A5080259766- Coral and Marine Ecosystems Studies
- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Marine Ecology and Invasive Species
- Protist diversity and phylogeny
- Marine and coastal plant biology
- Developmental Biology and Gene Regulation
- Venomous Animal Envenomation and Studies
- Identification and Quantification in Food
- Environmental DNA in Biodiversity Studies
- Antimicrobial Peptides and Activities
- Genetic diversity and population structure
- Congenital heart defects research
- Marine Sponges and Natural Products
- Amphibian and Reptile Biology
- Marine Bivalve and Aquaculture Studies
- Algal biology and biofuel production
- Cellular transport and secretion
- Coastal wetland ecosystem dynamics
- Parasite Biology and Host Interactions
- Seaweed-derived Bioactive Compounds
- Calcium Carbonate Crystallization and Inhibition
- Biocrusts and Microbial Ecology
- Photosynthetic Processes and Mechanisms
- Polar Research and Ecology
Okinawa Institute of Science and Technology Graduate University
2015-2024
Tohoku University
2020
Kyushu University
2020
Kōchi University
1998
Coral reefs are among the most biologically diverse ecosystems on planet and of great economic importance. They under threat because scleractinian corals at their core susceptible to ocean acidification rising seawater temperatures. The genome reef-building coral Acropora digitifera has been analysed with a view understanding molecular basis symbiosis responses environmental change. seems have lost key enzyme cysteine biosynthesis, so may be dependent its symbionts for this amino acid. It...
The study of the pearl oyster Pinctada fucata is key to increasing our understanding molecular mechanisms involved in biosynthesis and biology bivalve molluscs. We sequenced ∼1150-Mb genome at ∼40-fold coverage using Roche 454 GS-FLX Illumina GAIIx sequencers. sequences were assembled into contigs with N50 = 1.6 kb (total contig assembly reached 1024 Mb) scaffolds 14.5 kb. AT-rich, a GC content 34%. DNA transposons, retrotransposons, tandem repeat elements occupied 0.4, 1.5, 7.9% genome,...
Acorn worms, also known as enteropneust (literally, 'gut-breathing') hemichordates, are marine invertebrates that share features with echinoderms and chordates. Together, these three phyla comprise the deuterostomes. Here we report draft genome sequences of two acorn Saccoglossus kowalevskii Ptychodera flava. By comparing them diverse bilaterian genomes, identify shared traits were probably inherited from last common deuterostome ancestor, then explore evolutionary trajectories leading this...
Genome sequencing and proteomic analyses of the crown-of-thorns starfish identify species-specific secreted factors that are associated with aggregating might be useful for biocontrol strategies. Crown-of-thorns (COTS) a predator reef-building corals throughout Indo-Pacific, where population outbreaks have led to loss coral cover biodiversity. Bernie Degnan colleagues now report genomes two COTS, Acanthaster planci, from Great Barrier Reef in Australia reefs Okinawa, Japan. They also...
Bivalve molluscs have flourished in marine environments, and many species constitute important aquatic resources. Recently, whole genome sequences from two bivalves, the pearl oyster, Pinctada fucata, Pacific Crassostrea gigas, been decoded, making it possible to compare genomic among molluscs, explore general lineage-specific genetic features trends bivalves. In order improve quality of sequence data for these purposes, we updated entire P. fucata assembly. We present a new assembly...
The marine dinoflagellate, Symbiodinium, is a well-known photosynthetic partner for coral and other diverse, non-photosynthetic hosts in subtropical tropical shallows, where it comprises an essential component of ecosystems. Using molecular phylogenetics, the genus Symbiodinium has been classified into nine major clades, A-I, one reported differences among phenotypes their capacity to synthesize mycosporine-like amino acids (MAAs), which absorb UV radiation. However, genetic basis this...
Abstract Nemerteans (ribbon worms) and phoronids (horseshoe are closely related lophotrochozoans—a group of animals including leeches, snails other invertebrates. Lophotrochozoans represent a superphylum that is crucial to our understanding bilaterian evolution. However, given the inconsistency molecular morphological data for these groups, their origins have been unclear. Here, we present draft genomes nemertean Notospermus geniculatus phoronid Phoronis australis , together with...
Abstract Since its initial publication in 2002, the genome of Ciona intestinalis type A (Ciona robusta), first sequence an invertebrate chordate, has provided a valuable resource for wide range biological studies, including developmental biology, evolutionary and neuroscience. The assembly was updated 2008, it included 68% information 14 pairs chromosomes. However, more contiguous is required analyses higher order genomic structure chromosomal evolution. Here, we provide new inbred line this...
The brown alga, Cladosiphon okamuranus (Okinawa mozuku), is economically one of the most important edible seaweeds, and cultivated for market primarily in Okinawa, Japan. C. constitutes a significant source fucoidan, which has various physiological biological activities. To facilitate studies seaweed biology, we decoded draft genome S-strain. size was estimated as ∼140 Mbp, smaller than genomes two other algae, Ectocarpus siliculosus Saccharina japonica. Sequencing with ∼100× coverage...
Genome sequencing of Symbiodinium minutum revealed that 95 109 plastid-associated genes have been transferred to the nuclear genome and subsequently expanded by gene duplication. Only 14 remain in plastids occur as DNA minicircles. Each minicircle (1.8-3.3 kb) contains one a conserved noncoding region containing putative promoters RNA-binding sites. Nine types RNA editing, including novel G/U type, were discovered transcripts but not nucleus. In contrast editing sites dinoflagellate...
Abstract Evolution of novel traits is a challenging subject in biological research. Several snake lineages developed elaborate venom systems to deliver complex protein mixtures for prey capture. To understand mechanisms involved evolution, we decoded here the ~1.4-Gb genome habu, Protobothrops flavoviridis . We identified 60 genes (SV) and 224 non-venom paralogs (NV), belonging 18 gene families. Molecular phylogeny reveals early divergence SV NV genes, suggesting that one four copies...
Photosynthetic dinoflagellates of the Family Symbiodiniaceae live symbiotically with many organisms that inhabit coral reefs and are currently classified into fifteen groups, including seven genera. Draft genomes from four genera, Symbiodinium, Breviolum, Fugacium, Cladocopium, which have been isolated corals, reported. However, no genome is available genus Durusdinium, occupies an intermediate phylogenetic position in well known for thermal tolerance (resistance to bleaching). We sequenced,...
The striped catfish, Pangasianodon hypophthalmus, is a freshwater and benthopelagic fish common in the Mekong River delta. Catfish constitute valuable source of dietary protein. Therefore, they are cultured worldwide, P. hypophthalmus food staple area. However, genetic information about culture stock, unavailable for breeding improvement, although genetics channel Ictalurus punctatus, has been reported. To acquire genome sequence data as useful resource marker-assisted breeding, we decoded...
Genome evolution and development of unicellular, multinucleate macroalgae (siphonous algae) are poorly known, although various multicellular organisms have been studied extensively. To understand macroalgal developmental evolution, we assembled the ∼26 Mb genome a siphonous green alga, Caulerpa lentillifera, with high contiguity, containing 9,311 protein-coding genes. Molecular phylogeny using 107 nuclear genes indicates that diversification class Ulvophyceae, including C. occurred before...
Coral reefs have the highest biodiversity of all marine ecosystems in tropical and subtropical oceans. However, scleractinian corals, keystone organisms reef productivity, are facing a crisis due to climate change anthropogenic activities. A broad survey reef-building corals is essential for worldwide preservation. To this end, direct observations made by coral-specialist divers might be supported another robust method. We improved recently devised environmental DNA (eDNA) metabarcoding...
The kuruma shrimp Marsupenaeus japonicus (order Decapoda, family Penaeidae) is an economically important crustacean that occurs in shallow, warm seas across the Indo-Pacific. Here, using a combination of Illumina and Oxford Nanopore Technologies platforms, we produced draft genome assembly M. (1.70 Gbp; 18,210 scaffolds; scaffold N50 = 234.9 kbp; 34.38% GC, 93.4% BUSCO completeness) complete mitochondrial sequence (15,969 bp). As with other penaeid genomes, extremely rich simple repeats,...
Labyrinthulomycetes have been regarded as a promising industrial source of xanthophylls, including astaxanthin and canthaxanthin, polyunsaturated fatty acids such docosahexaenoic acid docosapentaenoic acid, ω-3 oils, terpenic hydrocarbons, sterols squalene. A Thraustochytrid, Aurantiochytrium sp. KH105 produces carotenoids, astaxanthin, with strong antioxidant activity. To gain genomic insights into this capacity, we decoded its 97-Mbp genome characterized genes for enzymes involved in...
Dinoflagellates are unicellular marine and freshwater eukaryotes. They possess large nuclear genomes (1.5-245 gigabases) produce structurally unique biologically active polyketide secondary metabolites. Although biosynthesis is well studied in terrestrial organisms, only recently have dinoflagellate polyketides been investigated. Transcriptomic analyses characterized synthase genes having single domains. The Genus Symbiodinium, with a comparatively small genome, group of major coral...
Abstract Symbiodiniaceae dinoflagellates possess smaller nuclear genomes than other and produce structurally specialized, biologically active, secondary metabolites. Till date, little is known about the evolution of metabolism in as comparative genomic approaches have been hampered by their large genome sizes. Here, we overcome this challenge combining metabolomics to investigate how chemical diversity arises three decoded (clades A3, B1 C). Our analyses identify extensive diversification...
Snake venoms are complex mixtures of toxic proteins encoded by various gene families that function synergistically to incapacitate prey. A huge repertoire snake venom genes and have been reported, alternative splicing is suggested be involved in the production divergent transcripts. However, a genome-wide survey transcript extent still remains determined. In this study, comprehensive analysis transcriptomes gland was achieved using PacBio sequencing. Extensive observed three protein...