Network


Latest external collaboration on country level. Dive into details by clicking on the dots.

Hotspot


Dive into the research topics where Chuya Shinzato is active.

Publication


Featured researches published by Chuya Shinzato.


Nature | 2011

Using the Acropora digitifera genome to understand coral responses to environmental change

Chuya Shinzato; Eiichi Shoguchi; Takeshi Kawashima; Mayuko Hamada; Kanako Hisata; Makiko Tanaka; Manabu Fujie; Mayuki Fujiwara; Ryo Koyanagi; Tetsuro Ikuta; Asao Fujiyama; David J. Miller; Nori Satoh

Despite the enormous ecological and economic importance of coral reefs, the keystone organisms in their establishment, the scleractinian corals, increasingly face a range of anthropogenic challenges including ocean acidification and seawater temperature rise. To understand better the molecular mechanisms underlying coral biology, here we decoded the approximately 420-megabase genome of Acropora digitifera using next-generation sequencing technology. This genome contains approximately 23,700 gene models. Molecular phylogenetics indicate that the coral and the sea anemone Nematostella vectensis diverged approximately 500 million years ago, considerably earlier than the time over which modern corals are represented in the fossil record (∼240 million years ago). Despite the long evolutionary history of the endosymbiosis, no evidence was found for horizontal transfer of genes from symbiont to host. However, unlike several other corals, Acropora seems to lack an enzyme essential for cysteine biosynthesis, implying dependency of this coral on its symbionts for this amino acid. Corals inhabit environments where they are frequently exposed to high levels of solar radiation, and analysis of the Acropora genome data indicates that the coral host can independently carry out de novo synthesis of mycosporine-like amino acids, which are potent ultraviolet-protective compounds. In addition, the coral innate immunity repertoire is notably more complex than that of the sea anemone, indicating that some of these genes may have roles in symbiosis or coloniality. A number of genes with putative roles in calcification were identified, and several of these are restricted to corals. The coral genome provides a platform for understanding the molecular basis of symbiosis and responses to environmental changes.


DNA Research | 2012

Draft Genome of the Pearl Oyster Pinctada fucata: A Platform for Understanding Bivalve Biology

Takeshi Takeuchi; Takeshi Kawashima; Ryo Koyanagi; Fuki Gyoja; Makiko Tanaka; Tetsuro Ikuta; Eiichi Shoguchi; Mayuki Fujiwara; Chuya Shinzato; Kanako Hisata; Manabu Fujie; Takeshi Usami; Kiyohito Nagai; Kaoru Maeyama; Kikuhiko Okamoto; Hideo Aoki; Takashi Ishikawa; Tetsuji Masaoka; Atushi Fujiwara; Kazuyoshi Endo; Hirotoshi Endo; Hiromichi Nagasawa; Shigeharu Kinoshita; Shuichi Asakawa; Shugo Watabe; Nori Satoh

The study of the pearl oyster Pinctada fucata is key to increasing our understanding of the molecular mechanisms involved in pearl biosynthesis and biology of bivalve molluscs. We sequenced ∼1150-Mb genome at ∼40-fold coverage using the Roche 454 GS-FLX and Illumina GAIIx sequencers. The sequences were assembled into contigs with N50 = 1.6 kb (total contig assembly reached to 1024 Mb) and scaffolds with N50 = 14.5 kb. The pearl oyster genome is AT-rich, with a GC content of 34%. DNA transposons, retrotransposons, and tandem repeat elements occupied 0.4, 1.5, and 7.9% of the genome, respectively (a total of 9.8%). Version 1.0 of the P. fucata draft genome contains 23 257 complete gene models, 70% of which are supported by the corresponding expressed sequence tags. The genes include those reported to have an association with bio-mineralization. Genes encoding transcription factors and signal transduction molecules are present in numbers comparable with genomes of other metazoans. Genome-wide molecular phylogeny suggests that the lophotrochozoan represents a distinct clade from ecdysozoans. Our draft genome of the pearl oyster thus provides a platform for the identification of selection markers and genes for calcification, knowledge of which will be important in the pearl industry.


eLife | 2016

Comparative genomics explains the evolutionary success of reef-forming corals

Debashish Bhattacharya; Shobhit Agrawal; Manuel Aranda; Sebastian Baumgarten; Mahdi Belcaid; Jeana L. Drake; Douglas H. Erwin; Sylvain Forêt; Ruth D. Gates; David F. Gruber; Bishoy Kamel; Michael P. Lesser; Oren Levy; Yi Jin Liew; Matthew D. MacManes; Tali Mass; Mónica Medina; Shaadi Mehr; Eli Meyer; Dana C. Price; Hollie M. Putnam; Huan Qiu; Chuya Shinzato; Eiichi Shoguchi; Alexander J. Stokes; Sylvie Tambutté; Dan Tchernov; Christian R. Voolstra; Nicole E. Wagner; Charles W. Walker

Transcriptome and genome data from twenty stony coral species and a selection of reference bilaterians were studied to elucidate coral evolutionary history. We identified genes that encode the proteins responsible for the precipitation and aggregation of the aragonite skeleton on which the organisms live, and revealed a network of environmental sensors that coordinate responses of the host animals to temperature, light, and pH. Furthermore, we describe a variety of stress-related pathways, including apoptotic pathways that allow the host animals to detoxify reactive oxygen and nitrogen species that are generated by their intracellular photosynthetic symbionts, and determine the fate of corals under environmental stress. Some of these genes arose through horizontal gene transfer and comprise at least 0.2% of the animal gene inventory. Our analysis elucidates the evolutionary strategies that have allowed symbiotic corals to adapt and thrive for hundreds of millions of years. DOI: http://dx.doi.org/10.7554/eLife.13288.001


Molecular Biology and Evolution | 2013

The Complex NOD-Like Receptor Repertoire of the Coral Acropora digitifera Includes Novel Domain Combinations

Mayuko Hamada; Eiichi Shoguchi; Chuya Shinzato; Takeshi Kawashima; David J. Miller; Nori Satoh

Innate immunity in corals is of special interest not only in the context of self-defense but also in relation to the establishment and collapse of their obligate symbiosis with dinoflagellates of the genus Symbiodinium. In innate immunity system of vertebrates, approximately 20 tripartite nucleotide oligomerization domain (NOD)-like receptor proteins that are defined by the presence of a NAIP, CIIA, HET-E and TP1 (NACHT) domain, a C-terminal leucine-rich repeat (LRR) domain, and one of three types of N-terminal effector domain, are known to function as the primary intracellular pattern recognition molecules. Surveying the coral genome revealed not only a larger number of NACHT- and related domain nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4 (NB-ARC)-encoding loci (~500) than in other metazoans but also surprising diversity of domain combinations among the coral NACHT/NB-ARC-containing proteins; N-terminal effector domains included the apoptosis-related domains caspase recruitment domain (CARD), death effector domain (DED), and Death, and C-terminal repeat domains included LRRs, tetratricopeptide repeats, ankyrin repeats, and WD40 repeats. Many of the predicted coral proteins that contain a NACHT/NB-ARC domain also contain a glycosyl transferase group 1 domain, a novel domain combination first found in metazoans. Phylogenetic analyses suggest that the NACHT/NB-ARC domain inventories of various metazoan lineages, including corals, are largely products of lineage-specific expansions. Many of the NACHT/NB-ARC loci are organized in pairs or triplets in the Acropora genome, suggesting that the large coral NACHT/NB-ARC repertoire has been generated at least in part by tandem duplication. In addition, shuffling of N-terminal effector domains may have occurred after expansions of specific NACHT/NB-ARC-repeat domain types. These results illustrate the extraordinary complexity of the innate immune repertoire of corals, which may in part reflect adaptive evolution to a symbiotic lifestyle in a uniquely complex and challenging environment.


Genome Biology and Evolution | 2014

Massive Gene Transfer and Extensive RNA Editing of a Symbiotic Dinoflagellate Plastid Genome

Sutada Mungpakdee; Chuya Shinzato; Takeshi Takeuchi; Takeshi Kawashima; Ryo Koyanagi; Kanako Hisata; Makiko Tanaka; Hiroki Goto; Manabu Fujie; Senjie Lin; Nori Satoh; Eiichi Shoguchi

Genome sequencing of Symbiodinium minutum revealed that 95 of 109 plastid-associated genes have been transferred to the nuclear genome and subsequently expanded by gene duplication. Only 14 genes remain in plastids and occur as DNA minicircles. Each minicircle (1.8–3.3 kb) contains one gene and a conserved noncoding region containing putative promoters and RNA-binding sites. Nine types of RNA editing, including a novel G/U type, were discovered in minicircle transcripts but not in genes transferred to the nucleus. In contrast to DNA editing sites in dinoflagellate mitochondria, which tend to be highly conserved across all taxa, editing sites employed in DNA minicircles are highly variable from species to species. Editing is crucial for core photosystem protein function. It restores evolutionarily conserved amino acids and increases peptidyl hydropathy. It also increases protein plasticity necessary to initiate photosystem complex assembly.


BMC Evolutionary Biology | 2008

Sox genes in the coral Acropora millepora: divergent expression patterns reflect differences in developmental mechanisms within the Anthozoa

Chuya Shinzato; Akira Iguchi; David C. Hayward; Ulrich Technau; Eldon E. Ball; David J. Miller

BackgroundSox genes encode transcription factors that function in a wide range of developmental processes across the animal kingdom. To better understand both the evolution of the Sox family and the roles of these genes in cnidarians, we are studying the Sox gene complement of the coral, Acropora millepora (Class Anthozoa).ResultsBased on overall domain structures and HMG box sequences, the Acropora Sox genes considered here clearly fall into four of the five major Sox classes. AmSoxC is expressed in the ectoderm during development, in cells whose morphology is consistent with their assignment as sensory neurons. The expression pattern of the Nematostella ortholog of this gene is broadly similar to that of AmSoxC, but there are subtle differences – for example, expression begins significantly earlier in Acropora than in Nematostella. During gastrulation, AmSoxBb and AmSoxB1 transcripts are detected only in the presumptive ectoderm while AmSoxE1 transcription is restricted to the presumptive endoderm, suggesting that these Sox genes might play roles in germ layer specification. A third type B Sox gene, AmSoxBa, and a Sox F gene AmSoxF also have complex and specific expression patterns during early development. Each of these genes has a clear Nematostella ortholog, but in several cases the expression pattern observed in Acropora differs significantly from that reported in Nematostella.ConclusionThese differences in expression patterns between Acropora and Nematostella largely reflect fundamental differences in developmental processes, underscoring the diversity of mechanisms within the anthozoan Sub-Class Hexacorallia (Zoantharia).


PLOS ONE | 2014

A snapshot of a coral "holobiont": a transcriptome assembly of the scleractinian coral, porites, captures a wide variety of genes from both the host and symbiotic zooxanthellae.

Chuya Shinzato; Mayuri Inoue; Makoto Kusakabe

Massive scleractinian corals of the genus Porites are important reef builders in the Indo-Pacific, and they are more resistant to thermal stress than other stony corals, such as the genus Acropora. Because coral health and survival largely depend on the interaction between a coral host and its symbionts, it is important to understand the molecular interactions of an entire “coral holobiont”. We simultaneously sequenced transcriptomes of Porites australiensis and its symbionts using the Illumina Hiseq2000 platform. We obtained 14.3 Gbp of sequencing data and assembled it into 74,997 contigs (average: 1,263 bp, N50 size: 2,037 bp). We successfully distinguished contigs originating from the host (Porites) and the symbiont (Symbiodinium) by aligning nucleotide sequences with the decoded Acropora digitifera and Symbiodinium minutum genomes. In contrast to previous coral transcriptome studies, at least 35% of the sequences were found to have originated from the symbionts, indicating that it is possible to analyze both host and symbiont transcriptomes simultaneously. Conserved protein domain and KEGG analyses showed that the dataset contains broad gene repertoires of both Porites and Symbiodinium. Effective utilization of sequence reads revealed that the polymorphism rate in P. australiensis is 1.0% and identified the major symbiotic Symbiodinium as Type C15. Analyses of amino acid biosynthetic pathways suggested that this Porites holobiont is probably able to synthesize most of the common amino acids and that Symbiodinium is potentially able to provide essential amino acids to its host. We believe this to be the first molecular evidence of complementarity in amino acid metabolism between coral hosts and their symbionts. We successfully assembled genes originating from both the host coral and the symbiotic Symbiodinium to create a snapshot of the coral holobiont transcriptome. This dataset will facilitate a deeper understanding of molecular mechanisms of coral symbioses and stress responses.


BMC Evolutionary Biology | 2008

Unexpected diversity of cnidarian integrins: expression during coral gastrulation

Brent Knack; Akira Iguchi; Chuya Shinzato; David C. Hayward; Eldon E. Ball; David J. Miller

BackgroundAdhesion mediated through the integrin family of cell surface receptors is central to early development throughout the Metazoa, playing key roles in cell-extra cellular matrix adhesion and modulation of cadherin activity during the convergence and extension movements of gastrulation. It has been suggested that Caenorhabditis elegans, which has a single β and two α integrins, might reflect the ancestral integrin complement. Investigation of the integrin repertoire of anthozoan cnidarians such as the coral Acropora millepora is required to test this hypothesis and may provide insights into the original roles of these molecules.ResultsTwo novel integrins were identified in Acropora. AmItgα1 shows features characteristic of α integrins lacking an I-domain, but phylogenetic analysis gives no clear indication of its likely binding specificity. AmItgβ2 lacks consensus cysteine residues at positions 8 and 9, but is otherwise a typical β integrin. In situ hybridization revealed that AmItgα1, AmItgβ1, and AmItgβ2 are expressed in the presumptive endoderm during gastrulation. A second anthozoan, the sea anemone Nematostella vectensis, has at least four β integrins, two resembling AmItgβ1 and two like AmItgβ2, and at least three α integrins, based on its genomic sequence.ConclusionIn two respects, the cnidarian data do not fit expectations. First, the cnidarian integrin repertoire is more complex than predicted: at least two βs in Acropora, and at least three αs and four βs in Nematostella. Second, whereas the bilaterian αs resolve into well-supported groups corresponding to those specific for RGD-containing or laminin-type ligands, the known cnidarian αs are distinct from these. During early development in Acropora, the expression patterns of the three known integrins parallel those of amphibian and echinoderm integrins.


Molecular Ecology | 2016

The transcriptomic response of the coral Acropora digitifera to a competent Symbiodinium strain: the symbiosome as an arrested early phagosome

A. R. Mohamed; Vivian R. Cumbo; Saki Harii; Chuya Shinzato; Cheong Xin Chan; Mark A. Ragan; David G. Bourne; Bette L. Willis; Eldon E. Ball; Nori Satoh; David J. Miller

Despite the ecological significance of the relationship between reef‐building corals and intracellular photosynthetic dinoflagellates of the genus Symbiodinium, very little is known about the molecular mechanisms involved in its establishment. Indeed, microarray‐based analyses point to the conclusion that host gene expression is largely or completely unresponsive during the establishment of symbiosis with a competent strain of Symbiodinium. In this study, the use of Illumina RNA‐Seq technology allowed detection of a transient period of differential expression involving a small number of genes (1073 transcripts; <3% of the transcriptome) 4 h after the exposure of Acropora digitifera planulae to a competent strain of Symbiodinium (a clade B strain). This phenomenon has not previously been detected as a consequence of both the lower sensitivity of the microarray approaches used and the sampling times used. The results indicate that complex changes occur, including transient suppression of mitochondrial metabolism and protein synthesis, but are also consistent with the hypothesis that the symbiosome is a phagosome that has undergone early arrest, raising the possibility of common mechanisms in the symbiotic interactions of corals and symbiotic sea anemones with their endosymbionts.


Nature | 2017

The crown-of-thorns starfish genome as a guide for biocontrol of this coral reef pest

Michael R. Hall; Kevin M. Kocot; Kenneth W. Baughman; Selene L. Fernandez-Valverde; Marie Gauthier; William L. Hatleberg; Arunkumar Krishnan; Carmel McDougall; Cherie A. Motti; Eiichi Shoguchi; Tianfang Wang; Xueyan Xiang; Min Zhao; Utpal Bose; Chuya Shinzato; Kanako Hisata; Manabu Fujie; Miyuki Kanda; Scott F. Cummins; Noriyuki Satoh; Sandie M. Degnan; Bernard M. Degnan

The crown-of-thorns starfish (COTS, the Acanthaster planci species group) is a highly fecund predator of reef-building corals throughout the Indo-Pacific region. COTS population outbreaks cause substantial loss of coral cover, diminishing the integrity and resilience of reef ecosystems. Here we sequenced genomes of COTS from the Great Barrier Reef, Australia and Okinawa, Japan to identify gene products that underlie species-specific communication and could potentially be used in biocontrol strategies. We focused on water-borne chemical plumes released from aggregating COTS, which make the normally sedentary starfish become highly active. Peptide sequences detected in these plumes by mass spectrometry are encoded in the COTS genome and expressed in external tissues. The exoproteome released by aggregating COTS consists largely of signalling factors and hydrolytic enzymes, and includes an expanded and rapidly evolving set of starfish-specific ependymin-related proteins. These secreted proteins may be detected by members of a large family of olfactory-receptor-like G-protein-coupled receptors that are expressed externally, sometimes in a sex-specific manner. This study provides insights into COTS-specific communication that may guide the generation of peptide mimetics for use on reefs with COTS outbreaks.

Collaboration


Dive into the Chuya Shinzato's collaboration.

Top Co-Authors

Avatar

Nori Satoh

Okinawa Institute of Science and Technology

View shared research outputs
Top Co-Authors

Avatar

Eiichi Shoguchi

Okinawa Institute of Science and Technology

View shared research outputs
Top Co-Authors

Avatar

Noriyuki Satoh

Okinawa Institute of Science and Technology

View shared research outputs
Top Co-Authors

Avatar
Top Co-Authors

Avatar

Kanako Hisata

Okinawa Institute of Science and Technology

View shared research outputs
Top Co-Authors

Avatar

Manabu Fujie

Okinawa Institute of Science and Technology

View shared research outputs
Top Co-Authors

Avatar

Takeshi Kawashima

Okinawa Institute of Science and Technology

View shared research outputs
Top Co-Authors

Avatar

Makiko Tanaka

Okinawa Institute of Science and Technology

View shared research outputs
Top Co-Authors

Avatar

Ryo Koyanagi

Okinawa Institute of Science and Technology

View shared research outputs
Top Co-Authors

Avatar

Takeshi Takeuchi

Okinawa Institute of Science and Technology

View shared research outputs
Researchain Logo
Decentralizing Knowledge