Biology subjects

Yonezawa, R.

Publications and source records attributed to Yonezawa, R..

5 recordsLinked to original sources

bioRxiv2025

Environmental exosomes: Evidence of extracellular RNA release by aquatic organisms

Aquatic organisms continuously interact with surrounding water, yet whether they release extracellular vesicles remains unknown. We hypothesized that pearl oysters (Pinctada fucata) release exosomes/small extracellular vesicles (sEVs) into the aquatic environment. To this end, we collected exosomes/sEV-sized components by ultrafiltration from tank water and open-sea culture areas. Microscopy revealed abundant vesicles consistent with exosome/sEV size, and RNA sequencing identified oyster-specific piRNAs that matched sequences previously detected in hemolymph exosomes. These findings demonstrated that pearl oysters actively released exosomes containing species-specific nucleic acids into surrounding water. We propose referring to these vesicles as environmental exosomes/environmental sEVs (eExosomes/esEVs). This finding suggests that aquatic exosomes serve as carriers of RNA and may contribute to inter-organismal communication networks. Beyond their functional role, eExosomes/esEVs also hold promise as novel targets for environmental DNA/RNA (eDNA/eRNA) analysis, offering new opportunities for ecological monitoring and biodiversity research.

ecology↗

bioRxiv2025

The minimal endosymbiosis between Spurilla braziliana (Aeolidiidae, Nudibranchia) and Symbiodiniaceae

Symbiotic relationships between dinoflagellates of the family Symbiodiniaceae and marine invertebrates underpin the functioning of certain shallow-water marine ecosystems. Although the Symbiodiniaceae-Cladobranchia nudibranch association has been proposed as a promising model for symbiosis research, interspecific variation in the extent of this association remains poorly resolved. Here, we assessed the algal symbiotic characteristics of the nudibranch Spurilla braziliana. Histological analyses revealed limited branching of the digestive gland and the presence of intact Symbiodiniaceae cells within lysosome-rich epithelial digestive cells. Metagenomic profiling further showed a complete absence of Endozoicomonas--bacteria typically linked to Symbiodiniaceae symbioses--in this species. These findings indicate that S. braziliana can harbor Symbiodiniaceae but exhibits only primitive morphological and microbial adaptations to the symbiotic state. Collectively, these results provide new insights into the evolutionary and structural diversity of nudibranch-algal symbioses.

zoology↗

bioRxiv2023

The highly developed symbiotic system between the solar-powered nudibranch Pteraeolidia semperi and Symbiodiniacean algae

The intricate coexistence of Symbiodiniacean algae with a diverse range of marine invertebrates underpins the flourishing biodiversity observed within coral reef ecosystems. However, the phenomenon of coral bleaching--precipitated by the dissolution of symbiotic relationships with Symbiodiniaceae--poses a significant threat to these ecosystems, thereby necessitating an urgent investigation into the underlying symbiotic mechanisms. The symbiosis between nudibranchs and Symbiodiniaceae has been identified as an efficacious model for examining these mechanisms, yet a comprehensive understanding of their histological structures and cellular processes remains elusive. In this study, we concentrate on the nudibranch host Pteraeolidia semperi, renowned for its exceptional symbiotic capabilities, and we elucidate its sophisticated symbiotic architecture. Furthermore, we delineate the bleaching process within the nudibranch, uncovering the associated cellular processes. Collectively, these findings furnish invaluable insights into the intricate relationship between nudibranchs and Symbiodiniaceae, thereby contributing to our understanding of the symbiosis that sustains these critical marine ecosystems.

cell biology↗

bioRxiv2023

The complete mitochondrial genome of Spurilla braziliana MacFarland 1909 (Nudibranchia, Aeolidiidae).

Spurilla braziliana MacFarland 1909 is a morphologically diverse nudibranch found in the Pacific and Western Atlantic. The complete mitochondrial genome of S. braziliana has been constructed using next-generation sequencing technology. The mitochondrial genome is 14,291 bp and contains 13 protein-coding genes, 2 rRNA genes, and 23 tRNA genes. Molecular phylogenetic analysis using the maximum likelihood method revealed that S. braziliana is included in the superfamily Aeolidioidea and forms a monophyletic group with Berghia stephanieae, a nudibranch of the family Aeolidiidae. This study reinforces existing taxonomic insights and provides a basis for further molecular phylogenetic analysis.

genomics↗

bioRxiv2020

Chromosome-level genome construction of a Japanese stickleback species using ultra-dense linkage analysis using single-cell sequencing of sperms

The presence of high quality genomes at the chromosome level is very useful in the search for the causal genes of mutants and in genetic breeding. The advent of next-generation sequencers has made it easier to decode genomes, but it is still difficult to construct the genomes of higher organisms. In order to construct the genome of a higher organism, the genome sequence of the organism is extended to the length of the chromosome by linkage analysis after assembly and scaffolding. However, in the past linkage analysis, it was difficult to make a high-density linkage map, and it was not possible to analyze organisms without an established breeding system. As an innovative alternative to conventional linkage analysis, we devised a method for genotyping sperm using 10x single-cell genome (CNV) sequencing libraries to generate a linkage map without interbreeding individuals. The genome was constructed using sperm from Gasterosteus nipponicus, and single-cell genotyping yielded 1,864,430 very dense hetero-SNPs. The average coverage per sperm cell is 0.13x. The number of sperm used is 1,738, which is an order of magnitude higher than the number of sperm used for conventional linkage analysis. We have improved the linkage analysis tool SELDLA (Scaffold Extender with Low Depth Linkage Analysis) so that we can analyze the data in accordance with the characteristics of single-cell genotyping data. Finally, we were able to determine the location and orientation on the chromosome for 85.6% of the contigs in the 456 Mbase genome of Gasterosteus nipponicus sequenced in nanopores. A total of 95.6% of the contigs in which a cross-reaction was detected within the contigs.

genomics↗