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Shoguchi E, Kawachi M, Shinzato C, Beedessee G. Functional analyses of bacterial genomes found in Symbiodiniaceae genome assemblies. Environ Microbiol Rep 2024; 16:e13238. [PMID: 38444256 PMCID: PMC10915500 DOI: 10.1111/1758-2229.13238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 01/25/2024] [Indexed: 03/07/2024]
Abstract
Bacterial-algal interactions strongly influence marine ecosystems. Bacterial communities in cultured dinoflagellates of the family Symbiodiniaceae have been characterized by metagenomics. However, little is known about whole-genome analysis of marine bacteria associated with these dinoflagellates. We performed in silico analysis of four bacterial genomes from cultures of four dinoflagellates of the genera Symbiodinium, Breviolum, Cladocopium and Durusdinium. Comparative analysis showed that the former three contain the alphaproteobacterial family Parvibaculaceae and that the Durusdinium culture includes the family Sphingomonadaceae. There were no large genomic reductions in the alphaproteobacteria with genome sizes of 2.9-3.9 Mb, implying they are not obligate intracellular bacteria. Genomic annotations of three Parvibaculaceae detected the gene for diacetylchitobiose deacetylase (Dac), which may be involved in the degradation of dinoflagellate cell surfaces. They also had metabolic genes for dissimilatory nitrate reduction to ammonium (DNRA) in the nitrogen (N) cycle and cobalamin (vitamin B12 ) biosynthetic genes in the salvage pathway. Those three characters were not found in the Sphingomonadaceae genome. Predicted biosynthetic gene clusters for secondary metabolites indicated that the Parvibaculaceae likely produce the same secondary metabolites. Our study suggests that the Parvibaculaceae is a major resident of Symbiodiniaceae cultures with antibiotics.
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Affiliation(s)
- Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate UniversityOnnaJapan
| | - Masanobu Kawachi
- Center for Environmental Biology and Ecosystem StudiesNational Institute for Environmental StudiesTsukubaJapan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of TokyoKashiwaJapan
| | - Girish Beedessee
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate UniversityOnnaJapan
- Department of BiochemistryUniversity of CambridgeCambridgeUK
- Present address:
Faculty of Health & Life SciencesNorthumbria UniversityNewcastle upon TyneUK
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Shinzato C, Yoshioka Y. Genomic Data Reveal Diverse Biological Characteristics of Scleractinian Corals and Promote Effective Coral Reef Conservation. Genome Biol Evol 2024; 16:evae014. [PMID: 38271267 PMCID: PMC10901607 DOI: 10.1093/gbe/evae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/11/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
Reef-building corals (Scleractinia, Anthozoa, Cnidaria) are the keystone organisms of coral reefs, which constitute the most diverse marine ecosystems. Since the first decoded coral genome reported in 2011, about 40 reference genomes are registered as of 2023. Comparative genomic analyses of coral genomes have revealed genomic characters that may underlie unique biological characteristics and coral diversification. These include existence of genes for biosynthesis of mycosporine-like amino acids, loss of an enzyme necessary for cysteine biosynthesis in family Acroporidae, and lineage-specific gene expansions of DMSP lyase-like genes in the genus Acropora. While symbiosis with endosymbiotic photosynthetic dinoflagellates is a common biological feature among reef-building corals, genes associated with the intricate symbiotic relationship encompass not only those shared by many coral species, but also genes that were uniquely duplicated in each coral lineage, suggesting diversified molecular mechanisms of coral-algal symbiosis. Coral genomic data have also enabled detection of hidden, complex population structures of corals, indicating the need for species-specific, local-scale, carefully considered conservation policies for effective maintenance of corals. Consequently, accumulating coral genomic data from a wide range of taxa and from individuals of a species not only promotes deeper understanding of coral reef biodiversity, but also promotes appropriate and effective coral reef conservation. Considering the diverse biological traits of different coral species and accurately understanding population structure and genetic diversity revealed by coral genomic analyses during coral reef restoration planning could enable us to "archive" coral reef environments that are nearly identical to natural coral reefs.
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Affiliation(s)
- Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-8564, Japan
| | - Yuki Yoshioka
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0412, Japan
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Yoshioka Y, Chiu YL, Uchida T, Yamashita H, Suzuki G, Shinzato C. Genes possibly related to symbiosis in early life stages of Acropora tenuis inoculated with Symbiodinium microadriaticum. Commun Biol 2023; 6:1027. [PMID: 37853100 PMCID: PMC10584924 DOI: 10.1038/s42003-023-05350-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/12/2023] [Indexed: 10/20/2023] Open
Abstract
Due to the ecological importance of mutualism between reef-building corals and symbiotic algae (Family Symbiodiniaceae), various transcriptomic studies on coral-algal symbiosis have been performed; however, molecular mechanisms, especially genes essential to initiate and maintain these symbioses remain unknown. We investigated transcriptomic responses of Acropora tenuis to inoculation with the native algal symbiont, Symbiodinium microadriaticum, during early life stages, and identified possible symbiosis-related genes. Genes involved in immune regulation, protection against oxidative stress, and metabolic interactions between partners are particularly important for symbiosis during Acropora early life stages. In addition, molecular phylogenetic analysis revealed that some possible symbiosis-related genes originated by gene duplication in the Acropora lineage, suggesting that gene duplication may have been the driving force to establish stable mutualism in Acropora, and that symbiotic molecular mechanisms may vary among coral lineages.
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Affiliation(s)
- Yuki Yoshioka
- Atmosphere and Ocean Research Institute (AORI), The University of Tokyo, Kashiwa, Chiba, Japan.
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan.
| | - Yi-Ling Chiu
- Atmosphere and Ocean Research Institute (AORI), The University of Tokyo, Kashiwa, Chiba, Japan
| | - Taiga Uchida
- Atmosphere and Ocean Research Institute (AORI), The University of Tokyo, Kashiwa, Chiba, Japan
| | - Hiroshi Yamashita
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Ishigaki, Okinawa, Japan
| | - Go Suzuki
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Ishigaki, Okinawa, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute (AORI), The University of Tokyo, Kashiwa, Chiba, Japan.
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4
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Uchida T, Yoshioka Y, Yoshida Y, Fujie M, Yamaki A, Sasaki A, Inoue K, Shinzato C. Genomic and transcriptomic analyses illuminate the molecular basis of the unique lifestyle of a tubeworm, Lamellibrachia satsuma. DNA Res 2023; 30:dsad014. [PMID: 37358253 DOI: 10.1093/dnares/dsad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 05/17/2023] [Accepted: 06/20/2023] [Indexed: 06/27/2023] Open
Abstract
Vestimentiferan tubeworms are representative members of deep-sea chemosynthetic ecosystems. In this study, we developed a draft genome and gene models and performed genomic and transcriptomic analyses of Lamellibrachia satsuma, the only vestimentiferan reported from the euphotic zone. The quality of the genome assembly and gene models is comparable to or higher than those of previously reported vestimentiferan tubeworms. Tissue-specific transcriptome sequencing revealed that Toll-like receptor genes and lineage-specific expanded bacteriolytic enzyme genes are highly expressed in the obturacular and vestimental regions, respectively, suggesting the importance of these tissues in defense against pathogens. On the other hand, globin subunit genes are expressed almost exclusively in the trunk region, supporting the hypothesis that the trophosome is the site of haemoglobin biosynthesis. Vestimentiferan-specific expanded gene families included chitinases, ion channels, and C-type lectins, suggesting the importance of these functions for vestimentiferans. C-type lectins in the trunk region, in particular, may be involved in recognition of pathogens, or in interactions between tubeworms and symbiotic bacteria. Our genomic and transcriptomic analyses enhance understanding of molecular mechanisms underlying the unique lifestyle of vestimentiferan tubeworms, particularly their obligate mutualism with chemosynthetic bacteria.
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Affiliation(s)
- Taiga Uchida
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Yuki Yoshioka
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Yu Yoshida
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Manabu Fujie
- DNA Sequencing Section (SQC), Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Ayuta Yamaki
- Kagoshima City Aquarium, Kagoshima, Japan
- Enoshima Aquarium, Fujisawa, Kanagawa, Japan
| | | | - Koji Inoue
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
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Nishitsuji K, Nagata T, Narisoko H, Kanai M, Hisata K, Shinzato C, Satoh N. An environmental DNA metabarcoding survey reveals generic-level occurrence of scleractinian corals at reef slopes of Okinawa Island. Proc Biol Sci 2023; 290:20230026. [PMID: 36987647 PMCID: PMC10050943 DOI: 10.1098/rspb.2023.0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
Abstract
Coral reefs have the highest biodiversity of all marine ecosystems in tropical and subtropical oceans. However, scleractinian corals, keystone organisms of reef productivity, are facing a crisis due to climate change and anthropogenic activities. A broad survey of reef-building corals is essential for worldwide reef preservation. To this end, direct observations made by coral-specialist divers might be supported by another robust method. We improved a recently devised environmental DNA (eDNA) metabarcoding method to identify more than 43 scleractinian genera by sampling 2 l of surface seawater above reefs. Together with direct observations by divers, we assessed the utility of eDNA at 63 locations spanning approximately 250 km near Okinawa Island. Slopes of these islands are populated by diverse coral genera, whereas shallow 'moats' sustain fewer and less varied coral taxa. Major genera recorded by divers included Acropora, Pocillopora, Porites and Montipora, the presence of which was confirmed by eDNA analyses. In addition, eDNA identified more genera than direct observations and documented the presence of previously unrecorded species. This scleractinian coral-specific eDNA method promises to be a powerful tool to survey coral reefs broadly, deeply and robustly.
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Affiliation(s)
- Koki Nishitsuji
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Tomofumi Nagata
- Incorporated Foundation Okinawa Environment Science Center, Urasoe, Okinawa 901-2111, Japan
| | - Haruhi Narisoko
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Megumi Kanai
- Incorporated Foundation Okinawa Environment Science Center, Urasoe, Okinawa 901-2111, Japan
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-8564, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
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Kitchen SA, Jiang D, Harii S, Satoh N, Weis VM, Shinzato C. Coral larvae suppress heat stress response during the onset of symbiosis decreasing their odds of survival. Mol Ecol 2022; 31:5813-5830. [PMID: 36168983 DOI: 10.1111/mec.16708] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 09/06/2022] [Accepted: 09/15/2022] [Indexed: 01/13/2023]
Abstract
The endosymbiosis between most corals and their photosynthetic dinoflagellate partners begins early in the host life history, when corals are larvae or juvenile polyps. The capacity of coral larvae to buffer climate-induced stress while in the process of symbiont acquisition could come with physiological trade-offs that alter behaviour, development, settlement and survivorship. Here we examined the joint effects of thermal stress and symbiosis onset on colonization dynamics, survival, metamorphosis and host gene expression of Acropora digitifera larvae. We found that thermal stress decreased symbiont colonization of hosts by 50% and symbiont density by 98.5% over 2 weeks. Temperature and colonization also influenced larval survival and metamorphosis in an additive manner, where colonized larvae fared worse or prematurely metamorphosed more often than noncolonized larvae under thermal stress. Transcriptomic responses to colonization and thermal stress treatments were largely independent, while the interaction of these treatments revealed contrasting expression profiles of genes that function in the stress response, immunity, inflammation and cell cycle regulation. The combined treatment either cancelled or lowered the magnitude of expression of heat-stress responsive genes in the presence of symbionts, revealing a physiological cost to acquiring symbionts at the larval stage with elevated temperatures. In addition, host immune suppression, a hallmark of symbiosis onset under ambient temperature, turned to immune activation under heat stress. Thus, by integrating the physical environment and biotic pressures that mediate presettlement event in corals, our results suggest that colonization may hinder larval survival and recruitment under projected climate scenarios.
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Affiliation(s)
- Sheila A Kitchen
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, USA
| | - Duo Jiang
- Statistics Department, Oregon State University, Corvallis, Oregon, USA
| | - Saki Harii
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Virginia M Weis
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, USA
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
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Zhang J, Richards ZT, Adam AAS, Chan CX, Shinzato C, Gilmour J, Thomas L, Strugnell JM, Miller DJ, Cooke I. Evolutionary responses of a reef-building coral to climate change at the end of the last glacial maximum. Mol Biol Evol 2022; 39:msac201. [PMID: 36219871 PMCID: PMC9578555 DOI: 10.1093/molbev/msac201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 09/04/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Climate change threatens the survival of coral reefs on a global scale, primarily through mass bleaching and mortality as a result of marine heatwaves. While these short-term effects are clear, predicting the fate of coral reefs over the coming century is a major challenge. One way to understand the longer-term effects of rapid climate change is to examine the response of coral populations to past climate shifts. Coastal and shallow-water marine ecosystems such as coral reefs have been reshaped many times by sea-level changes during the Pleistocene, yet, few studies have directly linked this with its consequences on population demographics, dispersal, and adaptation. Here we use powerful analytical techniques, afforded by haplotype phased whole-genomes, to establish such links for the reef-building coral, Acropora digitifera. We show that three genetically distinct populations are present in northwestern Australia, and that their rapid divergence since the last glacial maximum (LGM) can be explained by a combination of founder-effects and restricted gene flow. Signatures of selective sweeps, too strong to be explained by demographic history, are present in all three populations and overlap with genes that show different patterns of functional enrichment between inshore and offshore habitats. In contrast to rapid divergence in the host, we find that photosymbiont communities are largely undifferentiated between corals from all three locations, spanning almost 1000 km, indicating that selection on host genes and not acquisition of novel symbionts, has been the primary driver of adaptation for this species in northwestern Australia.
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Affiliation(s)
- Jia Zhang
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - Zoe T Richards
- Coral Conservation and Research Group, Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
- Collections and Research, Western Australian Museum, 49 Kew Street Welshpool, WA 6106, Australia
| | - Arne A S Adam
- Coral Conservation and Research Group, Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Cheong Xin Chan
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, QLD 4072, Australia
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo277-8564, Chiba, Japan
| | - James Gilmour
- Australia Institute of Marine Science, Indian Oceans Marine Research Centre, Crawley, WA, 6009, Australia
| | - Luke Thomas
- Australia Institute of Marine Science, Indian Oceans Marine Research Centre, Crawley, WA, 6009, Australia
- Oceans Graduate School, The UWA Oceans Institute, The University of Western Australia, Perth, WA, 6009, Australia
| | - Jan M Strugnell
- Department of Marine Biology and Aquaculture, James Cook University, Townsville, QLD, 4811, Australia
- Centre for Sustainable Fisheries and Aquaculture, James Cook University, Townsville, QLD, 4811, Australia
| | - David J Miller
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
- Marine Climate Change Unit, Okinawa Institute of Science and Technology, Onna-son, Okinawa, Japan 904-0495
| | - Ira Cooke
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia
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Tsuchiya K, Zayasu Y, Nakajima Y, Arakaki N, Suzuki G, Satoh N, Shinzato C. Genomic analysis of a reef-building coral, Acropora digitifera, reveals complex population structure and a migration network in the Nansei Islands, Japan. Mol Ecol 2022; 31:5270-5284. [PMID: 36082782 DOI: 10.1111/mec.16665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 06/04/2022] [Accepted: 08/08/2022] [Indexed: 12/15/2022]
Abstract
Understanding the structure and connectivity of coral populations is fundamental for developing marine conservation policies, especially in patchy environments such as archipelagos. The Nansei Islands, extending more than 1000 km in southwestern Japan, are characterized by high levels of biodiversity and endemism, supported by coral reefs, which make this region ideal for assessing genetic attributes of coral populations. In this study, we conducted population genomic analyses based on genome-wide, single-nucleotide polymorphisms (SNPs) of Acropora digitifera, a common species in the Nansei Islands. By merging newly obtained genome resequencing data with previously published data, we identified more than 4 million genome-wide SNPs in 303 colonies collected at 22 locations, with sequencing coverage ranging from 3.91× to 27.41×. While population structure analyses revealed genetic similarities between the southernmost and northernmost locations, separated by >1000 km, several subpopulations in intermediate locations suggested limited genetic admixture, indicating conflicting migration tendencies in the Nansei Islands. Although migration networks revealed a general tendency of northward migration along the Kuroshio Current, a substantial amount of southward migration was also detected, indicating important contributions of minor ocean currents to coral larval dispersal. Moreover, heterogeneity in the transition of effective population sizes among locations suggests different histories for individual subpopulations. The unexpected complexity of both past and present population dynamics in the Nansei Islands implies that heterogeneity of ocean currents and local environments, past and present, have influenced the population structure of this species, and similar unexpected population complexities may be expected for other marine species with similar reproductive modes.
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Affiliation(s)
- Kojin Tsuchiya
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
| | - Yuna Zayasu
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Yuichi Nakajima
- Center for Climate Change Adaptation, National Institute for Environmental Studies, Tsukuba, Japan
| | - Nana Arakaki
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Go Suzuki
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Ishigaki, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
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Jandang S, Viyakarn V, Yoshioka Y, Shinzato C, Chavanich S. The seasonal investigation of Symbiodiniaceae in broadcast spawning, Acropora humilis and brooding, Pocillopora cf. damicornis corals. PeerJ 2022; 10:e13114. [PMID: 35722256 PMCID: PMC9205303 DOI: 10.7717/peerj.13114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 02/23/2022] [Indexed: 01/12/2023] Open
Abstract
The density and diversity of Symbiodiniaceae associated with corals can be influenced by seasonal changes . This study provided the first annual investigation of Symbiodiniaceae density and diversity associated with Acropora humilis and Pocillopora cf. damicornis corals in the Gulf of Thailand using both zooxanthellae cell count and next-generation sequencing (ITS-1, ITS-2 regions) techniques, respectively. The results from this study indicated that zooxanthellae cell densities in both coral species differ significantly. The number of zooxanthellae was negatively correlated with the physical environment variable (light intensity). The diversity within A. humilis consisted of two genera, Cladocopium (Cspc_C3: 56.39%, C3w: 33.62%, C93type1: 4.42% and Cspf: 3.59%) and a small amount of Durusdinium (D1: 1.03%) whereas P. cf. damicornis was found to be 100% associated with Durusdinium (D1: 95.58%, D6: 1.01% and D10: 2.7%) suggesting that each coral species may select their appropriate genus/species of Symbiodiniaceae in response to local environmental stressors. The results of this study provided some information on the coral-Symbiodiniaceae relationship between seasons, which may be applied to predict the potential adaptation of corals in localized reef environments.
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Affiliation(s)
- Suppakarn Jandang
- Reef Biology Research Group, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Voranop Viyakarn
- Reef Biology Research Group, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand,Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, Thailand
| | - Yuki Yoshioka
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
| | - Suchana Chavanich
- Reef Biology Research Group, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand,Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, Thailand,Center of Excellence for Marine Biotechnology, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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Yoshioka Y, Suzuki G, Zayasu Y, Yamashita H, Shinzato C. Comparative genomics highlight the importance of lineage-specific gene families in evolutionary divergence of the coral genus, Montipora. BMC Ecol Evol 2022; 22:71. [PMID: 35624412 PMCID: PMC9145168 DOI: 10.1186/s12862-022-02023-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 05/13/2022] [Indexed: 12/23/2022] Open
Abstract
Background Scleractinian corals of the genus Montipora (Anthozoa, Cnidaria) possess some unusual biological traits, such as vertical transmission of algal symbionts; however, the genetic bases for those traits remain unknown. We performed extensive comparative genomic analyses among members of the family Acroporidae (Montipora, Acropora, and Astreopora) to explore genomic novelties that might explain unique biological traits of Montipora using improved genome assemblies and gene predictions for M. cactus, M. efflorescens and Astreopora myriophthalma. Results We obtained genomic data for the three species of comparable high quality to other published coral genomes. Comparative genomic analyses revealed that the gene families restricted to Montipora are significantly more numerous than those of Acropora and Astreopora, but their functions are largely unknown. The number of gene families specifically expanded in Montipora was much lower than the number specifically expanded in Acropora. In addition, we found that evolutionary rates of the Montipora-specific gene families were significantly higher than other gene families shared with Acropora and/or Astreopora. Of 40 gene families under positive selection (Ka/Ks ratio > 1) in Montipora, 30 were specifically detected in Montipora-specific gene families. Comparative transcriptomic analysis of early life stages of Montipora, which possesses maternally inherited symbionts, and Acropora, which lacks them, revealed that most gene families continuously expressed in Montipora, but not expressed in Acropora do not have orthologs in Acropora. Among the 30 Montipora-specific gene families under positive selection, 27 are expressed in early life stages. Conclusions Lineage-specific gene families were important to establish the genus Montipora, particularly genes expressed throughout early life stages, which under positive selection, gave rise to biological traits unique to Montipora. Our findings highlight evolutionarily acquired genomic bases that may support symbiosis in these stony corals and provide novel insights into mechanisms of coral-algal symbiosis, the physiological foundation of coral reefs. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02023-8.
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Affiliation(s)
- Yuki Yoshioka
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan.,Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Go Suzuki
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Ishigaki, Okinawa, Japan
| | - Yuna Zayasu
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Hiroshi Yamashita
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Ishigaki, Okinawa, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan.
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11
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Shinzato C, Takeuchi T, Yoshioka Y, Tada I, Kanda M, Broussard C, Iguchi A, Kusakabe M, Marin F, Satoh N, Inoue M. Whole-Genome Sequencing Highlights Conservative Genomic Strategies of a Stress-Tolerant, Long-Lived Scleractinian Coral, Porites australiensis Vaughan, 1918. Genome Biol Evol 2021; 13:6456307. [PMID: 34878117 PMCID: PMC8691061 DOI: 10.1093/gbe/evab270] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2021] [Indexed: 12/13/2022] Open
Abstract
Massive corals of the genus Porites, common, keystone reef builders in the Indo-Pacific Ocean, are distinguished by their relative stress tolerance and longevity. In order to identify genetic bases of these attributes, we sequenced the complete genome of a massive coral, Porites australiensis. We developed a genome assembly and gene models of comparable quality to those of other coral genomes. Proteome analysis identified 60 Porites skeletal matrix protein genes, all of which show significant similarities to genes from other corals and even to those from a sea anemone, which has no skeleton. Nonetheless, 30% of its skeletal matrix proteins were unique to Porites and were not present in the skeletons of other corals. Comparative genomic analyses showed that genes widely conserved among other organisms are selectively expanded in Porites. Specifically, comparisons of transcriptomic responses of P. australiensis and Acropora digitifera, a stress-sensitive coral, reveal significant differences in regard to genes that respond to increased water temperature, and some of the genes expanded exclusively in Porites may account for the different thermal tolerances of these corals. Taken together, widely shared genes may have given rise to unique biological characteristics of Porites, massive skeletons and stress tolerance.
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Affiliation(s)
- Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Takeshi Takeuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Yuki Yoshioka
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan.,Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Ipputa Tada
- Department of Genetics, SOKENDAI (Graduate University for Advanced Studies), Mishima, Shizuoka, Japan
| | - Miyuki Kanda
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | | | - Akira Iguchi
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | | | - Frédéric Marin
- Biogéosciences, Bâtiment des Sciences Gabriel, Université de Bourgogne, Dijon, France
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Mayuri Inoue
- Division of Earth Science, Graduate School of Natural Science and Technology, Okayama University, Japan
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12
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Maeda K, Shinzato C, Koyanagi R, Kunishima T, Kobayashi H, Satoh N, Palla HP. Two new species of Rhinogobius (Gobiiformes: Oxudercidae) from Palawan, Philippines, with their phylogenetic placement. Zootaxa 2021; 5068:81-98. [PMID: 34810721 DOI: 10.11646/zootaxa.5068.1.3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Indexed: 11/04/2022]
Abstract
Two new species of Rhinogobius found in streams on central part of Palawan Island, Philippines are described. The two new species, Rhinogobius estrellae and Rhinogobius tandikan share unique transverse rows of sensory papillae on the cheek with Rhinogobius similis Gill, 1859, but differ from the latter in fin ray counts, arrangement of the scales, etc. The two new species are distinguished from each other by the pectoral-fin ray count, the longitudinal- and predorsal-scale counts, and colouration of the body. Rhinogobius estrellae new species and R. tandikan new species have been found allopatrically in a stream within Malatgao River system flowing into the Sulu Sea and in the Cayulo River flowing into the South China Sea, respectively. The Malatgao River system is the southernmost habitat of the genus Rhinogobius. Rhinogobius similis had been considered as the only member of the most basal lineage of this genus, but our mitochondrial genome analysis suggested that the two new species are additional members of this lineage. They are considered to be relicts of their common ancestor with R. similis, which probably had a wider distribution.
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Affiliation(s)
- Ken Maeda
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa 904-0495, Japan..
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba 277-8564, Japan..
| | - Ryo Koyanagi
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa 904-0495, Japan..
| | - Taiga Kunishima
- Wakayama Prefectural Museum of Natural History, 370-1 Funoo, Kainan, Wakayama 642-0001, Japan. .
| | - Hirozumi Kobayashi
- University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan..
| | - Noriyuki Satoh
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa 904-0495, Japan..
| | - Herminie P Palla
- College of Fisheries and Aquatic Sciences, Western Philippines University - Puerto Princesa Campus, Puerto Princesa City, 5300 Palawan, Philippines. .
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13
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Kawato S, Nishitsuji K, Arimoto A, Hisata K, Kawamitsu M, Nozaki R, Kondo H, Shinzato C, Ohira T, Satoh N, Shoguchi E, Hirono I. Genome and transcriptome assemblies of the kuruma shrimp, Marsupenaeus japonicus. G3 (Bethesda) 2021; 11:jkab268. [PMID: 34515781 PMCID: PMC8527471 DOI: 10.1093/g3journal/jkab268] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/18/2021] [Indexed: 11/25/2022]
Abstract
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 a draft genome assembly of M. japonicus (1.70 Gbp; 18,210 scaffolds; scaffold N50 = 234.9 kbp; 34.38% GC, 93.4% BUSCO completeness) and a complete mitochondrial genome sequence (15,969 bp). As with other penaeid shrimp genomes, the M. japonicus genome is extremely rich in simple repeats, which occupies 27.4% of the assembly. A total of 26,381 protein-coding gene models (94.7% BUSCO completeness) were predicted, of which 18,005 genes (68.2%) were assigned functional description by at least one method. We also produced an Illumina-based transcriptome shotgun assembly (40,991 entries; 93.0% BUSCO completeness) and a PacBio Iso-Seq transcriptome assembly (25,415 entries; 67.5% BUSCO completeness). We envision that the M. japonicus genome and transcriptome assemblies will serve as useful resources for the basic research, fisheries management, and breeding programs of M. japonicus.
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Affiliation(s)
- Satoshi Kawato
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Koki Nishitsuji
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Asuka Arimoto
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Mayumi Kawamitsu
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Reiko Nozaki
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Hidehiro Kondo
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba 277-0882, Japan
| | - Tsuyoshi Ohira
- Faculty of Science, Department of Biological Sciences, Kanagawa University, Kanagawa 221-8686, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Ikuo Hirono
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
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14
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Maeda K, Kobayashi H, Palla HP, Shinzato C, Koyanagi R, Montenegro J, Nagano AJ, Saeki T, Kunishima T, Mukai T, Tachihara K, Laudet V, Satoh N, Yamahira K. Do colour-morphs of an amphidromous goby represent different species? Taxonomy of Lentipes (Gobiiformes) from Japan and Palawan, Philippines, with phylogenomic approaches. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1971792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Ken Maeda
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Hirozumi Kobayashi
- University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan
| | - Herminie P. Palla
- College of Fisheries and Aquatic Sciences, Western Philippines University, Puerto Princesa Campus, Puerto Princesa City, 5300, Palawan, Philippines
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan
| | - Ryo Koyanagi
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Javier Montenegro
- University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan
| | | | | | - Taiga Kunishima
- Wakayama Prefectural Museum of Natural History, 370-1 Funoo, Kainan, Wakayama, 642-0001, Japan
| | - Takahiko Mukai
- Faculty of Regional Studies, Gifu University, Gifu, 501-1193, Japan
| | | | - Vincent Laudet
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Noriyuki Satoh
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Kazunori Yamahira
- University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan
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15
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Shinzato C, Khalturin K, Inoue J, Zayasu Y, Kanda M, Kawamitsu M, Yoshioka Y, Yamashita H, Suzuki G, Satoh N. Corrigendum to: Eighteen Coral Genomes Reveal the Evolutionary Origin of Acropora Strategies to Accommodate Environmental Changes. Mol Biol Evol 2021; 38:3495. [PMID: 34151991 DOI: 10.1093/molbev/msab137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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16
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Shinzato C, Khalturin K, Inoue J, Zayasu Y, Kanda M, Kawamitsu M, Yoshioka Y, Yamashita H, Suzuki G, Satoh N. Eighteen Coral Genomes Reveal the Evolutionary Origin of Acropora Strategies to Accommodate Environmental Changes. Mol Biol Evol 2021; 38:16-30. [PMID: 32877528 PMCID: PMC7783167 DOI: 10.1093/molbev/msaa216] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The genus Acropora comprises the most diverse and abundant scleractinian corals (Anthozoa, Cnidaria) in coral reefs, the most diverse marine ecosystems on Earth. However, the genetic basis for the success and wide distribution of Acropora are unknown. Here, we sequenced complete genomes of 15 Acropora species and 3 other acroporid taxa belonging to the genera Montipora and Astreopora to examine genomic novelties that explain their evolutionary success. We successfully obtained reasonable draft genomes of all 18 species. Molecular dating indicates that the Acropora ancestor survived warm periods without sea ice from the mid or late Cretaceous to the Early Eocene and that diversification of Acropora may have been enhanced by subsequent cooling periods. In general, the scleractinian gene repertoire is highly conserved; however, coral- or cnidarian-specific possible stress response genes are tandemly duplicated in Acropora. Enzymes that cleave dimethlysulfonioproprionate into dimethyl sulfide, which promotes cloud formation and combats greenhouse gasses, are the most duplicated genes in the Acropora ancestor. These may have been acquired by horizontal gene transfer from algal symbionts belonging to the family Symbiodiniaceae, or from coccolithophores, suggesting that although functions of this enzyme in Acropora are unclear, Acropora may have survived warmer marine environments in the past by enhancing cloud formation. In addition, possible antimicrobial peptides and symbiosis-related genes are under positive selection in Acropora, perhaps enabling adaptation to diverse environments. Our results suggest unique Acropora adaptations to ancient, warm marine environments and provide insights into its capacity to adjust to rising seawater temperatures.
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Affiliation(s)
- Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
| | - Konstantin Khalturin
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Jun Inoue
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan.,Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Yuna Zayasu
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Miyuki Kanda
- DNA Sequence Section (SQC), Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Mayumi Kawamitsu
- DNA Sequence Section (SQC), Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Yuki Yoshioka
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan.,Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Hiroshi Yamashita
- Research Center for Subtropical Fisheries, Seikai National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Okinawa, Japan
| | - Go Suzuki
- Research Center for Subtropical Fisheries, Seikai National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Okinawa, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
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17
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Yamashita H, Koike K, Shinzato C, Jimbo M, Suzuki G. Can Acropora tenuis larvae attract native Symbiodiniaceae cells by green fluorescence at the initial establishment of symbiosis? PLoS One 2021; 16:e0252514. [PMID: 34061893 PMCID: PMC8168901 DOI: 10.1371/journal.pone.0252514] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 05/17/2021] [Indexed: 11/21/2022] Open
Abstract
Most corals acquire symbiodiniacean symbionts from the surrounding environment to initiate symbiosis. The cell densities of Symbiodiniaceae in the environment are usually low, and mechanisms may exist by which new coral generations attract suitable endosymbionts. Phototaxis of suitable symbiodiniacean cells toward green fluorescence in corals has been proposed as one such mechanism. In the present study, we observed the phototaxis action wavelength of various strains of Symbiodiniaceae and the fluorescence spectra of aposymbiotic Acropora tenuis larvae at the time of endosymbiont uptake. The phototaxis patterns varied among the Symbiodiniaceae species and “native” endosymbionts—commonly found in Acropora juveniles present in natural environments; that is, Symbiodinium microadriaticum was attracted to blue light rather than to green light. Another native endosymbiont, Durusdinium trenchii, showed no phototaxis specific to any wavelength. Although the larvae exhibited green and broad orange fluorescence under blue-violet excitation light, the maximum green fluorescence peak did not coincide with that of the phototaxis action spectrum of S. microadriaticum. Rather, around the peak wavelength of larval green fluorescence, this native endosymbiont showed slightly negative phototaxis, suggesting that the green fluorescence of A. tenuis larvae may not play a role in the initial attraction of native endosymbionts. Conversely, broad blue larval fluorescence under UV-A excitation covered the maximum phototaxis action wavelength of S. microadriaticum. We also conducted infection tests using native endosymbionts and aposymbiotic larvae under red LED light that does not excite visible larval fluorescence. Almost all larvae failed to acquire S. microadriaticum cells, whereas D. trenchii cells were acquired by larvae even under red illumination. Thus, attraction mechanisms other than visible fluorescence might exist, at least in the case of D. trenchii. Our results suggest that further investigation and discussion, not limited to green fluorescence, would be required to elucidate the initial attraction mechanisms.
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Affiliation(s)
- Hiroshi Yamashita
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Ishigaki, Okinawa, Japan
- * E-mail:
| | - Kazuhiko Koike
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Mitsuru Jimbo
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Go Suzuki
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Ishigaki, Okinawa, Japan
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18
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Sassa M, Takagi T, Kinjo A, Yoshioka Y, Zayasu Y, Shinzato C, Kanda S, Murakami-Sugihara N, Shirai K, Inoue K. Divalent metal transporter-related protein restricts animals to marine habitats. Commun Biol 2021; 4:463. [PMID: 33846549 PMCID: PMC8041893 DOI: 10.1038/s42003-021-01984-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 03/12/2021] [Indexed: 12/30/2022] Open
Abstract
Utilization and regulation of metals from seawater by marine organisms are important physiological processes. To better understand metal regulation, we searched the crown-of-thorns starfish genome for the divalent metal transporter (DMT) gene, a membrane protein responsible for uptake of divalent cations. We found two DMT-like sequences. One is an ortholog of vertebrate DMT, but the other is an unknown protein, which we named DMT-related protein (DMTRP). Functional analysis using a yeast expression system demonstrated that DMT transports various metals, like known DMTs, but DMTRP does not. In contrast, DMTRP reduced the intracellular concentration of some metals, especially zinc, suggesting its involvement in negative regulation of metal uptake. Phylogenetic distribution of the DMTRP gene in various metazoans, including sponges, protostomes, and deuterostomes, indicates that it originated early in metazoan evolution. However, the DMTRP gene is only retained in marine species, and its loss seems to have occurred independently in ecdysozoan and vertebrate lineages from which major freshwater and land animals appeared. DMTRP may be an evolutionary and ecological limitation, restricting organisms that possess it to marine habitats, whereas its loss may have allowed other organisms to invade freshwater and terrestrial habitats. Mieko Sassa et al. report a novel divalent metal transporter protein (DMTRP) in the crown-of-thorns starfish genome and determine that all organisms with a DMTRP gene are located in marine habitats. They also show in a functional yeast system that DMTRP can prevent uptake of certain metals, bringing insight into the evolution of metal regulation for marine organisms.
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Affiliation(s)
- Mieko Sassa
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan. .,Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan.
| | - Toshiyuki Takagi
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Azusa Kinjo
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Yuki Yoshioka
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan.,Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Yuna Zayasu
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Shinji Kanda
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | | | - Kotaro Shirai
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Koji Inoue
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan.,Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
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19
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Inoue K, Yoshioka Y, Tanaka H, Kinjo A, Sassa M, Ueda I, Shinzato C, Toyoda A, Itoh T. Genomics and Transcriptomics of the green mussel explain the durability of its byssus. Sci Rep 2021; 11:5992. [PMID: 33727571 PMCID: PMC7971044 DOI: 10.1038/s41598-021-84948-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/18/2021] [Indexed: 11/09/2022] Open
Abstract
Mussels, which occupy important positions in marine ecosystems, attach tightly to underwater substrates using a proteinaceous holdfast known as the byssus, which is tough, durable, and resistant to enzymatic degradation. Although various byssal proteins have been identified, the mechanisms by which it achieves such durability are unknown. Here we report comprehensive identification of genes involved in byssus formation through whole-genome and foot-specific transcriptomic analyses of the green mussel, Perna viridis. Interestingly, proteins encoded by highly expressed genes include proteinase inhibitors and defense proteins, including lysozyme and lectins, in addition to structural proteins and protein modification enzymes that probably catalyze polymerization and insolubilization. This assemblage of structural and protective molecules constitutes a multi-pronged strategy to render the byssus highly resistant to environmental insults.
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Affiliation(s)
- Koji Inoue
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan.
| | - Yuki Yoshioka
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan.,Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8563, Japan
| | - Hiroyuki Tanaka
- Department of Biological Information, Tokyo Institute of Technology, Meguro, Tokyo, 152-8550, Japan
| | - Azusa Kinjo
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan
| | - Mieko Sassa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan.,Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8563, Japan
| | - Ikuo Ueda
- School of Marine Biosciences, Kitasato University, Kanagawa, 252-0373, Japan.,Faculty of Science, Kanagawa University, Hiratsuka, 259-1293, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Takehiko Itoh
- Department of Biological Information, Tokyo Institute of Technology, Meguro, Tokyo, 152-8550, Japan
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20
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Kashimoto R, Hisata K, Shinzato C, Satoh N, Shoguchi E. Expansion and Diversification of Fluorescent Protein Genes in Fifteen Acropora Species during the Evolution of Acroporid Corals. Genes (Basel) 2021; 12:genes12030397. [PMID: 33799612 PMCID: PMC8001845 DOI: 10.3390/genes12030397] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 11/16/2022] Open
Abstract
In addition to a purple, non-fluorescent chromoprotein (ChrP), fluorescent proteins (FPs) account for the vivid colors of corals, which occur in green (GFP), cyan (CFP), and red (RFP) FPs. To understand the evolution of the coral FP gene family, we examined the genomes of 15 Acropora species and three confamilial taxa. This genome-wide survey identified 219 FP genes. Molecular phylogeny revealed that the 15 Acropora species each have 9–18 FP genes, whereas the other acroporids examined have only two, suggesting a pronounced expansion of the FP genes in the genus Acropora. The data estimates of FP gene duplication suggest that the last common ancestor of the Acropora species that survived in the period of high sea surface temperature (Paleogene period) has already gained 16 FP genes. Different evolutionary histories of lineage-specific duplication and loss were discovered among GFP/CFPs, RFPs, and ChrPs. Synteny analysis revealed core GFP/CFP, RFP, and ChrP gene clusters, in which a tandem duplication of the FP genes was evident. The expansion and diversification of Acropora FPs may have contributed to the present-day richness of this genus.
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Affiliation(s)
- Rio Kashimoto
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan; (K.H.); (N.S.); (E.S.)
- Correspondence:
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan; (K.H.); (N.S.); (E.S.)
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-8564, Japan;
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan; (K.H.); (N.S.); (E.S.)
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan; (K.H.); (N.S.); (E.S.)
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21
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Shoguchi E, Yoshioka Y, Shinzato C, Arimoto A, Bhattacharya D, Satoh N. Correlation between Organelle Genetic Variation and RNA Editing in Dinoflagellates Associated with the Coral Acropora digitifera. Genome Biol Evol 2021; 12:203-209. [PMID: 32108224 PMCID: PMC7144361 DOI: 10.1093/gbe/evaa042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2020] [Indexed: 12/11/2022] Open
Abstract
In order to develop successful strategies for coral reef preservation, it is critical that the biology of both host corals and symbiotic algae are investigated. In the Ryukyu Archipelago, which encompasses many islands spread over ∼500 km of the Pacific Ocean, four major populations of the coral Acropora digitifera have been studied using whole-genome shotgun (WGS) sequence analysis (Shinzato C, Mungpakdee S, Arakaki N, Satoh N. 2015. Genome-wide single-nucleotide polymorphism (SNP) analysis explains coral diversity and recovery in the Ryukyu Archipelago. Sci Rep. 5:18211.). In contrast, the diversity of the symbiotic dinoflagellates associated with these A. digitifera populations is unknown. It is therefore unclear if these two core components of the coral holobiont share a common evolutionary history. This issue can be addressed for the symbiotic algal populations by studying the organelle genomes of their mitochondria and plastids. Here, we analyzed WGS data from ∼150 adult A. digitifera, and by mapping reads to the available reference genome sequences, we extracted 2,250 sequences representing 15 organelle genes of Symbiodiniaceae. Molecular phylogenetic analyses of these mitochondrial and plastid gene sets revealed that A. digitifera from the southern Yaeyama islands harbor a different Symbiodiniaceae population than the islands of Okinawa and Kerama in the north, indicating that the distribution of symbiont populations partially matches that of the four host populations. Interestingly, we found that numerous SNPs correspond to known RNA-edited sites in 14 of the Symbiodiniaceae organelle genes, with mitochondrial genes showing a stronger correspondence than plastid genes. These results suggest a possible correlation between RNA editing and SNPs in the two organelle genomes of symbiotic dinoflagellates.
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Affiliation(s)
- Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Yuki Yoshioka
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan.,Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwanoha, Kashiwa, Japan
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan.,Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwanoha, Kashiwa, Japan
| | - Asuka Arimoto
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
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22
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Satoh N, Kinjo K, Shintaku K, Kezuka D, Ishimori H, Yokokura A, Hagiwara K, Hisata K, Kawamitsu M, Koizumi K, Shinzato C, Zayasu Y. Color morphs of the coral, Acropora tenuis, show different responses to environmental stress and different expression profiles of fluorescent-protein genes. G3 (Bethesda) 2021; 11:jkab018. [PMID: 33621334 PMCID: PMC8022974 DOI: 10.1093/g3journal/jkab018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 01/06/2021] [Indexed: 11/21/2022]
Abstract
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 polyps of each morph exhibit specific fluorescence spectra. This attribute is inherited asexually, and color morphs do not change seasonally. In Okinawa Prefecture, during the summer of 2017, N and P morphs experienced bleaching, in which many N morphs died. Dinoflagellates (Symbiodiniaceae) are essential partners of scleractinian corals, and photosynthetic activity of symbionts was reduced in N and P morphs. In contrast, G morphs successfully withstood the stress. Examination of the clade and type of Symbiodiniaceae indicated that the three color-morphs host similar sets of Clade-C symbionts, suggesting that beaching of N and P morphs is unlikely attributable to differences in the clade of Symbiodiniaceae the color morphs hosted. Fluorescent proteins play pivotal roles in physiological regulation of corals. Since the A. tenuis genome has been decoded, we identified five genes for green fluorescent proteins (GFPs), two for cyan fluorescent proteins (CFPs), three for red fluorescent proteins (RFPs), and seven genes for chromoprotein (ChrP). A summer survey of gene expression profiles under outdoor aquarium conditions demonstrated that (a) expression of CFP and REP was quite low during the summer in all three morphs, (b) P morphs expressed higher levels of ChrP than N and G morphs, (c) both N and G morphs expressed GFP more highly than P morphs, and (d) GFP expression in N morphs was reduced during summer whereas G morphs maintained high levels of GFP expression throughout the summer. Although further studies are required to understand the biological significance of these color morphs of A. tenuis, our results suggest that thermal stress resistance is modified by genetic mechanisms that coincidentally lead to diversification of color morphs of this coral.
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Affiliation(s)
- Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Koji Kinjo
- Umino-Tane Co. Ltd, Okinawa 905-0888, Japan
| | - Kohei Shintaku
- IDEA Consultants, Inc., Okinawa Branch Office, Okinawa 900-0003, Japan
| | - Daisuke Kezuka
- IDEA Consultants, Inc., Okinawa Branch Office, Okinawa 900-0003, Japan
| | - Hiroo Ishimori
- IDEA Consultants, Inc., Okinawa Branch Office, Okinawa 900-0003, Japan
| | - Atsushi Yokokura
- IDEA Consultants, Inc., Institute of Environmental Informatics, Kanagawa 224-0025, Japan
| | | | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Mayumi Kawamitsu
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Koji Koizumi
- Imaging Section, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba 277-8564, Japan
| | - Yuna Zayasu
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
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23
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Takagi T, Yoshioka Y, Zayasu Y, Satoh N, Shinzato C. Transcriptome Analyses of Immune System Behaviors in Primary Polyp of Coral Acropora digitifera Exposed to the Bacterial Pathogen Vibrio coralliilyticus under Thermal Loading. Mar Biotechnol (NY) 2020; 22:748-759. [PMID: 32696240 DOI: 10.1007/s10126-020-09984-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
Elevated sea surface temperature associated with global warming is a serious threat to coral reefs. Elevated temperatures directly or indirectly alter the distribution of coral-pathogen interactions and thereby exacerbate infectious coral diseases. The pathogenic bacterium Vibrio coralliilyticus is well-known as a causative agent of infectious coral disease. Rising sea surface temperature promotes the infection of corals by this bacterium, which causes several coral pathologies, such as bacterial bleaching, tissue lysis, and white syndrome. However, the effects of thermal stress on coral immune responses to the pathogen are poorly understood. To delineate the effects of thermal stress on coral immunity, we performed transcriptome analysis of aposymbiotic primary polyps of the reef-building coral Acropora digitifera exposed to V. coralliilyticus under thermal stress conditions. V. coralliilyticus infection of coral that was under thermal stress had negative effects on various molecular processes, including suppression of gene expression related to the innate immune response. In response to the pathogen, the coral mounted various responses including changes in protein metabolism, exosome release delivering signal molecules, extracellular matrix remodeling, and mitochondrial metabolism changes. Based on these results, we provide new insights into innate immunity of A. digitifera against pathogen infection under thermal stress conditions.
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Affiliation(s)
- Toshiyuki Takagi
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan.
| | - Yuki Yoshioka
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8564, Japan
| | - Yuna Zayasu
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, 904-0495, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, 904-0495, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan
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24
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Yoshioka Y, Yamashita H, Suzuki G, Zayasu Y, Tada I, Kanda M, Satoh N, Shoguchi E, Shinzato C. Whole-Genome Transcriptome Analyses of Native Symbionts Reveal Host Coral Genomic Novelties for Establishing Coral-Algae Symbioses. Genome Biol Evol 2020; 13:5981117. [PMID: 33185681 PMCID: PMC7850063 DOI: 10.1093/gbe/evaa240] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2020] [Indexed: 01/14/2023] Open
Abstract
Reef-building corals and photosynthetic, endosymbiotic algae of the family Symbiodiniaceae establish mutualistic relationships that are fundamental to coral biology, enabling coral reefs to support a vast diversity of marine species. Although numerous types of Symbiodiniaceae occur in coral reef environments, Acropora corals select specific types in early life stages. In order to study molecular mechanisms of coral–algal symbioses occurring in nature, we performed whole-genome transcriptomic analyses of Acropora tenuis larvae inoculated with Symbiodinium microadriaticum strains isolated from an Acropora recruit. In order to identify genes specifically involved in symbioses with native symbionts in early life stages, we also investigated transcriptomic responses of Acropora larvae exposed to closely related, nonsymbiotic, and occasionally symbiotic Symbiodinium strains. We found that the number of differentially expressed genes was largest when larvae acquired native symbionts. Repertoires of differentially expressed genes indicated that corals reduced amino acid, sugar, and lipid metabolism, such that metabolic enzymes performing these functions were derived primarily from S. microadriaticum rather than from A. tenuis. Upregulated gene expression of transporters for those metabolites occurred only when coral larvae acquired their natural symbionts, suggesting active utilization of native symbionts by host corals. We also discovered that in Acropora, genes for sugar and amino acid transporters, prosaposin-like, and Notch ligand-like, were upregulated only in response to native symbionts, and included tandemly duplicated genes. Gene duplications in coral genomes may have been essential to establish genomic novelties for coral–algae symbiosis.
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Affiliation(s)
- Yuki Yoshioka
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan.,Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Hiroshi Yamashita
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Ishigaki, Okinawa, Japan
| | - Go Suzuki
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Ishigaki, Okinawa, Japan
| | - Yuna Zayasu
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Ipputa Tada
- Department of Genetics, SOKENDAI (Graduate University for Advanced Studies), Mishima, Shizuoka, Japan
| | - Miyuki Kanda
- DNA Sequencing Section (SQC), Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
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25
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Shoguchi E, Beedessee G, Hisata K, Tada I, Narisoko H, Satoh N, Kawachi M, Shinzato C. A New Dinoflagellate Genome Illuminates a Conserved Gene Cluster Involved in Sunscreen Biosynthesis. Genome Biol Evol 2020; 13:5955767. [PMID: 33146374 PMCID: PMC7875005 DOI: 10.1093/gbe/evaa235] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2020] [Indexed: 12/18/2022] Open
Abstract
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, and Cladocopium, which have been isolated from corals, have been reported. However, no genome is available from the genus Durusdinium, which occupies an intermediate phylogenetic position in the Family Symbiodiniaceae and is well known for thermal tolerance (resistance to bleaching). We sequenced, assembled, and annotated the genome of Durusdinium trenchii, isolated from the coral, Favia speciosa, in Okinawa, Japan. Assembled short reads amounted to 670 Mb with ∼47% GC content. This GC content was intermediate among taxa belonging to the Symbiodiniaceae. Approximately 30,000 protein-coding genes were predicted in the D. trenchii genome, fewer than in other genomes from the Symbiodiniaceae. However, annotations revealed that the D. trenchii genome encodes a cluster of genes for synthesis of mycosporine-like amino acids, which absorb UV radiation. Interestingly, a neighboring gene in the cluster encodes a glucose-methanol-choline oxidoreductase with a flavin adenine dinucleotide domain that is also found in Symbiodinium tridacnidorum. This conservation seems to partially clarify an ancestral genomic structure in the Symbiodiniaceae and its loss in late-branching lineages, including Breviolum and Cladocopium, after splitting from the Durusdinium lineage. Our analysis suggests that approximately half of the taxa in the Symbiodiniaceae may maintain the ability to synthesize mycosporine-like amino acids. Thus, this work provides a significant genomic resource for understanding the genomic diversity of Symbiodiniaceae in corals.
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Affiliation(s)
- Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Girish Beedessee
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Ipputa Tada
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan.,Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
| | - Haruhi Narisoko
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Masanobu Kawachi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan.,Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
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26
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Chiu YL, Shikina S, Yoshioka Y, Shinzato C, Chang CF. De novo transcriptome assembly from the gonads of a scleractinian coral, Euphyllia ancora: molecular mechanisms underlying scleractinian gametogenesis. BMC Genomics 2020; 21:732. [PMID: 33087060 PMCID: PMC7579821 DOI: 10.1186/s12864-020-07113-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 09/29/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Sexual reproduction of scleractinians has captured the attention of researchers and the general public for decades. Although extensive ecological data has been acquired, underlying molecular and cellular mechanisms remain largely unknown. In this study, to better understand mechanisms underlying gametogenesis, we isolated ovaries and testes at different developmental phases from a gonochoric coral, Euphyllia ancora, and adopted a transcriptomic approach to reveal sex- and phase-specific gene expression profiles. In particular, we explored genes associated with oocyte development and maturation, spermiogenesis, sperm motility / capacitation, and fertilization. RESULTS 1.6 billion raw reads were obtained from 24 gonadal samples. De novo assembly of trimmed reads, and elimination of contigs derived from symbiotic dinoflagellates (Symbiodiniaceae) and other organisms yielded a reference E. ancora gonadal transcriptome of 35,802 contigs. Analysis of 4 developmental phases identified 2023 genes that were differentially expressed during oogenesis and 678 during spermatogenesis. In premature/mature ovaries, 631 genes were specifically upregulated, with 538 in mature testes. Upregulated genes included those involved in gametogenesis, gamete maturation, sperm motility / capacitation, and fertilization in other metazoans, including humans. Meanwhile, a large number of genes without homology to sequences in the SWISS-PROT database were also observed among upregulated genes in premature / mature ovaries and mature testes. CONCLUSIONS Our findings show that scleractinian gametogenesis shares many molecular characteristics with that of other metazoans, but it also possesses unique characteristics developed during cnidarian and/or scleractinian evolution. To the best of our knowledge, this study is the first to create a gonadal transcriptome assembly from any scleractinian. This study and associated datasets provide a foundation for future studies regarding gametogenesis and differences between male and female colonies from molecular and cellular perspectives. Furthermore, our transcriptome assembly will be a useful reference for future development of sex-specific and/or stage-specific germ cell markers that can be used in coral aquaculture and ecological studies.
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Affiliation(s)
- Yi-Ling Chiu
- Doctoral Program in Marine Biotechnology, National Taiwan Ocean University, Keelung, 20224, Taiwan.,Doctoral Program in Marine Biotechnology, Academia Sinica, Taipei, 11529, Taiwan
| | - Shinya Shikina
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan. .,Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Pei-Ning Rd, Keelung, 20224, Taiwan.
| | - Yuki Yoshioka
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan.
| | - Ching-Fong Chang
- Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Pei-Ning Rd, Keelung, 20224, Taiwan. .,Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan.
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27
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Hanahara N, Higashiji T, Shinzato C, Koyanagi R, Maeda K. First record of Larsonella pumilus (Teleostei: Gobiidae) from Japan, with phylogenetic placement of the genus Larsonella. Zootaxa 2019; 4695:zootaxa.4695.4.4. [PMID: 31719342 DOI: 10.11646/zootaxa.4695.4.4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Indexed: 11/04/2022]
Abstract
During a survey of deep-sea fauna, using a Remotely Operated Vehicle, a single specimen (21.6 mm in standard length) of Larsonella pumilus (Larson Hoese, 1980) was collected at a depth of 214 m off the coast of Okinawa Island, Japan. It represents the first record of this species from Japan. The collection site was far deeper than previous reports for this species. This suggests that the main habitat of L. pumilus is deeper than previously recognized and it may explain the paucity of records of this species. As the previously available morphological description of L. pumilus was based on only a single specimen (holotype), this new specimen is described herein. Its morphology corresponds closely to the original description of the holotype, except that faint melanophores are arranged radially around the eyes and scattered on the trunk and the fins. Mitochondrial genome sequences of L. pumilus and 19 related species demonstrate close relationships between L. pumilus and the genus Priolepis. These data also indicate that the genus Priolepis is not monophyletic.
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Affiliation(s)
- Nozomi Hanahara
- Okinawa Churashima Foundation Research Center, 888 Ishikawa, Motobu-cho, Okinawa 905-0206, Japan..
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28
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Zhang Y, Chiu YL, Chen CJ, Ho YY, Shinzato C, Shikina S, Chang CF. Discovery of a receptor guanylate cyclase expressed in the sperm flagella of stony corals. Sci Rep 2019; 9:14652. [PMID: 31601940 PMCID: PMC6787079 DOI: 10.1038/s41598-019-51224-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 09/16/2019] [Indexed: 12/27/2022] Open
Abstract
The receptor guanylate cyclases (rGCs) in animals serve as sensitive chemoreceptors to detect both chemical and environmental cues. In reproduction, rGCs were shown to be expressed on sperm and serve as receptors for egg-derived sperm-activating and sperm-attracting factors in some echinoderms and mammals. However, sperm-associated rGCs have only been identified in some deuterostomes thus far, and it remains unclear how widely rGCs are utilized in metazoan reproduction. To address this issue, this study investigated the existence and expression of rGCs, particularly asking if rGCs are involved in the reproduction of a basal metazoan, phylum Cnidaria, using the stony coral Euphyllia ancora. Six paralogous rGCs were identified from a transcriptome database of E. ancora, and one of the rGCs, GC-A, was shown to be specifically expressed in the testis. Immunohistochemical analyses demonstrated that E. ancora GC-A protein was expressed in the spermatocytes and spermatids and eventually congregated on the sperm flagella during spermatogenesis. These findings suggest that GC-A may be involved in the regulation of sperm activity and/or functions (e.g., fertilization) in corals. This study is the first to perform molecular characterization of rGCs in cnidarians and provides evidence for the possible involvement of rGCs in the reproduction of basal metazoans.
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Affiliation(s)
- Yan Zhang
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, 20224, Taiwan
| | - Yi-Ling Chiu
- Doctoral Program in Marine Biotechnology, National Taiwan Ocean University, Keelung, 20224, Taiwan.,Doctoral Program in Marine Biotechnology, Academia Sinica, Taipei, 11529, Taiwan
| | - Chieh-Jhen Chen
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, 20224, Taiwan
| | - Yu-Ying Ho
- Department of Aquaculture, National Taiwan Ocean University, Keelung, 20224, Taiwan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan
| | - Shinya Shikina
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, 20224, Taiwan. .,Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, 20224, Taiwan.
| | - Ching-Fong Chang
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, 20224, Taiwan. .,Department of Aquaculture, National Taiwan Ocean University, Keelung, 20224, Taiwan.
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29
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Guzman C, Atrigenio M, Shinzato C, Aliño P, Conaco C. Warm seawater temperature promotes substrate colonization by the blue coral, Heliopora coerulea. PeerJ 2019; 7:e7785. [PMID: 31579631 PMCID: PMC6768060 DOI: 10.7717/peerj.7785] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 08/29/2019] [Indexed: 12/29/2022] Open
Abstract
Background Heliopora coerulea, the blue coral, is a reef building octocoral that is reported to have a higher optimum temperature for growth compared to most scleractinian corals. This octocoral has been observed to grow over both live and dead scleractinians and to dominate certain reefs in the Indo-Pacific region. The molecular mechanisms underlying the ability of H. coerulea to tolerate warmer seawater temperatures and to effectively compete for space on the substrate remain to be elucidated. Methods In this study, we subjected H. coerulea colonies to various temperatures for up to 3 weeks. The growth and photosynthetic efficiency rates of the coral colonies were measured. We then conducted pairwise comparisons of gene expression among the different coral tissue regions to identify genes and pathways that are expressed under different temperature conditions. Results A horizontal growth rate of 1.13 ± 0.25 mm per week was observed for corals subjected to 28 or 31 °C. This growth rate was significantly higher compared to corals exposed at 26 °C. This new growth was characterized by the extension of whitish tissue at the edges of the colony and was enriched for a matrix metallopeptidase, a calcium and integrin binding protein, and other transcripts with unknown function. Tissues at the growth margin and the adjacent calcified encrusting region were enriched for transcripts related to proline and riboflavin metabolism, nitrogen utilization, and organic cation transport. The calcified digitate regions, on the other hand, were enriched for transcripts encoding proteins involved in cell-matrix adhesion, translation, receptor-mediated endocytosis, photosynthesis, and ion transport. Functions related to lipid biosynthesis, extracellular matrix formation, cell migration, and oxidation-reduction processes were enriched at the growth margin in corals subjected for 3 weeks to 28 or 31 °C relative to corals at 26 °C. In the digitate region of the coral, transcripts encoding proteins that protect against oxidative stress, modify cell membrane composition, and mediate intercellular signaling pathways were enriched after just 24 h of exposure to 31 °C compared to corals at 28 °C. The overall downregulation of gene expression observed after 3 weeks of sustained exposure to 31 °C is likely compensated by symbiont metabolism. Discussion These findings reveal that the different regions of H. coerulea have variable gene expression profiles and responses to temperature variation. Under warmer conditions, the blue coral invests cellular resources toward extracellular matrix formation and cellular migration at the colony margins, which may promote rapid tissue growth and extension. This mechanism enables the coral to colonize adjacent reef substrates and successfully overgrow slower growing scleractinian corals that may already be more vulnerable to warming ocean waters.
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Affiliation(s)
- Christine Guzman
- Marine Science Institute, College of Science, University of the Philippines Diliman, Quezon City, Philippines.,Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Michael Atrigenio
- Marine Science Institute, College of Science, University of the Philippines Diliman, Quezon City, Philippines
| | - Chuya Shinzato
- Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Porfirio Aliño
- Marine Science Institute, College of Science, University of the Philippines Diliman, Quezon City, Philippines
| | - Cecilia Conaco
- Marine Science Institute, College of Science, University of the Philippines Diliman, Quezon City, Philippines
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30
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Arimoto A, Nishitsuji K, Higa Y, Arakaki N, Hisata K, Shinzato C, Satoh N, Shoguchi E. A siphonous macroalgal genome suggests convergent functions of homeobox genes in algae and land plants. DNA Res 2019; 26:183-192. [PMID: 30918953 PMCID: PMC6476727 DOI: 10.1093/dnares/dsz002] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/15/2019] [Indexed: 11/13/2022] Open
Abstract
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 of a siphonous green alga, Caulerpa lentillifera, with high contiguity, containing 9,311 protein-coding genes. Molecular phylogeny using 107 nuclear genes indicates that the diversification of the class Ulvophyceae, including C. lentillifera, occurred before the split of the Chlorophyceae and Trebouxiophyceae. Compared with other green algae, the TALE superclass of homeobox genes, which expanded in land plants, shows a series of lineage-specific duplications in this siphonous macroalga. Plant hormone signalling components were also expanded in a lineage-specific manner. Expanded transport regulators, which show spatially different expression, suggest that the structural patterning strategy of a multinucleate cell depends on diversification of nuclear pore proteins. These results not only imply functional convergence of duplicated genes among green plants, but also provide insight into evolutionary roots of green plants. Based on the present results, we propose cellular and molecular mechanisms involved in the structural differentiation in the siphonous alga.
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Affiliation(s)
- Asuka Arimoto
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Koki Nishitsuji
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Yoshimi Higa
- Onna Village Fisheries Cooperative, Onna, Okinawa, Japan
| | - Nana Arakaki
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
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Miyake T, Aihara N, Maeda K, Shinzato C, Koyanagi R, Kobayashi H, Yamahira K. Bloodmeal host identification with inferences to feeding habits of a fish-fed mosquito, Aedes baisasi. Sci Rep 2019; 9:4002. [PMID: 30850720 PMCID: PMC6408532 DOI: 10.1038/s41598-019-40509-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 02/18/2019] [Indexed: 01/20/2023] Open
Abstract
The mosquito, Aedes baisasi, which inhabits brackish mangrove swamps, is known to feed on fish. However, its host assemblage has not been investigated at the species level. We amplified and sequenced the cytochrome oxidase subunit I barcoding regions as well as some other regions from blood-fed females to identify host assemblages in the natural populations from four islands in the Ryukyu Archipelago. Hosts were identified from 230 females. We identified 15 host fish species belonging to eight families and four orders. Contrary to expectations from previous observations, mudskippers were detected from only 3% of blood-engorged females. The dominant host was a four-eyed sleeper, Bostrychus sinensis (Butidae, Gobiiformes), in Iriomote-jima Island (61%), while it was a snake eel, Pisodonophis boro (Ophichthidae, Anguilliformes), in Amami-oshima and Okinawa-jima islands (78% and 79%, respectively). Most of the identified hosts were known as air-breathing or amphibious fishes that inhabit mangroves or lagoons. Our results suggest that A. baisasi females locate the bloodmeal hosts within the mangrove forests and sometimes in the adjacent lagoons and land on the surface of available amphibious or other air-breathing fishes exposed in the air to feed on their blood.
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Affiliation(s)
- Takashi Miyake
- Faculty of Education, Gifu University, Gifu, 501-1193, Japan.
| | - Natsuki Aihara
- Faculty of Education, Gifu University, Gifu, 501-1193, Japan
| | - Ken Maeda
- Okinawa Institute of Science and Technology Graduate University (OIST), Onna, Okinawa, 904-0495, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan
| | - Ryo Koyanagi
- Okinawa Institute of Science and Technology Graduate University (OIST), Onna, Okinawa, 904-0495, Japan
| | - Hirozumi Kobayashi
- Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan
| | - Kazunori Yamahira
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan
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32
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Kim OTP, Nguyen PT, Shoguchi E, Hisata K, Vo TTB, Inoue J, Shinzato C, Le BTN, Nishitsuji K, Kanda M, Nguyen VH, Nong HV, Satoh N. A draft genome of the striped catfish, Pangasianodon hypophthalmus, for comparative analysis of genes relevant to development and a resource for aquaculture improvement. BMC Genomics 2018; 19:733. [PMID: 30290758 PMCID: PMC6173838 DOI: 10.1186/s12864-018-5079-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/14/2018] [Indexed: 11/22/2022] Open
Abstract
Background The striped catfish, Pangasianodon hypophthalmus, is a freshwater and benthopelagic fish common in the Mekong River delta. Catfish constitute a valuable source of dietary protein. Therefore, they are cultured worldwide, and P. hypophthalmus is a food staple in the Mekong area. However, genetic information about the culture stock, is unavailable for breeding improvement, although genetics of the channel catfish, Ictalurus punctatus, has been reported. To acquire genome sequence data as a useful resource for marker-assisted breeding, we decoded a draft genome of P. hypophthalmus and performed comparative analyses. Results Using the Illumina platform, we obtained both nuclear and mitochondrial DNA sequences. Molecular phylogeny using the mitochondrial genome confirmed that P. hypophthalmus is a member of the family Pangasiidae and is nested within a clade including the families Cranoglanididae and Ictaluridae. The nuclear genome was estimated at approximately 700 Mb, assembled into 568 scaffolds with an N50 of 14.29 Mbp, and was estimated to contain ~ 28,600 protein-coding genes, comparable to those of channel catfish and zebrafish. Interestingly, zebrafish produce gadusol, but genes for biosynthesis of this sunscreen compound have been lost from catfish genomes. The differences in gene contents between these two catfishes were found in genes for vitamin D-binding protein and cytosolic phospholipase A2, which have lost only in channel catfish. The Hox cluster in catfish genomes comprised seven paralogous groups, similar to that of zebrafish, and comparative analysis clarified catfish lineage-specific losses of A5a, B10a, and A11a. Genes for insulin-like growth factor (IGF) signaling were conserved between the two catfish genomes. In addition to identification of MHC class I and sex determination-related gene loci, the hypothetical chromosomes by comparison with the channel catfish demonstrated the usefulness of the striped catfish genome as a marker resource. Conclusions We developed genomic resources for the striped catfish. Possible conservation of genes for development and marker candidates were confirmed by comparing the assembled genome to that of a model fish, Danio rerio, and to channel catfish. Since the catfish genomic constituent resembles that of zebrafish, it is likely that zebrafish data for gene functions is applicable to striped catfish as well. Electronic supplementary material The online version of this article (10.1186/s12864-018-5079-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Oanh T P Kim
- Institute of Genome Research, Vietnam Academy of Science and Technology, Cau Giay, Hanoi, Vietnam.
| | - Phuong T Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, Cau Giay, Hanoi, Vietnam
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Thuy T B Vo
- Institute of Genome Research, Vietnam Academy of Science and Technology, Cau Giay, Hanoi, Vietnam
| | - Jun Inoue
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.,Present address: Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, 277-8564, Japan
| | - Binh T N Le
- Institute of Genome Research, Vietnam Academy of Science and Technology, Cau Giay, Hanoi, Vietnam
| | - Koki Nishitsuji
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Miyuki Kanda
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Vu H Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, Cau Giay, Hanoi, Vietnam
| | - Hai V Nong
- Institute of Genome Research, Vietnam Academy of Science and Technology, Cau Giay, Hanoi, Vietnam
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
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Motone K, Takagi T, Aburaya S, Aoki W, Miura N, Minakuchi H, Takeyama H, Nagasaki Y, Shinzato C, Ueda M. Protection of Coral Larvae from Thermally Induced Oxidative Stress by Redox Nanoparticles. Mar Biotechnol (NY) 2018; 20:542-548. [PMID: 29705864 DOI: 10.1007/s10126-018-9825-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 04/03/2018] [Indexed: 06/08/2023]
Abstract
Coral reefs are one of the most biologically diverse and economically important ecosystems on earth. However, the destruction of coral reefs has been reported worldwide owing to rising seawater temperature associated with global warming. In this study, we investigated the potential of a redox nanoparticle (RNPO) to scavenge reactive oxygen species (ROS), which are overproduced under heat stress and play a crucial role in causing coral mortality. When reef-building coral (Acropora tenuis) larvae, without algal symbionts, were exposed to thermal stress at 33 °C, RNPO treatment significantly increased the survival rate. Proteome analysis of coral larvae was performed using nano-liquid chromatography-tandem mass spectrometry for the first time. The results revealed that several proteins related to ROS-induced oxidative stress were specifically identified in A. tenuis larvae without RNPO treatment, whereas these proteins were absent in RNPO-treated larvae, which suggested that RNPO effectively scavenged ROS from A. tenuis larvae. Results from this study indicate that RNPO treatment can reduce ROS in aposymbiotic coral larvae and would be a promising approach for protecting corals from thermal stress.
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Affiliation(s)
- Keisuke Motone
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
- Japan Society for the Promotion of Science, Kyoto, 606-8502, Japan
| | - Toshiyuki Takagi
- Japan Society for the Promotion of Science, Kyoto, 606-8502, Japan
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan
| | - Shunsuke Aburaya
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
- Japan Society for the Promotion of Science, Kyoto, 606-8502, Japan
| | - Wataru Aoki
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Natsuko Miura
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | | | - Haruko Takeyama
- Faculty of Science and Engineering, Waseda University, Tokyo, 162-0056, Japan
| | - Yukio Nagasaki
- Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba, 305-8573, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, 904-0495, Japan
| | - Mitsuyoshi Ueda
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
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Campbell MA, Sado T, Shinzato C, Koyanagi R, Okamoto M, Miya M. Multilocus phylogenetic analysis of the first molecular data from the rare and monotypic Amarsipidae places the family within the Pelagia and highlights limitations of existing data sets in resolving pelagian interrelationships. Mol Phylogenet Evol 2018. [DOI: 10.1016/j.ympev.2018.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Shoguchi E, Beedessee G, Tada I, Hisata K, Kawashima T, Takeuchi T, Arakaki N, Fujie M, Koyanagi R, Roy MC, Kawachi M, Hidaka M, Satoh N, Shinzato C. Two divergent Symbiodinium genomes reveal conservation of a gene cluster for sunscreen biosynthesis and recently lost genes. BMC Genomics 2018; 19:458. [PMID: 29898658 PMCID: PMC6001144 DOI: 10.1186/s12864-018-4857-9] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/06/2018] [Indexed: 11/10/2022] Open
Abstract
Background The marine dinoflagellate, Symbiodinium, is a well-known photosynthetic partner for coral and other diverse, non-photosynthetic hosts in subtropical and tropical shallows, where it comprises an essential component of marine ecosystems. Using molecular phylogenetics, the genus Symbiodinium has been classified into nine major clades, A-I, and one of the reported differences among phenotypes is their capacity to synthesize mycosporine-like amino acids (MAAs), which absorb UV radiation. However, the genetic basis for this difference in synthetic capacity is unknown. To understand genetics underlying Symbiodinium diversity, we report two draft genomes, one from clade A, presumed to have been the earliest branching clade, and the other from clade C, in the terminal branch. Results The nuclear genome of Symbiodinium clade A (SymA) has more gene families than that of clade C, with larger numbers of organelle-related genes, including mitochondrial transcription terminal factor (mTERF) and Rubisco. While clade C (SymC) has fewer gene families, it displays specific expansions of repeat domain-containing genes, such as leucine-rich repeats (LRRs) and retrovirus-related dUTPases. Interestingly, the SymA genome encodes a gene cluster for MAA biosynthesis, potentially transferred from an endosymbiotic red alga (probably of bacterial origin), while SymC has completely lost these genes. Conclusions Our analysis demonstrates that SymC appears to have evolved by losing gene families, such as the MAA biosynthesis gene cluster. In contrast to the conservation of genes related to photosynthetic ability, the terminal clade has suffered more gene family losses than other clades, suggesting a possible adaptation to symbiosis. Overall, this study implies that Symbiodinium ecology drives acquisition and loss of gene families. Electronic supplementary material The online version of this article (10.1186/s12864-018-4857-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
| | - Girish Beedessee
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Ipputa Tada
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.,Present address: Department of Genetics, School of Life Science, The Graduate University for Advanced Studies, 1111, Yata, Mishima-shi, Shizuoka, 411-8540, Japan
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Takeshi Kawashima
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.,Present address: Center for Information Biology, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Takeshi Takeuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Nana Arakaki
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Manabu Fujie
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Ryo Koyanagi
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Michael C Roy
- Instrumental Analysis Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Masanobu Kawachi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, 305-8506, Japan
| | - Michio Hidaka
- Department of Chemistry, Biology and Marine Science, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan. .,Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwanoha, Kashiwa, 277-8564, Japan.
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Hamada M, Schröder K, Bathia J, Kürn U, Fraune S, Khalturina M, Khalturin K, Shinzato C, Satoh N, Bosch TC. Metabolic co-dependence drives the evolutionarily ancient Hydra-Chlorella symbiosis. eLife 2018; 7:35122. [PMID: 29848439 PMCID: PMC6019070 DOI: 10.7554/elife.35122] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/26/2018] [Indexed: 11/13/2022] Open
Abstract
Many multicellular organisms rely on symbiotic associations for support of metabolic activity, protection, or energy. Understanding the mechanisms involved in controlling such interactions remains a major challenge. In an unbiased approach we identified key players that control the symbiosis between Hydra viridissima and its photosynthetic symbiont Chlorella sp. A99. We discovered significant up-regulation of Hydra genes encoding a phosphate transporter and glutamine synthetase suggesting regulated nutrition supply between host and symbionts. Interestingly, supplementing the medium with glutamine temporarily supports in vitro growth of the otherwise obligate symbiotic Chlorella, indicating loss of autonomy and dependence on the host. Genome sequencing of Chlorella sp. A99 revealed a large number of amino acid transporters and a degenerated nitrate assimilation pathway, presumably as consequence of the adaptation to the host environment. Our observations portray ancient symbiotic interactions as a codependent partnership in which exchange of nutrients appears to be the primary driving force.
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Affiliation(s)
- Mayuko Hamada
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.,Ushimado Marine Institute, Okayama University, Okayama, Japan
| | - Katja Schröder
- Interdisciplinary Research Center, Kiel Life Science, Kiel University, Kiel, Germany.,Zoological Institute, Kiel Life Science, Kiel University, Kiel, Germany
| | - Jay Bathia
- Interdisciplinary Research Center, Kiel Life Science, Kiel University, Kiel, Germany.,Zoological Institute, Kiel Life Science, Kiel University, Kiel, Germany
| | - Ulrich Kürn
- Interdisciplinary Research Center, Kiel Life Science, Kiel University, Kiel, Germany.,Zoological Institute, Kiel Life Science, Kiel University, Kiel, Germany
| | - Sebastian Fraune
- Interdisciplinary Research Center, Kiel Life Science, Kiel University, Kiel, Germany.,Zoological Institute, Kiel Life Science, Kiel University, Kiel, Germany
| | - Mariia Khalturina
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Konstantin Khalturin
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.,Atmosphere and Ocean Research Institute, The University of Tokyo, Tokyo, Japan
| | - Nori Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Thomas Cg Bosch
- Interdisciplinary Research Center, Kiel Life Science, Kiel University, Kiel, Germany.,Zoological Institute, Kiel Life Science, Kiel University, Kiel, Germany
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Guzman C, Shinzato C, Lu TM, Conaco C. Transcriptome analysis of the reef-building octocoral, Heliopora coerulea. Sci Rep 2018; 8:8397. [PMID: 29849113 PMCID: PMC5976621 DOI: 10.1038/s41598-018-26718-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 05/09/2018] [Indexed: 01/15/2023] Open
Abstract
The blue coral, Heliopora coerulea, is a reef-building octocoral that prefers shallow water and exhibits optimal growth at a temperature close to that which causes bleaching in scleractinian corals. To better understand the molecular mechanisms underlying its biology and ecology, we generated a reference transcriptome for H. coerulea using next-generation sequencing. Metatranscriptome assembly yielded 90,817 sequences of which 71% (64,610) could be annotated by comparison to public databases. The assembly included transcript sequences from both the coral host and its symbionts, which are related to the thermotolerant C3-Gulf ITS2 type Symbiodinium. Analysis of the blue coral transcriptome revealed enrichment of genes involved in stress response, including heat-shock proteins and antioxidants, as well as genes participating in signal transduction and stimulus response. Furthermore, the blue coral possesses homologs of biomineralization genes found in other corals and may use a biomineralization strategy similar to that of scleractinians to build its massive aragonite skeleton. These findings thus offer insights into the ecology of H. coerulea and suggest gene networks that may govern its interactions with its environment.
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Affiliation(s)
- Christine Guzman
- Marine Science Institute, College of Science, University of the Philippines, Diliman, Quezon City, 1101, Philippines.,Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Chuya Shinzato
- Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, 277-8564, Japan
| | - Tsai-Ming Lu
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Cecilia Conaco
- Marine Science Institute, College of Science, University of the Philippines, Diliman, Quezon City, 1101, Philippines.
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Takeuchi T, Plasseraud L, Ziegler-Devin I, Brosse N, Shinzato C, Satoh N, Marin F. Biochemical characterization of the skeletal matrix of the massive coral, Porites australiensis - The saccharide moieties and their localization. J Struct Biol 2018; 203:219-229. [PMID: 29859330 DOI: 10.1016/j.jsb.2018.05.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 05/28/2018] [Accepted: 05/29/2018] [Indexed: 02/01/2023]
Abstract
To construct calcium carbonate skeletons of sophisticated architecture, scleractinian corals secrete an extracellular skeletal organic matrix (SOM) from aboral ectodermal cells. The SOM, which is composed of proteins, saccharides, and lipids, performs functions critical for skeleton formation. Even though polysaccharides constitute the major component of the SOM, its contribution to coral skeleton formation is poorly understood. To this end, we analyzed the SOM of the massive colonial coral, Porites australiensis, the skeleton of which has drawn great research interest because it records environmental conditions throughout the life of the colony. The coral skeleton was extensively cleaned, decalcified with acetic acid, and organic fractions were separated based on solubility. These fractions were analyzed using various techniques, including SDS-PAGE, FT-IR, in vitro crystallization, CHNS analysis, chromatography analysis of monosaccharide and enzyme-linked lectin assay (ELLA). We confirmed the acidic nature of SOM and the presence of sulphate, which is thought to initiate CaCO3 crystallization. In order to analyze glycan structures, we performed ELLA on the soluble SOM for the first time and found that it exhibits strong specificity to Datura stramonium lectin (DSL). Furthermore, using biotinylated DSL with anti-biotin antibody conjugated to nanogold, in situ localization of DSL-binding polysaccharides in the P. australiensis skeleton was performed. Signals were distributed on the surfaces of fiber-like crystals of the skeleton, suggesting that polysaccharides may modulate crystal shape. Our study emphasizes the importance of sugar moieties in biomineralization of scleractinian corals.
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Affiliation(s)
- Takeshi Takeuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
| | - Laurent Plasseraud
- Institut de Chimie Moléculaire de l'Université de Bourgogne, UMR CNRS 6302, Faculté des Sciences Mirande, Université de Bourgogne - Franche-Comté (UBFC), Dijon, France
| | - Isabelle Ziegler-Devin
- LERMAB, Faculté des Sciences & Technologies -Campus Aiguillettes, Université de Lorraine, Vandœuvre-Lès-Nancy, France
| | - Nicolas Brosse
- LERMAB, Faculté des Sciences & Technologies -Campus Aiguillettes, Université de Lorraine, Vandœuvre-Lès-Nancy, France
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan; Department of Marine Bioscience Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwanoha, Kashiwa-shi, Chiba 277-8564, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Frédéric Marin
- UMR CNRS 6282 Biogéosciences, Bâtiment des Sciences Gabriel, Université de Bourgogne - Franche-Comté (UBFC), Dijon, France
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Affiliation(s)
- Yuna Zayasu
- Marine Genomics Unit; Okinawa Institute of Science and Technology Graduate University; 1919-1 Tancha, Onna-son, Okinawa, 904-0495 Japan
| | - Noriyuki Satoh
- Marine Genomics Unit; Okinawa Institute of Science and Technology Graduate University; 1919-1 Tancha, Onna-son, Okinawa, 904-0495 Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute; The University of Tokyo; Chiba, 277-8564 Japan
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Hall MR, Kocot KM, Baughman KW, Fernandez-Valverde SL, Gauthier MEA, Hatleberg WL, Krishnan A, McDougall C, Motti CA, Shoguchi E, Wang T, Xiang X, Zhao M, Bose U, Shinzato C, Hisata K, Fujie M, Kanda M, Cummins SF, Satoh N, Degnan SM, Degnan BM. The crown-of-thorns starfish genome as a guide for biocontrol of this coral reef pest. Nature 2017; 544:231-234. [PMID: 28379940 DOI: 10.1038/nature22033] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 03/05/2017] [Indexed: 01/02/2023]
Abstract
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.
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Affiliation(s)
- Michael R Hall
- Australian Institute of Marine Science (AIMS), Cape Ferguson, Townsville, Queensland 4810, Australia
| | - Kevin M Kocot
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Kenneth W Baughman
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Selene L Fernandez-Valverde
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Marie E A Gauthier
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - William L Hatleberg
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Arunkumar Krishnan
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Carmel McDougall
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Cherie A Motti
- Australian Institute of Marine Science (AIMS), Cape Ferguson, Townsville, Queensland 4810, Australia
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Tianfang Wang
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Xueyan Xiang
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Min Zhao
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia.,Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Utpal Bose
- Australian Institute of Marine Science (AIMS), Cape Ferguson, Townsville, Queensland 4810, Australia.,Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Manabu Fujie
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Miyuki Kanda
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Scott F Cummins
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Sandie M Degnan
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Bernard M Degnan
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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Campbell MA, Nielsen JG, Sado T, Shinzato C, Kanda M, Satoh TP, Miya M. Evolutionary affinities of the unfathomable Parabrotulidae: Molecular data indicate placement of Parabrotula within the family Bythitidae, Ophidiiformes. Mol Phylogenet Evol 2017; 109:337-342. [PMID: 28185947 DOI: 10.1016/j.ympev.2017.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/30/2017] [Accepted: 02/02/2017] [Indexed: 11/28/2022]
Abstract
Fishes are widely diverse in shape and body size and can quite rapidly undergo these changes. Consequently, some relationships are not clearly resolved with morphological analyses. In the case of fishes of small body size, informative characteristics can be absent due to simplification of body structures. The Parabrotulidae, a small family of diminutive body size consisting of two genera and three species has most recently been classified as either a perciform within the suborder Zoarcoidei or an ophidiiform. Classification of parabrotulids as ophidiiforms has become predominant; however the Parabrotulidae has not yet been investigated in a molecular phylogenetic framework. We examine molecular data from ten genetic loci to more specifically place the Parabrotulidae within the fish tree of life. In a hypothesis testing framework, the Parabrotulidae as a zoarcoid taxon is rejected. Previous identity with zoarcoids due to the one fin ray for each vertebra being present, a characteristic for the Zoarcidae, appears to be an example of convergence. Our results indicate that parabrotulids are viviparous ophidiiforms within the family Bythitidae.
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Affiliation(s)
- Matthew A Campbell
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA; Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA 95060, USA.
| | - Jørgen G Nielsen
- Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Tetsuya Sado
- Department of Ecology and Environmental Sciences, Natural History Museum and Institute, Chiba 260-8682, Japan
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0485, Japan
| | - Miyuki Kanda
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0485, Japan
| | - Takashi P Satoh
- Seto Marine Biological Laboratory, Field Science Education and Research Center, Kyoto University, 459 Shirahama, Nishimuro, Wakayama 649-2211, Japan
| | - Masaki Miya
- Department of Ecology and Environmental Sciences, Natural History Museum and Institute, Chiba 260-8682, Japan.
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42
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Ohno Y, Iguchi A, Shinzato C, Gushi M, Inoue M, Suzuki A, Sakai K, Nakamura T. Calcification process dynamics in coral primary polyps as observed using a calcein incubation method. Biochem Biophys Rep 2017; 9:289-294. [PMID: 29114586 PMCID: PMC5627507 DOI: 10.1016/j.bbrep.2017.01.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 11/13/2016] [Accepted: 01/23/2017] [Indexed: 11/29/2022] Open
Abstract
Calcification processes are largely unknown in scleractinian corals. In this study, live confocal imaging was used to elucidate the spatiotemporal dynamics of the calcification process in aposymbiotic primary polyps of the coral species Acropora digitifera. The fluorophore calcein was used as a calcium deposition marker and a visible indicator of extracellular fluid distribution at the tissue-skeleton interface (subcalicoblastic medium, SCM) in primary polyp tissues. Under continuous incubation in calcein-containing seawater, initial crystallization and skeletal growth were visualized among the calicoblastic cells in live primary polyp tissues. Additionally, the distribution of calcein-stained SCM and contraction movements of the pockets of SCM were captured at intervals of a few minutes. Our experimental system provided several new insights into coral calcification, particularly as a first step in monitoring the relationship between cellular dynamics and calcification in vivo. Our study suggests that coral calcification initiates at intercellular spaces, a finding that may contribute to the general understanding of coral calcification processes. Coral calcification dynamics were observed by using aposymbiotic primary polyps. CaCO3 deposits during skeletal formation were visualized by calcein fluorescence labeling and time-lapse confocal microscopy. Periodic pulsing activity of the pockets of subcalicoblastic medium (SCM) was detected.
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Affiliation(s)
- Yoshikazu Ohno
- Marine and Environmental Sciences Course, Graduate School of Engineering and Science, University of the Ryukyus, Senbaru 1, Nishihara, Okinawa 903-0213, Japan
| | - Akira Iguchi
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, 905 Henoko, Nago, Okinawa 905-2192, Japan
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Mikako Gushi
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, 905 Henoko, Nago, Okinawa 905-2192, Japan
| | - Mayuri Inoue
- Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Okayama 700-8530, Japan
| | - Atsushi Suzuki
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Kazuhiko Sakai
- Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, 3422 Sesoko, Motobu, Okinawa 905-0227, Japan
| | - Takashi Nakamura
- Marine and Environmental Sciences Course, Graduate School of Engineering and Science, University of the Ryukyus, Senbaru 1, Nishihara, Okinawa 903-0213, Japan.,Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, 3422 Sesoko, Motobu, Okinawa 905-0227, Japan.,Japan Science and Technology Agency (JST)/Japan International Cooperation Agency (JICA) SATREPS, Tokyo, Japan
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Ohno Y, Iguchi A, Shinzato C, Inoue M, Suzuki A, Sakai K, Nakamura T. An aposymbiotic primary coral polyp counteracts acidification by active pH regulation. Sci Rep 2017; 7:40324. [PMID: 28098180 PMCID: PMC5241827 DOI: 10.1038/srep40324] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 12/05/2016] [Indexed: 01/12/2023] Open
Abstract
Corals build their skeletons using extracellular calcifying fluid located in the tissue-skeleton interface. However, the mechanism by which corals control the transport of calcium and other ions from seawater and the mechanism of constant alkalization of calcifying fluid are largely unknown. To address these questions, we performed direct pH imaging at calcification sites (subcalicoblastic medium, SCM) to visualize active pH upregulation in live aposymbiotic primary coral polyps treated with HCl-acidified seawater. Active alkalization was observed in all individuals using vital staining method while the movement of HPTS and Alexa Fluor to SCM suggests that certain ions such as H+ could diffuse via a paracellular pathway to SCM. Among them, we discovered acid-induced oscillations in the pH of SCM (pHSCM), observed in 24% of polyps examined. In addition, we discovered acid-induced pH up-regulation waves in 21% of polyps examined, which propagated among SCMs after exposure to acidified seawater. Our results showed that corals can regulate pHSCM more dynamically than was previously believed. These observations will have important implications for determining how corals regulate pHSCM during calcification. We propose that corals can sense ambient seawater pH via their innate pH-sensitive systems and regulate pHSCM using several unknown pH-regulating ion transporters that coordinate with multicellular signaling occurring in coral tissue.
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Affiliation(s)
- Yoshikazu Ohno
- Marine and Environmental Sciences Course, Graduate School of Engineering and Science, University of the Ryukyus, Senbaru 1, Nishihara, Okinawa 903-0213, Japan
| | - Akira Iguchi
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, 905 Henoko, Nago, Okinawa 905-2192, Japan
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Mayuri Inoue
- Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Okayama 700-8530, Japan
| | - Atsushi Suzuki
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Kazuhiko Sakai
- Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, 3422 Sesoko, Motobu, Okinawa 905-0227, Japan
| | - Takashi Nakamura
- Marine and Environmental Sciences Course, Graduate School of Engineering and Science, University of the Ryukyus, Senbaru 1, Nishihara, Okinawa 903-0213, Japan
- Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, 3422 Sesoko, Motobu, Okinawa 905-0227, Japan
- Japan Science and Technology Agency (JST)/Japan International Cooperation Agency (JICA) SATREPS, Tokyo, Japan
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Nishitsuji K, Arimoto A, Iwai K, Sudo Y, Hisata K, Fujie M, Arakaki N, Kushiro T, Konishi T, Shinzato C, Satoh N, Shoguchi E. A draft genome of the brown alga, Cladosiphon okamuranus, S-strain: a platform for future studies of 'mozuku' biology. DNA Res 2016; 23:561-570. [PMID: 27501718 PMCID: PMC5144679 DOI: 10.1093/dnares/dsw039] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 06/29/2016] [Indexed: 11/15/2022] Open
Abstract
The brown alga, Cladosiphon okamuranus (Okinawa mozuku), is economically one of the most important edible seaweeds, and is cultivated for market primarily in Okinawa, Japan. C. okamuranus constitutes a significant source of fucoidan, which has various physiological and biological activities. To facilitate studies of seaweed biology, we decoded the draft genome of C. okamuranus S-strain. The genome size of C. okamuranus was estimated as ∼140 Mbp, smaller than genomes of two other brown algae, Ectocarpus siliculosus and Saccharina japonica Sequencing with ∼100× coverage yielded an assembly of 541 scaffolds with N50 = 416 kbp. Together with transcriptomic data, we estimated that the C. okamuranus genome contains 13,640 protein-coding genes, approximately 94% of which have been confirmed with corresponding mRNAs. Comparisons with the E. siliculosus genome identified a set of C. okamuranus genes that encode enzymes involved in biosynthetic pathways for sulfated fucans and alginate biosynthesis. In addition, we identified C. okamuranus genes for enzymes involved in phlorotannin biosynthesis. The present decoding of the Cladosiphon okamuranus genome provides a platform for future studies of mozuku biology.
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Affiliation(s)
- Koki Nishitsuji
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Asuka Arimoto
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Kenji Iwai
- Okinawa Prefectural Fisheries Research and Extension Center, Itoman, Okinawa 901-0354, Japan
| | - Yusuke Sudo
- Okinawa Prefectural Fisheries Research and Extension Center, Itoman, Okinawa 901-0354, Japan
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Manabu Fujie
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Nana Arakaki
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Tetsuo Kushiro
- School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Teruko Konishi
- Department of Bioscience and Biotechnology, Faculty of Agriculture, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
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Yasuoka Y, Shinzato C, Satoh N. The Mesoderm-Forming Gene brachyury Regulates Ectoderm-Endoderm Demarcation in the Coral Acropora digitifera. Curr Biol 2016; 26:2885-2892. [PMID: 27693135 DOI: 10.1016/j.cub.2016.08.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 07/25/2016] [Accepted: 08/04/2016] [Indexed: 12/27/2022]
Abstract
Blastoporal expression of the T-box transcription factor gene brachyury is conserved in most metazoans [1, 2]. Its role in mesoderm formation has been intensively studied in vertebrates [3-6]. However, its fundamental function near the blastopore is poorly understood in other phyla. Cnidarians are basal metazoans that are important for understanding evolution of metazoan body plans [7, 8]. Because they lack mesoderm, they have been used to investigate the evolutionary origins of mesoderm [1, 9-11]. Here, we focus on corals, a primitive clade of cnidarians that diverged from sea anemones ∼500 mya [12]. We developed a microinjection method for coral eggs to examine Brachyury functions during embryogenesis of the scleractinian coral, Acropora digitifera. Because Acropora embryos undergo pharynx formation after the blastopore closes completely [13-15], they are useful to understand Brachyury functions in gastrulation movement and pharynx formation. We show that blastoporal expression of brachyury is directly activated by Wnt/β-catenin signaling in the ectoderm of coral embryos, indicating that the regulatory axis from Wnt/β-catenin signaling to brachyury is highly conserved among eumetazoans. Loss-of-function analysis demonstrated that Brachyury is required for pharynx formation but not for gastrulation movement. Genome-wide transcriptome analysis demonstrated that genes positively regulated by Brachyury are expressed in the ectoderm of Acropora gastrulae, while negatively regulated genes are in endoderm. Therefore, germ layer demarcation around the blastopore appears to be the evolutionarily conserved role of Brachyury during gastrulation. Compared with Brachyury functions in vertebrate mesoderm-ectoderm and mesoderm-endoderm demarcation [4-6], our results suggest that the vertebrate-type mesoderm may have originated from brachyury-expressing ectoderm adjacent to endoderm.
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Affiliation(s)
- Yuuri Yasuoka
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan.
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
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Zayasu Y, Nakajima Y, Sakai K, Suzuki G, Satoh N, Shinzato C. Unexpectedly complex gradation of coral population structure in the Nansei Islands, Japan. Ecol Evol 2016; 6:5491-505. [PMID: 27551399 PMCID: PMC4984520 DOI: 10.1002/ece3.2296] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/08/2016] [Accepted: 06/10/2016] [Indexed: 12/11/2022] Open
Abstract
To establish effective locations and sizes of potential protected areas for reef ecosystems, detailed information about source and sink relationships between populations is critical, especially in archipelagic regions. Therefore, we assessed population structure and genetic diversity of Acropora tenuis, one of the dominant stony coral species in the Pacific, using 13 microsatellite markers to investigate 298 colonies from 15 locations across the Nansei Islands in southwestern Japan. Genetic diversity was not significant among sampling locations, even in possibly peripheral locations. In addition, our results showed that there are at least two populations of A. tenuis in the study area. The level of genetic differentiation between these populations was relatively low, but significant between many pairs of sampling locations. Directions of gene flow, which were estimated using a coalescence-based approach, suggest that gene flow not only occurs from south to north, but also from north to south in various locations. Consequently, the Yaeyama Islands and the Amami Islands are potential northern and southern sources of corals. On the other hand, the Miyako Islands and west central Okinawa Island are potential sink populations. The Kerama Islands and the vicinity of Taketomi Island are potential contact points of genetic subdivision of coral populations in the Nansei Islands. We found that genetic population structure of A. tenuis in the Nansei Islands is more complex than previously thought. These cryptic populations are very important for preserving genetic diversity and should be maintained.
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Affiliation(s)
- Yuna Zayasu
- Marine Genomics UnitOkinawa Institute of Science and Technology Graduate University1919‐1 TanchaOnna‐sonOkinawa904‐0405Japan
| | - Yuichi Nakajima
- Marine Biophysics UnitOkinawa Institute of Science and Technology Graduate University1919‐1 TanchaOnna‐sonOkinawa904‐0405Japan
| | - Kazuhiko Sakai
- Sesoko StationUniversity of the Ryukyus3422 SesokoMotobuOkinawa905‐0227Japan
| | - Go Suzuki
- Ishigaki Tropical StationSeikai National Fisheries Research InstituteFisheries Research Agency148‐446 Fukai‐otaIshigakiOkinawa907‐0451Japan
| | - Noriyuki Satoh
- Marine Genomics UnitOkinawa Institute of Science and Technology Graduate University1919‐1 TanchaOnna‐sonOkinawa904‐0405Japan
| | - Chuya Shinzato
- Marine Genomics UnitOkinawa Institute of Science and Technology Graduate University1919‐1 TanchaOnna‐sonOkinawa904‐0405Japan
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Takeuchi T, Yamada L, Shinzato C, Sawada H, Satoh N. Stepwise Evolution of Coral Biomineralization Revealed with Genome-Wide Proteomics and Transcriptomics. PLoS One 2016; 11:e0156424. [PMID: 27253604 PMCID: PMC4890752 DOI: 10.1371/journal.pone.0156424] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/14/2016] [Indexed: 11/19/2022] Open
Abstract
Despite the importance of stony corals in many research fields related to global issues, such as marine ecology, climate change, paleoclimatogy, and metazoan evolution, very little is known about the evolutionary origin of coral skeleton formation. In order to investigate the evolution of coral biomineralization, we have identified skeletal organic matrix proteins (SOMPs) in the skeletal proteome of the scleractinian coral, Acropora digitifera, for which large genomic and transcriptomic datasets are available. Scrupulous gene annotation was conducted based on comparisons of functional domain structures among metazoans. We found that SOMPs include not only coral-specific proteins, but also protein families that are widely conserved among cnidarians and other metazoans. We also identified several conserved transmembrane proteins in the skeletal proteome. Gene expression analysis revealed that expression of these conserved genes continues throughout development. Therefore, these genes are involved not only skeleton formation, but also in basic cellular functions, such as cell-cell interaction and signaling. On the other hand, genes encoding coral-specific proteins, including extracellular matrix domain-containing proteins, galaxins, and acidic proteins, were prominently expressed in post-settlement stages, indicating their role in skeleton formation. Taken together, the process of coral skeleton formation is hypothesized as: 1) formation of initial extracellular matrix between epithelial cells and substrate, employing pre-existing transmembrane proteins; 2) additional extracellular matrix formation using novel proteins that have emerged by domain shuffling and rapid molecular evolution and; 3) calcification controlled by coral-specific SOMPs.
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Affiliation(s)
- Takeshi Takeuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904–0495, Japan
- * E-mail:
| | - Lixy Yamada
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Sugashima, Toba, 517–0004, Japan
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904–0495, Japan
| | - Hitoshi Sawada
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Sugashima, Toba, 517–0004, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904–0495, Japan
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Bhattacharya D, Agrawal S, Aranda M, Baumgarten S, Belcaid M, Drake JL, Erwin D, Foret S, Gates RD, Gruber DF, Kamel B, Lesser MP, Levy O, Liew YJ, MacManes M, Mass T, Medina M, Mehr S, Meyer E, Price DC, Putnam HM, Qiu H, Shinzato C, Shoguchi E, Stokes AJ, Tambutté S, Tchernov D, Voolstra CR, Wagner N, Walker CW, Weber AP, Weis V, Zelzion E, Zoccola D, Falkowski PG. Comparative genomics explains the evolutionary success of reef-forming corals. eLife 2016; 5. [PMID: 27218454 PMCID: PMC4878875 DOI: 10.7554/elife.13288] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 04/20/2016] [Indexed: 12/30/2022] Open
Abstract
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 For millions of years, reef-building stony corals have created extensive habitats for numerous marine plants and animals in shallow tropical seas. Stony corals consist of many small, tentacled animals called polyps. These polyps secrete a mineral called aragonite to create the reef – an external ‘skeleton’ that supports and protects the corals. Photosynthesizing algae live inside the cells of stony corals, and each species depends on the other to survive. The algae produce the coral’s main source of food, although they also produce some waste products that can harm the coral if they build up inside cells. If the oceans become warmer and more acidic, the coral are more likely to become stressed and expel the algae from their cells in a process known as coral bleaching. This makes the coral more likely to die or become diseased. Corals have survived previous periods of ocean warming, although it is not known how they evolved to do so. The evolutionary history of an organism can be traced by studying its genome – its complete set of DNA – and the RNA molecules encoded by these genes. Bhattacharya et al. performed this analysis for twenty stony coral species, and compared the resulting genome and RNA sequences with the genomes of other related marine organisms, such as sea anemones and sponges. In particular, Bhattacharya et al. examined “ortholog” groups of genes, which are present in different species and evolved from a common ancestral gene. This analysis identified the genes in the corals that encode the proteins responsible for constructing the aragonite skeleton. The coral genome also encodes a network of environmental sensors that coordinate how the polyps respond to temperature, light and acidity. Bhattacharya et al. also uncovered a variety of stress-related pathways, including those that detoxify the polyps of the damaging molecules generated by algae, and the pathways that enable the polyps to adapt to environmental stress. Many of these genes were recruited from other species in a process known as horizontal gene transfer. The oceans are expected to become warmer and more acidic in the coming centuries. Provided that humans do not physically destroy the corals’ habitats, the evidence found by Bhattacharya et al. suggests that the genome of the corals contains the diversity that will allow them to adapt to these new conditions. DOI:http://dx.doi.org/10.7554/eLife.13288.002
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Affiliation(s)
- Debashish Bhattacharya
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, United States.,Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, United States
| | - Shobhit Agrawal
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Manuel Aranda
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sebastian Baumgarten
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mahdi Belcaid
- Hawaii Institute of Marine Biology, Kaneohe, United States
| | - Jeana L Drake
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, United States
| | - Douglas Erwin
- Smithsonian Institution, National Museum of Natural History, Washington, United States
| | - Sylvian Foret
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Australia.,Research School of Biology, Australian National University, Canberra, Australia
| | - Ruth D Gates
- Hawaii Institute of Marine Biology, Kaneohe, United States
| | - David F Gruber
- American Museum of Natural History, Sackler Institute for Comparative Genomics, New York, United States.,Department of Natural Sciences, City University of New York, Baruch College and The Graduate Center, New York, United States
| | - Bishoy Kamel
- Department of Biology, Mueller Lab, Penn State University, University Park, United States
| | - Michael P Lesser
- School of Marine Science and Ocean Engineering, University of New Hampshire, Durham, United States
| | - Oren Levy
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gam, Israel
| | - Yi Jin Liew
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Matthew MacManes
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, United States
| | - Tali Mass
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, United States.,Marine Biology Department, The Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel, Israel
| | - Monica Medina
- Department of Biology, Mueller Lab, Penn State University, University Park, United States
| | - Shaadi Mehr
- American Museum of Natural History, Sackler Institute for Comparative Genomics, New York, United States.,Biological Science Department, State University of New York, College at Old Westbury, New York, United States
| | - Eli Meyer
- Department of Integrative Biology, Oregon State University, Corvallis, United States
| | - Dana C Price
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, United States
| | | | - Huan Qiu
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, United States
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Alexander J Stokes
- Laboratory of Experimental Medicine and Department of Cell and Molecular Biology, John A. Burns School of Medicine, Honolulu, United States.,Chaminade University, Honolulu, United States
| | | | - Dan Tchernov
- Marine Biology Department, The Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel, Israel
| | - Christian R Voolstra
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Nicole Wagner
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, United States
| | - Charles W Walker
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, United States
| | - Andreas Pm Weber
- Institute of Plant Biochemistry, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Virginia Weis
- Department of Integrative Biology, Oregon State University, Corvallis, United States
| | - Ehud Zelzion
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, United States
| | | | - Paul G Falkowski
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, United States.,Department of Earth and Planetary Sciences, Rutgers University, New Jersey, United States
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49
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Mohamed AR, Cumbo V, Harii S, Shinzato C, Chan CX, Ragan MA, Bourne DG, Willis BL, Ball EE, Satoh N, Miller DJ. The transcriptomic response of the coral
Acropora digitifera
to a competent
Symbiodinium
strain: the symbiosome as an arrested early phagosome. Mol Ecol 2016; 25:3127-41. [DOI: 10.1111/mec.13659] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 04/04/2016] [Accepted: 04/14/2016] [Indexed: 12/15/2022]
Affiliation(s)
- A. R. Mohamed
- ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville Qld 4811 Australia
- Comparative Genomics Centre and Department of Molecular and Cell Biology James Cook University Townsville Qld 4811 Australia
- Zoology Department Faculty of Science Benha University Benha 13518 Egypt
- AIMS@JCU Department of Molecular and Cell Biology Australian Institute of Marine Science James Cook University Townsville Qld 4811 Australia
| | - V. Cumbo
- ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville Qld 4811 Australia
- Department of Biological Sciences Macquarie University Sydney NSW 2109 Australia
| | - S. Harii
- Sesoko Station Tropical Biosphere Research Center University of the Ryukyus 3422 Sesoko Motobu Okinawa 905‐0227 Japan
| | - C. Shinzato
- Marine Genomics Unit Okinawa Institute of Science and Technology Promotion Corporation Onna Okinawa 904‐0412 Japan
| | - C. X. Chan
- ARC Centre of Excellence in Bioinformatics and Institute for Molecular Bioscience The University of Queensland Brisbane Qld 4072 Australia
| | - M. A. Ragan
- ARC Centre of Excellence in Bioinformatics and Institute for Molecular Bioscience The University of Queensland Brisbane Qld 4072 Australia
| | - D. G. Bourne
- Australian Institute for Marine Science PMB 3 Townsville Qld 4811 Australia
| | - B. L. Willis
- ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville Qld 4811 Australia
- Department of Marine Ecosystems and Impacts James Cook University Townsville Qld 4811 Australia
| | - E. E. Ball
- ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville Qld 4811 Australia
- Evolution, Ecology and Genetics Research School of Biology Australian National University Canberra ACT 0200 Australia
| | - N. Satoh
- Marine Genomics Unit Okinawa Institute of Science and Technology Promotion Corporation Onna Okinawa 904‐0412 Japan
| | - D. J. Miller
- ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville Qld 4811 Australia
- Comparative Genomics Centre and Department of Molecular and Cell Biology James Cook University Townsville Qld 4811 Australia
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50
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Nakajima Y, Shinzato C, Khalturina M, Nakamura M, Watanabe H, Satoh N, Mitarai S. The mitochondrial genome sequence of a deep-sea, hydrothermal vent limpet, Lepetodrilus nux, presents a novel vetigastropod gene arrangement. Mar Genomics 2016; 28:121-126. [PMID: 27102631 DOI: 10.1016/j.margen.2016.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 04/08/2016] [Accepted: 04/08/2016] [Indexed: 01/27/2023]
Abstract
While mitochondrial (mt) genomes are used extensively for comparative and evolutionary genomics, few mt genomes of deep-sea species, including hydrothermal vent species, have been determined. The Genus Lepetodrilus is a major deep-sea gastropod taxon that occurs in various deep-sea ecosystems. Using next-generation sequencing, we determined nearly the complete mitochondrial genome sequence of Lepetodrilus nux, which inhabits hydrothermal vents in the Okinawa Trough. The total length of the mitochondrial genome is 16,353bp, excluding the repeat region. It contains 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region, typical of most metazoan genomes. Compared with other vetigastropod mt genome sequences, L. nux employs a novel mt gene arrangement. Other novel arrangements have been identified in the vetigastropod, Fissurella volcano, and in Chrysomallon squamiferum, a neomphaline gastropod; however, all three gene arrangements are different, and Bayesian inference suggests that each lineage diverged independently. Our findings suggest that vetigastropod mt gene arrangements are more diverse than previously realized.
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Affiliation(s)
- Yuichi Nakajima
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Mariia Khalturina
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Masako Nakamura
- School of Marine Science and Technology, Tokai University, Shimizu, Shizuoka 424-8610, Japan
| | - Hiromi Watanabe
- Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa 237-0061, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Satoshi Mitarai
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
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