Search Results (3)

Background/Objectives: The long-spined sea urchin Diadema antillarum is a keystone herbivore whose grazing maintains Caribbean coral reefs; basin-wide mass mortalities in 1983–1984 and 2022 have made genomic resources a conservation priority, yet no nuclear genome existed for the species. We aimed to generate the first nuclear reference and to resolve the high heterozygosity that complicates genome assembly in broadcast-spawning marine invertebrates. Methods: For the assembly, we combined PacBio HiFi, Oxford Nanopore, and Illumina sequencing. Genome size and heterozygosity were estimated by k-mer profiling. We compared standard and haplotype-aware assembly strategies (hifiasm), evaluated completeness with BUSCO, and annotated repeats using a species-specific RepeatModeler library. Results: k-mer profiling estimated a haploid genome of ~703 Mb with 2.52% heterozygosity. Standard assembly then produced an inflated 1.75 Gb assembly (98.4% BUSCO-complete but 84.4% duplicated), indicating retention of both haplotypes. Haplotype-aware reassembly separated this into a collapsed primary assembly (1.03 Gb) and two phased haplotypes (0.95 and 0.89 Gb), each comparable in size to the chromosome-level congener D. antillarum (886 Mb). BUSCO completeness reached 99.0%, with single-copy orthologs rising to 85–90%, and reference-free consensus quality reached QV 44.5 (Merqury; initial assembly). This genome is repeat-rich (42.84% repetitive; 29.96% unclassified). Conclusions: We provide the collapsed primary assembly together with both phased haplotypes as a haplotype-resolved reference for D. antillarum, establishing a foundation for immunogenomic, comparative, and population-genetic studies and for monitoring and restoration of this ecologically critical species. More broadly, the study shows that haplotype-aware assembly is essential for resolving such highly heterozygous genomes and delivers the genomic foundation needed to guide the conservation of this keystone Caribbean reef species. Full article

Caribbean sea urchins are marine invertebrates that have experienced a decline over the years. Studies on sea urchins have focused primarily on the microbiome of the coelomic fluid or the gut microbiota. In this study, the epibiota community associated with four wild Caribbean sea urchin species, Lytechinus variegatus, Echinometra lucunter, Tripneustes ventricosus, and Diadema antillarum, was characterized for the first time. Using 57 sea urchin animal samples, we evaluated the influence of animal species, trophic niches, and geographical location on the composition of the epibiotic microbiota. We found significant differences in the bacterial biota among species and trophic niches, but not among geographical locations. L. variegatus exhibited the highest alpha diversity with high dominance of Fusobacteria, Planctomycetes, and Cyanobacteria, whereas T. ventricosus and D. antillarum were dominated by Firmicutes. T. ventricosus inhabiting the seagrass biotope dominated by Thalassia testudinum meadows had mostly Endozoicomonas. In contrast, samples located in the reef (dominated by corals and other reef builders) had a higher abundance of Kistimonas and Photobacterium. Our findings confirm that the epibiotic microbiota is species-specific, but also niche-dependent, revealing the trophic networks emerging from the organic matter being recycled in the seagrass and reef niches. As echinoids are important grazers of benthic communities, their microbiota will likely influence ecosystem processes. Full article

Extracts of the Floridian marine cyanobacterium Lyngbya cf. confervoides were found to deter feeding by reef fish and sea urchins (Diadema antillarum). This antifeedant activity may be a reflection of the secondary metabolite content, known to be comprised of many serine protease inhibitors. Further chemical and NMR spectroscopic investigation led us to isolate and structurally characterize a new serine protease inhibitor 1 that is formally derived from an intramolecular condensation of largamide D (2). The cyclization resulted in diminished activity, but to different extents against two serine proteases tested. This finding suggests that cyanobacteria can endogenously modulate the activity of their protease inhibitors. Full article