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Matsuyama T, Miwa S, Mekata T, Kiryu I, Kuriyama I, Atsumi T, Itano T, Kawakami H. A novel birnavirus identified as the causative agent of summer atrophy of pearl oyster ( Pinctada fucata (Gould)). PeerJ 2024; 12:e17321. [PMID: 38708355 PMCID: PMC11067908 DOI: 10.7717/peerj.17321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 04/09/2024] [Indexed: 05/07/2024] Open
Abstract
The Akoya pearl oyster (Pinctada fucata (Gould)) is the most important species for pearl cultivation in Japan. Mass mortality of 0-year-old juvenile oysters and anomalies in adults, known as summer atrophy, have been observed in major pearl farming areas during the season when seawater temperatures exceed about 20 °C since 2019. In this study, we identified a novel birnavirus as the pathogen of summer atrophy and named it Pinctada birnavirus (PiBV). PiBV was first presumed to be the causative agent when it was detected specifically and frequently in the infected oysters in a comparative metatranscriptomics of experimentally infected and healthy pearl oysters. Subsequently, the symptoms of summer atrophy were reproduced by infection tests using purified PiBV. Infection of juvenile oysters with PiBV resulted in an increase in the PiBV genome followed by the atrophy of soft body and subsequent mortality. Immunostaining with a mouse antiserum against a recombinant PiBV protein showed that the virus antigen was localized mainly in the epithelial cells on the outer surface of the mantle. Although the phylogenetic analysis using maximum likelihood method placed PiBV at the root of the genus Entomobirnavirus, the identity of the bi-segmented, genomic RNA to that of known birnaviruses at the full-length amino acid level was low, suggesting that PiBV forms a new genus. The discovery of PiBV will be the basis for research to control this emerging disease.
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Affiliation(s)
- Tomomasa Matsuyama
- Japan Fisheries Research and Education Agency, Pathology Division, Aquaculture Research Department, Fisheries Technology Institute, Minami-Ise, Mie, Japan
| | - Satoshi Miwa
- Japan Fisheries Research and Education Agency, Pathology Division, Aquaculture Research Department, Fisheries Technology Institute, Minami-Ise, Mie, Japan
| | - Tohru Mekata
- Japan Fisheries Research and Education Agency, Pathology Division, Aquaculture Research Department, Fisheries Technology Institute, Minami-Ise, Mie, Japan
- Okayama University of Science, Department of Veterinary Medicine, Faculty of Veterinary Medicine, Imabari, Ehime, Japan
| | - Ikunari Kiryu
- Japan Fisheries Research and Education Agency, Pathology Division, Aquaculture Research Department, Fisheries Technology Institute, Minami-Ise, Mie, Japan
| | - Isao Kuriyama
- Mie Prefecture Fisheries Research Institute, Shima, Mie, Japan
- Mie Prefectural Government Department of Agriculture, Forestry and Fisheries, Tsu, Mie, Japan
| | - Takashi Atsumi
- Mie Prefecture Fisheries Research Institute, Shima, Mie, Japan
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Sakatoku A, Hatano K, Takada K, Shimizu R, Suzuki T, Seki M, Suzuki N, Tanaka D, Nakamura S, Isshiki T. Purification and Characterization of the Lecithin-Dependent Thermolabile Hemolysin Vhe1 from the Vibrio sp. Strain MA3 Associated with Mass Mortality of Pearl Oyster (Pinctada fucata). Curr Microbiol 2023; 80:288. [PMID: 37458864 DOI: 10.1007/s00284-023-03409-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023]
Abstract
In a previous study, we isolated a Vibrio sp. strain MA3 and its virulence factor, a hemolysin encoded by vhe1. This strain is associated with mass mortalities of the pearl oyster Pinctada fucata. In the present study, the vhe1 gene from strain MA3 was cloned and its encoded product was purified and characterized. Our results show that the vhe1 gene encodes a protein of 417 amino acids with an estimated molecular mass of 47.2 kDa and a pI of 5.14. The deduced protein, Vhe1, was found to contain the conserved amino acid sequence (GDSL motif) of the hydrolase/esterase superfamily and five conserved blocks characteristic of SGNH hydrolases. A BLAST homology search indicated that Vhe1 belongs the lecithin-dependent hemolysin/thermolabile hemolysin (LDH/TLH) family. In activity analyses, the optimal temperature for both the hemolytic and phospholipase activities of Vhe1 was 50 °C. Vhe1 hemolytic activity and phospholipase activity were highest at pH 8.5 and pH 8.0, respectively. However, both enzymatic activities sharply decreased at high temperature (> 50 °C) and pH < 7.0. Compared with previously reported hemolysins, Vhe1 appeared to be more thermal- and pH-labile. Both its hemolytic activity and phospholipase activity were significantly inhibited by CuCl2, CdCl2, ZnCl2, and NiCl2, and slightly inhibited by MnCl2 and CoCl2. Vhe1 showed higher phospholipase activity toward medium-chain fatty acids (C8-C12) than toward shorter- and longer-chain fatty acids. These results accumulate knowledge about the LDH/TLH of V. alginolyticus, which detailed characterization has not been reported, and contribute to solving of the mass mortality of pearl oyster.
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Affiliation(s)
- Akihiro Sakatoku
- School of Science, Academic Assembly, University of Toyama, Toyama, 930-8555, Japan.
| | - Kaito Hatano
- Noto Marine Laboratory, Institute of Nature and Environmental Technology, Kanazawa University, Ogi, Noto‑cho, Ishikawa, 927‑0553, Japan
| | - Kosei Takada
- School of Science, Academic Assembly, University of Toyama, Toyama, 930-8555, Japan
| | - Ryota Shimizu
- School of Science, Academic Assembly, University of Toyama, Toyama, 930-8555, Japan
| | - Takaya Suzuki
- School of Science, Academic Assembly, University of Toyama, Toyama, 930-8555, Japan
| | - Makoto Seki
- School of Science, Academic Assembly, University of Toyama, Toyama, 930-8555, Japan
| | - Nobuo Suzuki
- Noto Marine Laboratory, Institute of Nature and Environmental Technology, Kanazawa University, Ogi, Noto‑cho, Ishikawa, 927‑0553, Japan
| | - Daisuke Tanaka
- School of Science, Academic Assembly, University of Toyama, Toyama, 930-8555, Japan
| | - Shogo Nakamura
- School of Science, Academic Assembly, University of Toyama, Toyama, 930-8555, Japan
| | - Tadashi Isshiki
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya, Tsu, Mie, 514-8507, Japan
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Development and evaluation of a rapid, specific, and sensitive loop-mediated isothermal amplification assay to detect Tenacibaculum sp. strain pbs-1 associated with black-spot shell disease in Akoya pearl oysters. Arch Microbiol 2022; 205:43. [PMID: 36575332 DOI: 10.1007/s00203-022-03384-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022]
Abstract
Black-spot shell disease decreases pearl quality and threatens pearl oyster survival. Establishment of a rapid, specific, and sensitive assay to detect Tenacibaculum sp. strain Pbs-1 associated with black-spot shell disease is of commercial importance. We developed a rapid, specific, and highly sensitive loop-mediated isothermal amplification (LAMP) assay to detect Tenacibaculum sp. Pbs-1 in Akoya pearl oysters Pinctada fucata. A set of five specific primers (two inner, two outer, and a loop) were designed based on the 16S-23S internal spacer region of strain Pbs-1. The optimum reaction temperature was 63 °C, and concentrations of the inner and loop primers were 1.4 and 1.0 µM, respectively. The LAMP product can be detected using agarose gel electrophoresis, and the color change in the reaction tube can be detected visually (by the naked eye) following the addition of malachite green. Our assay proved to be specific for strain Pbs-1, with no cross-reactivity with five other species of Tenacibaculum. The detection limit of the LAMP assay at 35 min is 50 pg, and at 60 min it is 5 fg. We evaluated the LAMP assay using diseased and healthy pearl oysters. The results demonstrate the suitability and simplicity of this test for rapid field diagnosis of strain Pbs-1.
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Takeuchi T, Suzuki Y, Watabe S, Nagai K, Masaoka T, Fujie M, Kawamitsu M, Satoh N, Myers EW. A high-quality, haplotype-phased genome reconstruction reveals unexpected haplotype diversity in a pearl oyster. DNA Res 2022; 29:dsac035. [PMID: 36351462 PMCID: PMC9646362 DOI: 10.1093/dnares/dsac035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/18/2022] [Accepted: 09/12/2022] [Indexed: 07/30/2023] Open
Abstract
Homologous chromosomes in the diploid genome are thought to contain equivalent genetic information, but this common concept has not been fully verified in animal genomes with high heterozygosity. Here we report a near-complete, haplotype-phased, genome assembly of the pearl oyster, Pinctada fucata, using hi-fidelity (HiFi) long reads and chromosome conformation capture data. This assembly includes 14 pairs of long scaffolds (>38 Mb) corresponding to chromosomes (2n = 28). The accuracy of the assembly, as measured by an analysis of k-mers, is estimated to be 99.99997%. Moreover, the haplotypes contain 95.2% and 95.9%, respectively, complete and single-copy BUSCO genes, demonstrating the high quality of the assembly. Transposons comprise 53.3% of the assembly and are a major contributor to structural variations. Despite overall collinearity between haplotypes, one of the chromosomal scaffolds contains megabase-scale non-syntenic regions, which necessarily have never been detected and resolved in conventional haplotype-merged assemblies. These regions encode expanded gene families of NACHT, DZIP3/hRUL138-like HEPN, and immunoglobulin domains, multiplying the immunity gene repertoire, which we hypothesize is important for the innate immune capability of pearl oysters. The pearl oyster genome provides insight into remarkable haplotype diversity in animals.
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Affiliation(s)
| | - Yoshihiko Suzuki
- Present address: Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Shugo Watabe
- Kitasato University School of Marine Biosciences, Sagamihara, Kanagawa, Japan
| | - Kiyohito Nagai
- Pearl Research Institute, K. MIKIMOTO & CO., LTD, Shima, Mie, Japan
| | - Tetsuji Masaoka
- Aquatic Breeding Division, Aquaculture Research Department, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Tamaki, Mie, Japan
| | - Manabu Fujie
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Mayumi Kawamitsu
- DNA Sequencing Section, 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
| | - Eugene W Myers
- Algorithms for Eco and Evo Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
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Somrup S, Sangsawang A, McMillan N, Winitchai S, Inthoncharoen J, Liu S, Muangmai N. Pinctadaphuketensis sp. nov. (Bivalvia, Ostreida, Margaritidae), a new pearl oyster species from Phuket, western coast of Thailand. Zookeys 2022; 1119:181-195. [PMID: 36762354 PMCID: PMC9848700 DOI: 10.3897/zookeys.1119.87724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/11/2022] [Indexed: 11/12/2022] Open
Abstract
A new species of the genus Pinctada is described from samples collected from the east coast of Phuket Island, Thailand in the Andaman Sea. Pinctadaphuketensis sp. nov. is distinguished from other species on both molecular and morphological data. Morphologically, the valves of P.phuketensis are characterized by a slightly developed to undeveloped posterior auricle, a small, narrow slit-like byssal notch, the absence of hinge teeth, and a pale to transparent non-nacreous border, with a few dark brown or red blotches. This new species resembles P.fucata but differs by its smaller size and the absence of hinge teeth. Phylogenetic analyses based on both mitochondrial (COI) and nuclear (18S rDNA, ITS1 and ITS2) genes and species delimitation using COI data strongly support that P.phuketensis is a distinct species, which is closely related to Pinctadaalbina and Pinctadanigra.
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Affiliation(s)
- Supannee Somrup
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China,Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | - Akkarasiri Sangsawang
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | - Nichanun McMillan
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | - Supanida Winitchai
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | - Jitti Inthoncharoen
- Kasetsart Agricultural and Agro-Industrial Product Improvement Institute (KAPI), Kasetsart University, Bangkok 10900, Thailand
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Narongrit Muangmai
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand,Phuket Pearl Industry, Co. Ltd., Phuket 83000, Thailand
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