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Ke J, Yoshikuni Y. Multi-chassis engineering for heterologous production of microbial natural products. Curr Opin Biotechnol 2019; 62:88-97. [PMID: 31639618 DOI: 10.1016/j.copbio.2019.09.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/30/2019] [Accepted: 09/09/2019] [Indexed: 12/11/2022]
Abstract
Microbial genomes encode numerous biosynthetic gene clusters (BGCs) that may produce natural products with diverse applications in medicine, agriculture, the environment, and materials science. With the advent of genome sequencing and bioinformatics, heterologous expression of BGCs is of increasing interest in bioactive natural product (NP) discovery. However, this approach has had limited success because expression of BGCs relies heavily on the physiology of just a few commonly available host chassis. Expanding and diversifying the chassis portfolio for heterologous BGC expression may greatly increase the chances for successful NP production. In this review, we first discuss genetic and genome engineering technologies used to clone, modify, and transform BGCs into multiple strains and to engineer chassis strains. We then highlight studies that employed the multi-chassis approach successfully to optimize NP production, discover previously uncharacterized NPs, and better understand BGC function.
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Affiliation(s)
- Jing Ke
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA 94598, USA
| | - Yasuo Yoshikuni
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA 94598, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, IL 61801, USA; Global Institution for Collaborative Research and Education, Hokkaido University, Hokkaido, 060-8589, Japan.
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Improvement of the Pacific bluefin tuna (Thunnus orientalis) reference genome and development of male-specific DNA markers. Sci Rep 2019; 9:14450. [PMID: 31595011 PMCID: PMC6783451 DOI: 10.1038/s41598-019-50978-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 09/17/2019] [Indexed: 12/30/2022] Open
Abstract
The Pacific bluefin tuna, Thunnus orientalis, is a highly migratory species that is widely distributed in the North Pacific Ocean. Like other marine species, T. orientalis has no external sexual dimorphism; thus, identifying sex-specific variants from whole genome sequence data is a useful approach to develop an effective sex identification method. Here, we report an improved draft genome of T. orientalis and male-specific DNA markers. Combining PacBio long reads and Illumina short reads sufficiently improved genome assembly, with a 38-fold increase in scaffold contiguity (to 444 scaffolds) compared to the first published draft genome. Through analysing re-sequence data of 15 males and 16 females, 250 male-specific SNPs were identified from more than 30 million polymorphisms. All male-specific variants were male-heterozygous, suggesting that T. orientalis has a male heterogametic sex-determination system. The largest linkage disequilibrium block (3,174 bp on scaffold_064) contained 51 male-specific variants. PCR primers and a PCR-based sex identification assay were developed using these male-specific variants. The sex of 115 individuals (56 males and 59 females; sex was diagnosed by visual examination of the gonads) was identified with high accuracy using the assay. This easy, accurate, and practical technique facilitates the control of sex ratios in tuna farms. Furthermore, this method could be used to estimate the sex ratio and/or the sex-specific growth rate of natural populations.
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Yasuike M, Iwasaki Y, Nishiki I, Nakamura Y, Matsuura A, Yoshida K, Noda T, Andoh T, Fujiwara A. The yellowtail (Seriola quinqueradiata) genome and transcriptome atlas of the digestive tract. DNA Res 2018; 25:547-560. [PMID: 30329019 PMCID: PMC6191305 DOI: 10.1093/dnares/dsy024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 06/28/2018] [Indexed: 12/30/2022] Open
Abstract
Seriola quinqueradiata (yellowtail) is the most widely farmed and economically important fish in aquaculture in Japan. In this study, we used the genome of haploid yellowtail fish larvae for de novo assembly of whole-genome sequences, and built a high-quality draft genome for the yellowtail. The total length of the assembled sequences was 627.3 Mb, consisting of 1,394 scaffold sequences (>2 kb) with an N50 length of 1.43 Mb. A total of 27,693 protein-coding genes were predicted for the draft genome, and among these, 25,832 predicted genes (93.3%) were functionally annotated. Given our lack of knowledge of the yellowtail digestive system, and using the annotated draft genome as a reference, we conducted an RNA-Seq analysis of its three digestive organs (stomach, intestine and rectum). The RNA-Seq results highlighted the importance of certain genes in encoding proteolytic enzymes necessary for digestion and absorption in the yellowtail gastrointestinal tract, and this finding will accelerate development of formulated feeds for this species. Since this study offers comprehensive annotation of predicted protein-coding genes, it has potential broad application to our understanding of yellowtail biology and aquaculture.
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Affiliation(s)
- Motoshige Yasuike
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Yuki Iwasaki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Issei Nishiki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Yoji Nakamura
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Aiko Matsuura
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Kazunori Yoshida
- Goto Laboratory, Stock Enhancement and Aquaculture Division, Seikai National Fisheries Research Institute Japan Fisheries Research and Education Agency, Tamanoura-cho, Goto, Nagasaki, Japan
| | - Tsutomu Noda
- Goto Laboratory, Stock Enhancement and Aquaculture Division, Seikai National Fisheries Research Institute Japan Fisheries Research and Education Agency, Tamanoura-cho, Goto, Nagasaki, Japan
| | - Tadashi Andoh
- Stock Enhancement and Aquaculture Division, Seikai National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Nagasaki, Japan
| | - Atushi Fujiwara
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
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Insights into teleost sex determination from the Seriola dorsalis genome assembly. BMC Genomics 2018; 19:31. [PMID: 29310588 PMCID: PMC5759298 DOI: 10.1186/s12864-017-4403-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 12/19/2017] [Indexed: 12/15/2022] Open
Abstract
Background The assembly and annotation of a genome is a valuable resource for a species, with applications ranging from conservation genomics to gene discovery. Genomic resource development is especially important for species in culture, such as the California Yellowtail (Seriola dorsalis), the likely candidate for the establishment of commercial offshore aquaculture production in southern California. Genomic resource development for this species will improve the understanding of sex and other phenotypic traits, and allow for rapid increases in genetic improvement for and economic gain in culture production. Results We describe the assembly and annotation of the S. dorsalis genome, and present resequencing data from 45 male and 45 female wild-caught S. dorsalis used to identify a sex-determining region and marker in this species. The genome assembly captured approximately 93% of the total 685 MB genome with an average coverage depth of 180×. Using the assembled genome, resequencing data from the 90 fish were aligned to place boundaries on the sex-determining region. Sex-specific markers were developed based on a female-specific, 61 nucleotide deletion identified in that region. We hypothesize that Estradiol 17-beta-dehydrogenase is the putative sex-determining gene and propose a plausible genetic mechanism for ZW sex determination in S. dorsalis involving a female-specific deletion of a transcription factor binding motif that may be targeted by Sox3. Conclusions Understanding the mechanism of sex determination and development of assays to determine sex is critical both for management of wild fisheries and for development of efficient and sustainable aquaculture practices. In addition, this genome assembly for S. dorsalis will be a substantial resource for a variety of future research applications. Electronic supplementary material The online version of this article (10.1186/s12864-017-4403-1) contains supplementary material, which is available to authorized users.
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Kawase J, Aoki JY, Araki K. Constructing a 'Chromonome' of Yellowtail ( Seriola quinqueradiata) for Comparative Analysis of Chromosomal Rearrangements. J Genomics 2018; 6:9-19. [PMID: 29290830 PMCID: PMC5744233 DOI: 10.7150/jgen.23222] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 11/18/2017] [Indexed: 01/28/2023] Open
Abstract
To investigate chromosome evolution in fish species, we newly mapped 181 markers that allowed us to construct a yellowtail (Seriola quinqueradiata) radiation hybrid (RH) physical map with 1,713 DNA markers, which was far denser than a previous map, and we anchored the de novo assembled sequences onto the RH physical map. Finally, we mapped a total of 13,977 expressed sequence tags (ESTs) on a genome sequence assembly aligned with the physical map. Using the high-density physical map and anchored genome sequences, we accurately compared the yellowtail genome structure with the genome structures of five model fishes to identify characteristics of the yellowtail genome. Between yellowtail and Japanese medaka (Oryzias latipes), almost all regions of the chromosomes were conserved and some blocks comprising several markers were translocated. Using the genome information of the spotted gar (Lepisosteus oculatus) as a reference, we further documented syntenic relationships and chromosomal rearrangements that occurred during evolution in four other acanthopterygian species (Japanese medaka, zebrafish, spotted green pufferfish and three-spined stickleback). The evolutionary chromosome translocation frequency was 1.5-2-times higher in yellowtail than in medaka, pufferfish, and stickleback.
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Affiliation(s)
- Junya Kawase
- Department of Life Sciences, Graduate School of Bioresources, Mie University, Tsu city, Mie Prefecture, Japan
| | - Jun-Ya Aoki
- National Research Institute of Aquaculture, Fisheries Research Agency, Tamaki-cho, Mie Prefecture, Japan
| | - Kazuo Araki
- Department of Life Sciences, Graduate School of Bioresources, Mie University, Tsu city, Mie Prefecture, Japan.,National Research Institute of Aquaculture, Fisheries Research Agency, Tamaki-cho, Mie Prefecture, Japan
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Nakamoto M, Takeuchi Y, Akita K, Kumagai R, Suzuki J, Koyama T, Noda T, Yoshida K, Ozaki A, Araki K, Sakamoto T. A novel C-type lectin gene is a strong candidate gene for Benedenia disease resistance in Japanese yellowtail, Seriola quinqueradiata. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 76:361-369. [PMID: 28705457 DOI: 10.1016/j.dci.2017.07.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/08/2017] [Accepted: 07/08/2017] [Indexed: 06/07/2023]
Abstract
Little is known about mechanisms of resistance to parasitic diseases in marine finfish. Benedenia disease is caused by infection by the monogenean parasite Benedenia seriolae. Previous quantitative trait locus (QTL) analyses have identified a major QTL associated with resistance to Benedenia disease in linkage group Squ2 of the Japanese yellowtail/amberjack Seriola quinqueradiata. To uncover the bioregulatory mechanism of Benedenia disease resistance, complete Illumina sequencing of BAC clones carrying genomic DNA for the QTL region in linkage group Squ2 was performed to reveal a novel C-type lectin in this region. Expression of the mRNA of this C-type lectin was detected in skin tissue parasitized by B. seriolae. Scanning for single nucleotide polymorphisms (SNPs) uncovered a SNP in the C-type lectin/C-type lectin-like domain that was significantly associated with B. seriolae infection levels. These results strongly suggest that the novel C-type lectin gene controls resistance to Benedenia disease in Japanese yellowtails.
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Affiliation(s)
- Masatoshi Nakamoto
- Department of Aquatic Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Yusuke Takeuchi
- Department of Aquatic Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Kazuki Akita
- Department of Aquatic Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Ryo Kumagai
- Department of Aquatic Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Junpei Suzuki
- Department of Aquatic Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Takashi Koyama
- Department of Aquatic Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Tsutomu Noda
- Goto Laboratory of the Seikai National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Nagasaki 853-0508, Japan
| | - Kazunori Yoshida
- Goto Laboratory of the Seikai National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Nagasaki 853-0508, Japan
| | - Akiyuki Ozaki
- National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Mie 516-0193, Japan
| | - Kazuo Araki
- National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Mie 516-0193, Japan
| | - Takashi Sakamoto
- Department of Aquatic Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan.
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Nah HJ, Pyeon HR, Kang SH, Choi SS, Kim ES. Cloning and Heterologous Expression of a Large-sized Natural Product Biosynthetic Gene Cluster in Streptomyces Species. Front Microbiol 2017; 8:394. [PMID: 28360891 PMCID: PMC5350119 DOI: 10.3389/fmicb.2017.00394] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 02/24/2017] [Indexed: 12/14/2022] Open
Abstract
Actinomycetes family including Streptomyces species have been a major source for the discovery of novel natural products (NPs) in the last several decades thanks to their structural novelty, diversity and complexity. Moreover, recent genome mining approach has provided an attractive tool to screen potentially valuable NP biosynthetic gene clusters (BGCs) present in the actinomycetes genomes. Since many of these NP BGCs are silent or cryptic in the original actinomycetes, various techniques have been employed to activate these NP BGCs. Heterologous expression of BGCs has become a useful strategy to produce, reactivate, improve, and modify the pathways of NPs present at minute quantities in the original actinomycetes isolates. However, cloning and efficient overexpression of an entire NP BGC, often as large as over 100 kb, remain challenging due to the ineffectiveness of current genetic systems in manipulating large NP BGCs. This mini review describes examples of actinomycetes NP production through BGC heterologous expression systems as well as recent strategies specialized for the large-sized NP BGCs in Streptomyces heterologous hosts.
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Affiliation(s)
- Hee-Ju Nah
- Department of Biological Engineering, Inha University Incheon, South Korea
| | - Hye-Rim Pyeon
- Department of Biological Engineering, Inha University Incheon, South Korea
| | - Seung-Hoon Kang
- Department of Biological Engineering, Inha University Incheon, South Korea
| | - Si-Sun Choi
- Department of Biological Engineering, Inha University Incheon, South Korea
| | - Eung-Soo Kim
- Department of Biological Engineering, Inha University Incheon, South Korea
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Uchino T, Nakamura Y, Sekino M, Kai W, Fujiwara A, Yasuike M, Sugaya T, Fukuda H, Sano M, Sakamoto T. Constructing Genetic Linkage Maps Using the Whole Genome Sequence of Pacific Bluefin Tuna (<i>Thunnus orientalis</i>) and a Comparison of Chromosome Structure among Teleost Species. ACTA ACUST UNITED AC 2016. [DOI: 10.4236/abb.2016.72010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Koyama T, Ozaki A, Yoshida K, Suzuki J, Fuji K, Aoki JY, Kai W, Kawabata Y, Tsuzaki T, Araki K, Sakamoto T. Identification of Sex-Linked SNPs and Sex-Determining Regions in the Yellowtail Genome. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2015; 17:502-510. [PMID: 25975833 DOI: 10.1007/s10126-015-9636-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 04/15/2015] [Indexed: 06/04/2023]
Abstract
Unlike the conservation of sex-determining (SD) modes seen in most mammals and birds, teleost fishes exhibit a wide variety of SD systems and genes. Hence, the study of SD genes and sex chromosome turnover in fish is one of the most interesting topics in evolutionary biology. To increase resolution of the SD gene evolutionary trajectory in fish, identification of the SD gene in more fish species is necessary. In this study, we focused on the yellowtail, a species widely cultivated in Japan. It is a member of family Carangidae in which no heteromorphic sex chromosome has been observed, and no SD gene has been identified to date. By performing linkage analysis and BAC walking, we identified a genomic region and SNPs with complete linkage to yellowtail sex. Comparative genome analysis revealed the yellowtail SD region ancestral chromosome structure as medaka-fugu. Two inversions occurred in the yellowtail linage after it diverged from the yellowtail-medaka ancestor. An association study using wild yellowtails and the SNPs developed from BAC ends identified two SNPs that can reasonably distinguish the sexes. Therefore, these will be useful genetic markers for yellowtail breeding. Based on a comparative study, it was suggested that a PDZ domain containing the GIPC protein might be involved in yellowtail sex determination. The homomorphic sex chromosomes widely observed in the Carangidae suggest that this family could be a suitable marine fish model to investigate the early stages of sex chromosome evolution, for which our results provide a good starting point.
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Affiliation(s)
- Takashi Koyama
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7, Konan, Minato-ku, Tokyo, 108-8477, Japan
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Aoki JY, Kai W, Kawabata Y, Ozaki A, Yoshida K, Koyama T, Sakamoto T, Araki K. Second generation physical and linkage maps of yellowtail (Seriola quinqueradiata) and comparison of synteny with four model fish. BMC Genomics 2015; 16:406. [PMID: 26003112 PMCID: PMC4493941 DOI: 10.1186/s12864-015-1600-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 04/29/2015] [Indexed: 01/07/2023] Open
Abstract
Background Physical and linkage maps are important aids for the assembly of genome sequences, comparative analyses of synteny, and to search for candidate genes by quantitative trait locus analysis. Yellowtail, Seriola quinqueradiata, is an economically important species in Japanese aquaculture, and genetic information will be useful for DNA-assisted breeding. We report the construction of a second generation radiation hybrid map, its synteny analysis, and a second generation linkage map containing SNPs (single nucleotide polymorphisms) in yellowtail. Results Approximately 1.4 million reads were obtained from transcriptome sequence analysis derived from 11 tissues of one individual. To identify SNPs, cDNA libraries were generated from a pool of 500 whole juveniles, and the gills and kidneys of 100 adults. 9,356 putative SNPs were detected in 6,025 contigs, with a minor allele frequency ≥25%. The linkage and radiation hybrid maps were constructed based on these contig sequences. 2,081 markers, including 601 SNPs markers, were mapped onto the linkage map, and 1,532 markers were mapped in the radiation hybrid map. Conclusions The second generation linkage and physical maps were constructed using 6,025 contigs having SNP markers. These maps will aid the de novo assembly of sequencing reads, linkage studies and the identification of candidate genes related to important traits. The comparison of marker contigs in the radiation hybrid map indicated that yellowtail is evolutionarily closer to medaka than to green-spotted pufferfish, three-spined stickleback or zebrafish. The synteny analysis may aid studies of chromosomal evolution in yellowtail compared with model fish. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1600-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jun-ya Aoki
- National Research Institute of Aquaculture, Fisheries Research Agency, 224-1 Hiruta, Tamaki-cho, Watarai-gun, Mie, 519-0423, Japan.
| | - Wataru Kai
- National Research Institute of Aquaculture, Fisheries Research Agency, 224-1 Hiruta, Tamaki-cho, Watarai-gun, Mie, 519-0423, Japan.
| | - Yumi Kawabata
- National Research Institute of Aquaculture, Fisheries Research Agency, 224-1 Hiruta, Tamaki-cho, Watarai-gun, Mie, 519-0423, Japan.
| | - Akiyuki Ozaki
- National Research Institute of Aquaculture, Fisheries Research Agency, 422-1 Nakatsuhamaura, Minamiise-cho, Watarai-gun, Mie, 516-0193, Japan.
| | - Kazunori Yoshida
- Goto Laboratory, Seikai National Fisheries Research Institute, Fisheries Research Agency, 122-7, Nunoura, Tamanoura-cho, Goto, Nagasaki, 853-0508, Japan.
| | - Takashi Koyama
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan.
| | - Takashi Sakamoto
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan.
| | - Kazuo Araki
- National Research Institute of Aquaculture, Fisheries Research Agency, 224-1 Hiruta, Tamaki-cho, Watarai-gun, Mie, 519-0423, Japan.
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