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Baek IG, Kim YH, Han HS, Huynh DT, Bang IC. Complete mitochondrial genome sequence and phylogenetic analysis of the hybrid flat fish Platichthys stellatus (♀) × Platichthys bicoloratus (♂). Mitochondrial DNA B Resour 2024; 9:1317-1321. [PMID: 39359377 PMCID: PMC11445915 DOI: 10.1080/23802359.2024.2410438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 09/24/2024] [Indexed: 10/04/2024] Open
Abstract
We report the complete mitochondrial genome of the hybrid flounder Platichthys stellatus (♀) × Platichthys bicoloratus (♂). The mitochondrial genome contained 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and 1 control region (D-loop), for a total length of 16,874 bp. The nucleotide composition of the heavy strand was 29.15% C, 26.99% A, 26.14% T, and 17.71% G. A maximum-likelihood phylogenetic analysis showed that the hybrid flat fish was a member of the same clade as P. stellatus (maternal inheritance). Our findings add to the extant data on the subfamily Pleuronecidae and provide insight into their molecular phylogeny and taxonomy.
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Affiliation(s)
- In-Gug Baek
- Department of Biology, Soonchunhyang University, Asan, Republic of Korea
| | - Yong Hwi Kim
- Bio R&D Lab, BioTNS Co., Ltd, Daejeon, Republic of Korea
| | - Ho-Seop Han
- Department of Biology, Soonchunhyang University, Asan, Republic of Korea
| | - Duc Tam Huynh
- Research Institute for Aquaculture no.3, Nha Trang, Viet Nam
| | - In-Chul Bang
- Department of Biology, Soonchunhyang University, Asan, Republic of Korea
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Kundu S, Palimirmo FS, Kang HE, Kim AR, Lee SR, Gietbong FZ, Song SH, Kim HW. Insights into the Mitochondrial Genetic Makeup and Miocene Colonization of Primitive Flatfishes (Pleuronectiformes: Psettodidae) in the East Atlantic and Indo-West Pacific Ocean. BIOLOGY 2023; 12:1317. [PMID: 37887027 PMCID: PMC10604034 DOI: 10.3390/biology12101317] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/25/2023] [Accepted: 10/06/2023] [Indexed: 10/28/2023]
Abstract
The mitogenomic evolution of the Psettodes flatfishes is still poorly known from their range distribution in eastern Atlantic and Indo-West Pacific Oceans. The study delves into the matrilineal evolutionary pathway of these primitive flatfishes, with a specific focus on the complete mitogenome of the Psettodes belcheri species, as determined through next-generation sequencing. The mitogenome in question spans a length of 16,747 base pairs and comprises a total of 37 genes, including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. Notably, the mitogenome of P. belcheri exhibits a bias towards AT base pairs, with a composition of 54.15%, mirroring a similar bias observed in its close relative, Psettodes erumei, which showcases percentages of 53.07% and 53.61%. Most of the protein-coding genes commence with an ATG initiation codon, except for Cytochrome c oxidase I (COI), which initiates with a GTG codon. Additionally, four protein-coding genes commence with a TAA termination codon, while seven others exhibit incomplete termination codons. Furthermore, two protein-coding genes, namely NAD1 and NAD6, terminate with AGG and TAG stop codons, respectively. In the mitogenome of P. belcheri, the majority of transfer RNAs demonstrate the classical cloverleaf secondary structures, except for tRNA-serine, which lacks a DHU stem. Comparative analysis of conserved blocks within the control regions of two Psettodidae species unveiled that the CSB-II block extended to a length of 51 base pairs, surpassing the other blocks and encompassing highly variable sites. A comprehensive phylogenetic analysis using mitochondrial genomes (13 concatenated PCGs) categorized various Pleuronectiformes species, highlighting the basal position of the Psettodidae family and showed monophyletic clustering of Psettodes species. The approximate divergence time (35-10 MYA) between P. belcheri and P. erumei was estimated, providing insights into their separation and colonization during the early Miocene. The TimeTree analysis also estimated the divergence of two suborders, Psettodoidei and Pleuronectoidei, during the late Paleocene to early Eocene (56.87 MYA). The distribution patterns of Psettodes flatfishes were influenced by ocean currents and environmental conditions, contributing to their ecological speciation. In the face of climate change and anthropogenic activities, the conservation implications of Psettodes flatfishes are emphasized, underscoring the need for regulated harvesting and adaptive management strategies to ensure their survival in changing marine ecosystems. Overall, this study contributes to understanding the evolutionary history, genetic diversity, and conservation needs of Psettodes flatfishes globally. However, the multifaceted exploration of mitogenome and larger-scale genomic data of Psettodes flatfish will provide invaluable insights into their genetic characterization, evolutionary history, environmental adaptation, and conservation in the eastern Atlantic and Indo-West Pacific Oceans.
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Affiliation(s)
- Shantanu Kundu
- Institute of Fisheries Science, Pukyong National University, Busan 48513, Republic of Korea
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
| | - Flandrianto Sih Palimirmo
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
- Research Center for Conservation of Marine and Inland Water Resources, National Research and Innovation Agency, Cibinong 16911, Indonesia
| | - Hye-Eun Kang
- Institute of Marine Life Science, Pukyong National University, Busan 48513, Republic of Korea
| | - Ah Ran Kim
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
| | - Soo Rin Lee
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
| | | | - Se Hyun Song
- Fisheries Resources Management Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea
| | - Hyun-Woo Kim
- Institute of Fisheries Science, Pukyong National University, Busan 48513, Republic of Korea
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
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Chae JY, Kim J, Kang TW, Kim J, Lee HH, Kim MS. The study on the complete mitochondrial genome of Acanthopsetta nadeshnyi and its phylogenetic position. Mitochondrial DNA B Resour 2023; 8:852-856. [PMID: 37583940 PMCID: PMC10424613 DOI: 10.1080/23802359.2023.2241670] [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: 09/16/2022] [Accepted: 07/21/2023] [Indexed: 08/17/2023] Open
Abstract
Pleuronectidae is a well-studied familyin the order Pleuronectiformes. In contrast, genetic research on the flatfish Acanthopsetta nadeshnyi of the Pleuronectidae family is limited. This study reports the complete mitogenome of A. nadeshnyi. The mitogenome was 17,206 bases long and included 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a putative control region. Phylogenetic analysis based on the nucleotide sequences of the 13 PCGs confirmed that A. nadeshnyi belongs to the Pleuronectidae family.
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Affiliation(s)
- Jun Young Chae
- Department of Bioinformatics, the MOAGEN, Daejeon, South Korea
- Department of Biotechnology, Pukyong National University, Busan, South Korea
| | - JinHo Kim
- Department of Bioinformatics, the MOAGEN, Daejeon, South Korea
| | - Tae-Wook Kang
- Department of Bioinformatics, the MOAGEN, Daejeon, South Korea
| | - Jinkoo Kim
- Major of Marine Biology, Pukyong National University, Busan, South Korea
| | - Hyung-Ho Lee
- Department of Biotechnology, Pukyong National University, Busan, South Korea
| | - Moo-Sang Kim
- Department of Bioinformatics, the MOAGEN, Daejeon, South Korea
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Zhao N, Guo H, Jia L, Guo B, Zheng D, Liu S, Zhang B. Genome assembly and annotation at the chromosomal level of first Pleuronectidae: Verasper variegatus provides a basis for phylogenetic study of Pleuronectiformes. Genomics 2021; 113:717-726. [PMID: 33535123 DOI: 10.1016/j.ygeno.2021.01.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/26/2021] [Accepted: 01/28/2021] [Indexed: 01/09/2023]
Abstract
High quality genome is of great significance for the mining of biological information resources of species. Up to now, the genomic information of several important economic flatfishes has been well explained. All these fishes are eyes on left side-type, and no high-quality genome of eyes on right side-type species has been reported. In this study, we applied a combined strategy involving stLFR and Hi-C technologies to generate sequencing data for constructing the chromosomal genome of Verasper variegates, which belongs to Pleuronectidae with characteristic of eyes on right side. The size of genome of V. variegatus is 556 Mb. More than 97.2% of BUSCO genes were detected, and N50 lengths of the contigs and scaffolds reached 79.8 Kb and 23.8 Mb, respectively, demonstrating the outstanding completeness and sequence continuity of the genome. A total of 22,199 protein-coding genes were predicted in the assembled genome, and more than 95% of those genes could be functionally annotated. Meanwhile, the genomic collinearity, gene family and phylogenetic analyses of similar species in Pleuronectiformes were also investigated and portrayed for metamorphosis and benthic adaptation. Sex related genes mapping has also been achieved at the chromosome level. This study is the first chromosomal level genome of a Pleuronectidae fish (V. variegatus). The chromosomal genome assembly constructed in this work will not only be valuable for conservation and aquaculture studies of the V. variegatus but will also be of general interest in the phylogenetic and taxonomic studies of Pleuronectiformes.
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Affiliation(s)
- Na Zhao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, International Research Center for Marine Biosciences at Shanghai Ocean University, Shanghai Ocean University, Shanghai 201306, China
| | - Haobing Guo
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Lei Jia
- Tianjin Fisheries Research Institute, Tianjin 300200, China
| | - Biao Guo
- Tianjin Fisheries Research Institute, Tianjin 300200, China
| | - Debin Zheng
- Tianjin Fisheries Research Institute, Tianjin 300200, China
| | - Shanshan Liu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, International Research Center for Marine Biosciences at Shanghai Ocean University, Shanghai Ocean University, Shanghai 201306, China
| | - Bo Zhang
- Tianjin Fisheries Research Institute, Tianjin 300200, China.
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Wang Y, Sun W, Gu Q, Yao J, Tan H, Huang X, Qin Q, Tao M, Zhang C, Liu S. Variations in the Mitochondrial Genome of a Goldfish-Like Hybrid [Koi Carp (♀) × Blunt Snout Bream (♂)] Indicate Paternal Leakage. Front Genet 2021; 11:613520. [PMID: 33552134 PMCID: PMC7861200 DOI: 10.3389/fgene.2020.613520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/01/2020] [Indexed: 11/13/2022] Open
Abstract
Previously, a homodiploid goldfish-like fish (2n = 100; GF-L) was spontaneously generated by self-crossing a homodiploid red crucian carp-like fish (2n = 100; RCC-L), which was in turn produced via the distant hybridization of female koi carp (Cyprinus carpio haematopterus, KOC, 2n = 100) and male blunt snout bream (Megalobrama amblycephala, BSB, 2n = 48). The phenotypes and genotypes of RCC-L and GF-L differed from those of the parental species but were similar to diploid red crucian carp (2n = 100; RCC) and goldfish (2n = 100; GF), respectively. We sequenced the complete mitochondrial DNAs (mtDNAs) of the KOC, BSB, RCC-L, GF-L, and subsequent generations produced by self-crossing [the self-mating offspring of RCC-L (RCC-L-F2) to the self-mating offspring of RCC-L-F2 (RCC-L-F3) and the self-mating offspring of GF-L (GF-L-F2)]. Paternal mtDNA fragments were stably embedded in the mtDNAs of both lineages, forming chimeric DNA fragments. In addition to these chimeras, several nucleotide positions in the RCC-L and GF-L lineages differed from the parental bases, and were instead identical with RCC and GF, respectively. Moreover, RCC-L and GF-L mtDNA organization and nucleotide composition were more similar to those of RCC and GF, respectively, compared to parental mtDNA. Finally, phylogenetic analyses indicated that RCC-L and GF-L clustered with RCC and GF, not with the parental species. The molecular dating time shows that the divergence time of KOC and GF was about 21.26 Mya [95% highest posterior density (HPD): 24.41-16.67 Mya], which fell within the period of recent. The heritable chimeric DNA fragments and mutant loci identified in the mtDNA of the RCC-L and GF-L lineages provided important evidence that hybridizations might lead to changes in the mtDNA and the subsequent generation of new lineages. Our findings also demonstrated for the first time that the paternal mtDNA was transmitted into the mtDNA of homodiploid lineages (RCC-L and GF-L), which provided evidence that paternal DNA plays a role in inherited mtDNA. These evolutionary analyses in mtDNA suggest that GF might have diverged from RCC after RCC diverged from koi carp.
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Affiliation(s)
- Yude Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Wenzhen Sun
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Qianhong Gu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Jiajun Yao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Huifang Tan
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Xu Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Qinbo Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Chun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
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Shi W, Dong XL, Wang ZM, Miao XG, Wang SY, Kong XY. Complete mitogenome sequences of four flatfishes (Pleuronectiformes) reveal a novel gene arrangement of L-strand coding genes. BMC Evol Biol 2013; 13:173. [PMID: 23962312 PMCID: PMC3751894 DOI: 10.1186/1471-2148-13-173] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 08/12/2013] [Indexed: 11/19/2022] Open
Abstract
Background Few mitochondrial gene rearrangements are found in vertebrates and large-scale changes in these genomes occur even less frequently. It is difficult, therefore, to propose a mechanism to account for observed changes in mitogenome structure. Mitochondrial gene rearrangements are usually explained by the recombination model or tandem duplication and random loss model. Results In this study, the complete mitochondrial genomes of four flatfishes, Crossorhombus azureus (blue flounder), Grammatobothus krempfi, Pleuronichthys cornutus, and Platichthys stellatus were determined. A striking finding is that eight genes in the C. azureus mitogenome are located in a novel position, differing from that of available vertebrate mitogenomes. Specifically, the ND6 and seven tRNA genes (the Q, A, C, Y, S1, E, P genes) encoded by the L-strand have been translocated to a position between tRNA-T and tRNA-F though the original order of the genes is maintained. Conclusions These special features are used to suggest a mechanism for C. azureus mitogenome rearrangement. First, a dimeric molecule was formed by two monomers linked head-to-tail, then one of the two sets of promoters lost function and the genes controlled by the disabled promoters became pseudogenes, non-coding sequences, and even were lost from the genome. This study provides a new gene-rearrangement model that accounts for the events of gene-rearrangement in a vertebrate mitogenome.
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Affiliation(s)
- Wei Shi
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, PR China
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Sekino M, Saitoh K, Shimizu D, Wada T, Kamiyama K, Gambe S, Chen S, Aritaki M. Genetic structure in species with shallow evolutionary lineages: a case study of the rare flatfish Verasper variegatus. CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0128-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kong X, Dong X, Zhang Y, Shi W, Wang Z, Yu Z. A novel rearrangement in the mitochondrial genome of tongue sole, Cynoglossus semilaevis: control region translocation and a tRNA gene inversion. Genome 2009; 52:975-84. [PMID: 19953125 DOI: 10.1139/g09-069] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The organization of fish mitochondrial genomes (mitogenomes) is quite conserved, usually with the heavy strand encoding 12 of 13 protein-coding genes and 14 of 22 tRNA genes, and the light strand encoding ND6 and the remaining 8 tRNA genes. Currently, there are only a few reports on gene reorganization of fish mitogenomes, with only two types of rearrangements (shuffling and translocation) observed. No gene inversion has been detected in approximately 420 complete fish mitogenomes available so far. Here we report a novel rearrangement in the mitogenome of Cynoglossus semilaevis (Cynoglossinae, Cynoglossidae, Pleuronectiformes). The genome is 16 371 bp in length and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 2 main noncoding regions, the putative control region and the light-strand replication origin. A striking finding of this study is that the tRNAGln gene is translocated from the light to the heavy strand (Q inversion). This is accompanied by shuffling of the tRNAIle gene and long-range translocation of the putative control region downstream to a site between ND1 and the tRNAGln gene. The remaining gene order is identical to that of typical fish mitogenomes. Additionally, unique characters of this mitogenome, including a high A+T content and length variations of 8 protein-coding genes, were found through comparison of the mitogenome sequence with those from other flatfishes. All the features detected and their relationships with the rearrangements, as well as a possible rearrangement pathway, are discussed. These data provide interesting information for better understanding the molecular mechanisms of gene reorganization in fish mitogenomes.
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Affiliation(s)
- Xiaoyu Kong
- Marine Biodiversity Collection of South China Sea, Laboratory of Marine Bioresource Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, China
- Laboratory of Mariculture Research, College of Fisheries, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Xiaoli Dong
- Marine Biodiversity Collection of South China Sea, Laboratory of Marine Bioresource Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, China
- Laboratory of Mariculture Research, College of Fisheries, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Yanchun Zhang
- Marine Biodiversity Collection of South China Sea, Laboratory of Marine Bioresource Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, China
- Laboratory of Mariculture Research, College of Fisheries, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Wei Shi
- Marine Biodiversity Collection of South China Sea, Laboratory of Marine Bioresource Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, China
- Laboratory of Mariculture Research, College of Fisheries, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Zhongming Wang
- Marine Biodiversity Collection of South China Sea, Laboratory of Marine Bioresource Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, China
- Laboratory of Mariculture Research, College of Fisheries, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Ziniu Yu
- Marine Biodiversity Collection of South China Sea, Laboratory of Marine Bioresource Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, China
- Laboratory of Mariculture Research, College of Fisheries, Ocean University of China, 5 Yushan Road, Qingdao, China
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