Genomic and transcriptomic resources for the tropical ascidian Phallusia philippinensis2026 · Abstract Due to remarkably stereotyped development and small numbers of cells, ascidian embryos are invaluable as models for investigating the principles of chordate development at single-cell resolution. Established model species of ascidians, such as Ciona spp. and Phallusia mammillata, are primarily distributed in temperate waters, and natural populations become scarce in the summer due to rising water temperatures. However, Phallusia philippinensis is a tropical/subtropical species that is closely related to P. mammillata and shares the feature of highly transparent embryos, which facilitates live imaging and optical analyses. Its accessibility in warmwater habitats makes P. philippinensis a promising alternative model for imaging-based analyses, particularly in tropical regions or during the summer. We present comprehensive genomic transcriptomic resources that have been resolved according to the developmental stage for P. philippinensis. The assembled genome spans 150.2 Mb and comprises 407 contigs with an N50 of 909 kb and a GC content of 42.0%. Transcriptomes from 5 organs and 9 distinct embryonic stages were used to construct a gene model, which revealed 20,928 genes with a high BUSCO completeness score of 88.6%. Functional annotations were assigned to 16,507 genes using the UniProt and RefSeq databases. We integrated these resources into a new constructed genomic browser, which can be used easily by all researchers. These new resources are immediately applicable to comparative developmental studies of gene expression and regulation in ascidian embryos and will comprehensively cover the off-season of reproduction for model ascidians.
Optical properties of the jellyfish surface above the waterline: microvillar array in pleustonic hydrozoans2025 · Abstract Background The transparent jellyfish body is often difficult to see underwater, as its refractive index is similar to that of seawater, resulting in a low light reflectance on the body surface. Nevertheless, the outlines of jellyfish can be recognized by the slight reflection of light from their body surfaces. In some jellyfish species, the epidermis covering the body surface has an array of microvilli, nanostructures that can potentially reduce light reflection. However, the anti-reflective effect is minimal in water, as the difference in the refractive indices of tissue and seawater is so small that reflectance is low, even on flat surfaces. In jellyfish that have pneumatophores, structures used in floating and drifting on the sea surface, light reflection on the surface is expected to be large and noticeable owing to the large differences in refractive indices between the pneumatophore exposed above the water surface and air. In the current study, we examined the epidermal ultrastructure and refractive index of the pneumatophores of a Portuguese man o’ war (Physalia physalis) and a by-the-wind sailor (Velella velella). Results The refractive index of P. physalis pneumatophores measured with an Abbe refractometer was approximately 1.344. Microvillar arrays were found in epidermal cells of both P. physalis and V. velella. Based on the length, thickness, and pitch of the microvilli, we constructed simplified structural models for the simulation of light reflection using rigorous coupled wave analysis (RCWA). Our simulations showed that reflectance on the microvillar models could be greater or less than that on the flat surface, depending on light conditions (wavelength and angle of incidence), but with an overall effect of reduced reflection. Reflection reduction in microvillar models was particularly significant at large incident angles, where reflectance was extremely high on the flat surface. Conclusions Microvillar arrays found on the epidermis potentially reduce surface reflections of the pneumatophore and contribute to the reduction in visibility of the pleustonic hydrozoans above the sea surface. Moreover, less reflection at the pneumatophore surface indicates greater transmission of light through transparent bodies, potentially providing a counter-illumination effect that obscures the shadow of the hydrozoan bodies, depending on the intensity of ambient light.
