Biology subjects

Kawamitsu, M.

Publications and source records attributed to Kawamitsu, M..

5 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↗

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↗

bioRxiv2025

De novo genome assembly of an interspecific hybrid grapevine 'Maeve'

The grapevine is one of the most ancient and economically important horticultural crops in the world. The grapevine species Vitis vinifera is cultivated globally; however, due to its susceptibility to pathogens and environmental stresses, wild Vitis species and their hybrids are often used as rootstocks in vineyards. Here, we report the genome analysis of a Vitis strain named Maeve, which was identified in a vineyard in Japan, though its genetic origin remains unclear. We performed haplotype-resolved de novo assembly of the Maeve genome using PacBio HiFi sequencing and Hi-C assembly. Our genome analysis revealed that Maeve has originated from an interspecific hybridization between an unknown V. vinifera cultivar and the V. riparia Gloire cultivar, likely arising through breeding or natural pollination. This novel cultivar has a potential to expand wine grape production across a wider range of environmental conditions where conventional cultivars are unsuitable for viticulture.

plant biology↗

bioRxiv2023

A genome and tissue-specific transcriptomes of the large-polyp coral, Fimbriaphyllia (Euphyllia) ancora: Recipe for a coral polyp

Coral "polyps" are composed of several tissues; however, their characteristics are largely unexplored. Here we report biological characteristics of the four tissues that comprise polyps: tentacle (Te), mesenterial filament (Me), body wall (Bo), and mouth with pharynx (MP), using comparative genomic, morpho-histological, and transcriptomic analyses of the large-polyp coral, Fimbriaphyllia ancora. A draft F. ancora genome assembly of 434 Mbp was created. Morpho-histological and transcriptomic characterization of the four tissues showed that they have distinct differences in structure, primary cellular composition, and transcriptional profiles. Tissue-specific, highly expressed genes (HEGs) of Te are related to biological defense, predation, and coral-algal symbiosis. Me expresses multiple digestive enzymes, whereas Bo expresses innate immunity and biomineralization-related molecules. Many receptors for neuropeptides and neurotransmitters are expressed in MP. The established dataset and new insights into tissue functions will facilitate a deeper understanding of coral biology.

genomics↗

bioRxiv2020

Color morphs of the coral, Acropora tenuis, show different responses to environmental stress and different expression profiles of fluorescent-protein genes

Corals of the family Acroporidae are key structural components of reefs that support the most diverse marine ecosystems. Due to increasing anthropogenic stresses, coral reefs are in decline. Along the coast of Okinawa, Japan, three different color morphs of Acropora tenuis have been recognized for decades. These include brown (N morph), yellow-green (G) and purple (P) forms. The tips of axial coral polyps exhibit specific fluorescence spectra. This attribute is inherited asexually, and color morphs do not change seasonally. In Okinawa Prefecture, during the summer of 2017, the N and P morphs experienced bleaching, in which some N morphs died while P morphs recovered. In contrast, G morphs successfully withstood the stress. Symbiotic dinoflagellates are essential symbiotic partners of scleractinian corals. Photosynthetic activity of symbionts was reduced in July in N and P morphs; however, the three color-morphs host similar sets of Clade-C zoothanthellae, suggesting that beaching of N and P morphs cannot be attributed to differences in symbiont clades. The decoded Acropora tenuis genome includes five genes for green fluorescent proteins (GFP), two for cyan fluorescent proteins (CFP), three for red fluorescent proteins (RFP), and seven genes for chromoprotein (ChrP). A summer survey of gene expression profiles demonstrated that (a) expression of CFP and REP was quite low in all three morphs, (b) P morphs expressed higher levels of ChrP, (c) both N and G morphs expressed GFP highly, and (d) GFP expression was reduced in N morphs, compared to G morphs, which maintained higher levels of GFP expression throughout the summer. Although further studies are required to understand the biological significance of these color morphs of Acropora tenuis, our results suggest that thermal stress resistance is modified by genetic mechanisms that coincidentally lead to diversification of color morphs.

evolutionary biology↗