboring symbionts enriched in SQDG. Together, these results suggest that in aquatic invertebrates, SQase functions as a digestive enzyme for algal-derived sulfolipids and that photosymbiotic bivalves have expanded its deployment to tissues specialized for symbiosis. Our findings uncover a previously unrecognized metabolic interface between photosymbiosis and sulfur utilization in aquatic invertebrates, with broader implications for host-symbiont interactions and marine sulfur cycling.

zoology↗

bioRxiv2025

Genomic insights into photosymbiosis in giant clams: Comparisons with coral strategies

Giant clams are representative bivalves in coral reef ecosystems that host photosynthetic dinoflagellates extracellularly and rely on their photosynthates, functioning as "solar-powered animals." Unlike corals, which harbor intracellular dinoflagellates, molecular mechanisms and evolutionary history underlying this symbiosis remain largely unknown. Here, we integrated chromosome-scale genome assembly, transcriptome profiling, and bleaching experiments involving Tridacna crocea to explore the genetic basis of extracellular symbiosis. Signals associated with sterol transport by Niemann-Pick disease type C2 (NPC2) transporters and carbon-concentrating mechanisms suggest that giant clams share some nutrient exchange strategies with corals. Strikingly, the nitrate transporter NRT2, a "plant-like" gene previously thought to be absent in animals, represents an unexpected evolutionary retention that enables nitrate-based nutrient supply, highlighting a fundamental divergence from coral symbiosis. Together, our findings reveal both conserved and distinct molecular strategies of photosymbiosis in reef-dwelling marine invertebrates and provide insights into evolution and ecological resilience of coral reef ecosystems.

zoology↗

bioRxiv2021

Coral symbionts exhibit a polycistronic flavodiiron gene leading to functional proteins in photosynthesis

Photosynthesis in cyanobacteria, green algae, and basal land plants is protected against excess reducing pressure on the photosynthetic chain by flavodiiron proteins (FLV) that dissipate photosynthetic electrons by reducing O2. In these organisms, the genes encoding FLV are always conserved in the form of a pair of two-type isozymes (FLVA and FLVB) that are believed to function in O2 photo-reduction as a heterodimer. While coral symbionts (dinoflagellates of the family Symbiodiniaceae) are the only algae to harbor FLV in photosynthetic red plastid lineage, only one gene is found in transcriptomes and its role and activity remain unknown. Here, we characterized the FLV genes in Symbiodiniaceae and found that its coding region is composed of tandemly repeated FLV sequences. By measuring the O2-dependent electron flow and P700 oxidation, we suggest that this atypical FLV is active in vivo. Based on the amino-acid sequence alignment and the phylogenetic analysis, we conclude that in coral symbionts, the gene pair for FLVA and FLVB have been fused to construct one coding region for a hybrid enzyme, which presumably occurred when or after both genes were inherited from basal green algae to the dinoflagellate. Immunodetection suggested the FLV polypeptide to be cleaved by a post-translational mechanism, adding it to the rare cases of polycistronic genes in eukaryotes. Our results demonstrate that FLV are active in coral symbionts with genomic arrangement that is unique to these species. The implication of these unique features on their symbiotic living environment is discussed.

plant biology↗

bioRxiv2020

Response of coral reef dinoflagellates to nanoplastics under experimental conditions

Plastic products contribute heavily to anthropogenic pollution of the oceans. Small plastic particles in the micro- and nanoscale ranges have been found in all marine ecosystems, but little is known about their effects upon marine organisms. In this study we examine changes in cell growth, aggregation, and gene expression of two symbiotic dinoflagellates of the family Symbiodiniaceae, Symbiodinium tridacnidorum (clade A3) and Cladocopium sp. (clade C), under exposure to 42-nm polystyrene beads. In laboratory experiments, cell number and aggregation were reduced after 10 days of nanoplastic exposure at 0.01, 0.1, and 10 mg/L concentrations, but no clear correlation with plastic concentration was observed. Genes involved in dynein motor function were upregulated compared to control conditions, while genes related to photosynthesis, mitosis, and intracellular degradation were downregulated. Overall, nanoplastic exposure led to more genes being downregulated than upregulated and the number of genes with altered expression was larger in Cladocopium sp. than in S. tridacnidorum, suggesting different sensitivity to nanoplastic between species. Our data show that nanoplastic inhibits growth and alters aggregation properties of microalgae, which may negatively affect the uptake of these indispensable symbionts by coral reef organisms.

ecology↗

bioRxiv2018

Comparative genomics-first approach to understand diversification of secondary metabolite biosynthetic pathways in symbiotic dinoflagellates

Symbiotic dinoflagellates of the genus Symbiodinium are photosynthetic and unicellular. They possess smaller nuclear genomes than other dinoflagellates and produce structurally specialized, biologically active, secondary metabolites. Polyketide biosynthetic genes of toxic dinoflagellates have been studied extensively using transcriptomic analyses; however, a comparative genomic approach to understand secondary metabolism has been hampered by their large genome sizes. Here, we use a combined genomic and metabolomics approach to investigate the structure and diversification of secondary metabolite genes to understand how chemical diversity arises in three decoded Symbiodinium genomes (A3, B1 and C). Our analyses identify 71 polyketide synthase and 41 non-ribosomal peptide synthetase genes from two newly decoded genomes of clades A3 and C. Additionally, phylogenetic analyses indicate that almost all of the gene families are derived from lineage-specific gene duplications in Symbiodinium clades, suggesting divergence for environmental adaptation. Few metabolic pathways are conserved among the three clades and we detect metabolic similarity only in the recently diverged clades, B1 and C. We establish that secondary metabolism protein architecture guides substrate specificity and that gene duplication and domain shuffling have resulted in diversification of secondary metabolism genes.

genomics↗