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Eastment RV, Wong BBM, McGee MD. Convergent genomic signatures associated with vertebrate viviparity. BMC Biol 2024; 22:34. [PMID: 38331819 PMCID: PMC10854053 DOI: 10.1186/s12915-024-01837-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/30/2024] [Indexed: 02/10/2024] Open
Abstract
BACKGROUND Viviparity-live birth-is a complex and innovative mode of reproduction that has evolved repeatedly across the vertebrate Tree of Life. Viviparous species exhibit remarkable levels of reproductive diversity, both in the amount of care provided by the parent during gestation, and the ways in which that care is delivered. The genetic basis of viviparity has garnered increasing interest over recent years; however, such studies are often undertaken on small evolutionary timelines, and thus are not able to address changes occurring on a broader scale. Using whole genome data, we investigated the molecular basis of this innovation across the diversity of vertebrates to answer a long held question in evolutionary biology: is the evolution of convergent traits driven by convergent genomic changes? RESULTS We reveal convergent changes in protein family sizes, protein-coding regions, introns, and untranslated regions (UTRs) in a number of distantly related viviparous lineages. Specifically, we identify 15 protein families showing evidence of contraction or expansion associated with viviparity. We additionally identify elevated substitution rates in both coding and noncoding sequences in several viviparous lineages. However, we did not find any convergent changes-be it at the nucleotide or protein level-common to all viviparous lineages. CONCLUSIONS Our results highlight the value of macroevolutionary comparative genomics in determining the genomic basis of complex evolutionary transitions. While we identify a number of convergent genomic changes that may be associated with the evolution of viviparity in vertebrates, there does not appear to be a convergent molecular signature shared by all viviparous vertebrates. Ultimately, our findings indicate that a complex trait such as viviparity likely evolves with changes occurring in multiple different pathways.
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Affiliation(s)
- Rhiannon V Eastment
- School of Biological Sciences, Monash University, Melbourne, 3800, Australia.
| | - Bob B M Wong
- School of Biological Sciences, Monash University, Melbourne, 3800, Australia
| | - Matthew D McGee
- School of Biological Sciences, Monash University, Melbourne, 3800, Australia
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Sun Z, Li S, Liu Y, Li W, Liu K, Cao X, Lin J, Wang H, Wang Q, Shao C. Telomere-to-telomere gapless genome assembly of the Chinese sea bass (Lateolabrax maculatus). Sci Data 2024; 11:175. [PMID: 38326339 PMCID: PMC10850130 DOI: 10.1038/s41597-024-02988-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/18/2024] [Indexed: 02/09/2024] Open
Abstract
Chinese sea bass (Lateolabrax maculatus) is a highly sought-after commercial seafood species in Asian regions due to its excellent nutritional value. With the rapid advancement of bioinformatics, higher standards for genome analysis compared to previously published reference genomes are now necessary. This study presents a gapless assembly of the Chinese sea bass genome, which has a length of 632.75 Mb. The sequences were assembled onto 24 chromosomes with a coverage of over 99% (626.61 Mb), and telomeres were detected on 34 chromosome ends. Analysis using Merqury indicated a high level of accuracy, with an average consensus quality value of 54.25. The ONT ultralong and PacBio HiFi data were aligned with the assembly using minimap2, resulting in a mapping rate of 99.9%. The study also identified repeating elements in 20.90% (132.25 Mb) of the genome and inferred 22,014 protein-coding genes. These results establish meaningful groundwork for exploring the evolution of the Chinese sea bass genome and advancing molecular breeding techniques.
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Affiliation(s)
- Zhilong Sun
- College of Marine Technology and Environment, Dalian Ocean University, Dalian, 116023, China
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
| | - Shuo Li
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
| | - Yuyan Liu
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
| | - Weijing Li
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
| | - Kaiqiang Liu
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
| | - Xuebin Cao
- Yantai Jinghai Marine Fisheries Co., Ltd, Yantai, 264000, China
| | - Jiliang Lin
- Yantai Jinghai Marine Fisheries Co., Ltd, Yantai, 264000, China
| | - Hongyan Wang
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
| | - Qian Wang
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
| | - Changwei Shao
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China.
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3
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Lu X, Yi M, Hu Z, Yang T, Zhang W, Marsh ENG, Jia K. Feedback loop regulation between viperin and viral hemorrhagic septicemia virus through competing protein degradation pathways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574905. [PMID: 38260481 PMCID: PMC10802422 DOI: 10.1101/2024.01.09.574905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Viperin is an antiviral protein that exhibits a remarkably broad spectrum of antiviral activity. Viperin-like proteins are found all kingdoms of life, suggesting it is an ancient component of the innate immune system. However, viruses have developed strategies to counteract viperin's effects. Here, we describe a feedback loop between viperin and viral hemorrhagic septicemia virus (VHSV), a common fish pathogen. We show that Lateolabrax japonicus viperin (Ljviperin) is induced by both IFN-independent and IFN-dependent pathways, with the C-terminal domain of Ljviperin being important for its anti-VHSV activity. Ljviperin exerts an antiviral effect by binding both the nucleoprotein (N) and phosphoprotein (P) of VHSV and induces their degradation through the autophagy pathway, which is an evolutionarily conserved antiviral mechanism. However, counteracting viperin's activity, N protein targets and degrades transcription factors that up-regulate Ljviperin expression, interferon regulatory factor (IRF) 1 and IRF9, through ubiquitin-proteasome pathway. Together, our results reveal a previously unknown feedback loop between viperin and virus, providing potential therapeutic targets for VHSV prevention. Importance Viral hemorrhagic septicaemia (VHS) is a contagious disease caused by the viral hemorrhagic septicaemia virus (VHSV), which poses a threat to over 80 species of marine and freshwater fish. Currently, there are no effective treatments available for this disease. Understanding the mechanisms of VHSV-host interaction is crucial for preventing viral infections. Here, we found that, as an ancient antiviral protein, viperin degrades the N and P proteins of VHSV through the autophagy pathway. Additionally, the N protein also impacts the biological functions of IRF1 and IRF9 through the ubiquitin-proteasome pathway, leading to the suppression of viperin expression. Therefore, the N protein may serve as a potential virulence factor for the development of VHSV vaccines and screening of antiviral drugs. Our research will serve as a valuable reference for the development of strategies to prevent VHSV infections.
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Affiliation(s)
- Xiaobing Lu
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 519082, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, Guangdong, 519082, China
| | - Meisheng Yi
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 519082, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, Guangdong, 519082, China
| | - Zhe Hu
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 519082, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, Guangdong, 519082, China
| | - Taoran Yang
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 519082, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, Guangdong, 519082, China
| | - Wanwan Zhang
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 519082, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, Guangdong, 519082, China
| | - E. Neil G. Marsh
- Departments of Chemistry and Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Kuntong Jia
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 519082, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, Guangdong, 519082, China
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Wang Y, Zhang H, Xian W, Iwasaki W. Chromosome genome assembly and annotation of the spiny red gurnard (Chelidonichthys spinosus). Sci Data 2023; 10:443. [PMID: 37438353 DOI: 10.1038/s41597-023-02357-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/30/2023] [Indexed: 07/14/2023] Open
Abstract
Chelidonichthys spinosus, a secondary economic fish, is increasingly being exploited and valued in China. However, overfishing has led to it being recognized as one of the most depleted marine species in China. In this study, we generated a chromosome-level genome of C. spinosus using PacBio, Illumina, and Hi-C sequencing data. Ultimately, we assembled a 624.7 Mb genome of C. spinosus, with a contig N50 of 13.77 Mb and scaffold N50 of 28.11 Mb. We further anchored and oriented the assembled sequences onto 24 pseudo-chromosomes using Hi-C techniques. In total, 25,358 protein-coding genes were predicted, of which 24,072 (94.93%) genes were functionally annotated. The dot plot reveals a prominent co-linearity between C. spinosus and Cyclopterus lumpus, indicating a remarkably close phylogenetic relationship between these two species. The assembled genome sequences provide valuable information for elucidating the genetic adaptation and potential molecular basis of C. spinosus. They also have the potential to provide insight into the evolutionary investigation of teleost fish and vertebrates.
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Affiliation(s)
- Yibang Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hui Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Weiwei Xian
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
| | - Wataru Iwasaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Japan
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Chen B, Zhou Z, Shi Y, Gong J, Li C, Zhou T, Li Y, Zhang D, Xu P. Genome-wide evolutionary signatures of climate adaptation in spotted sea bass inhabiting different latitudinal regions. Evol Appl 2023; 16:1029-1043. [PMID: 37216029 PMCID: PMC10197228 DOI: 10.1111/eva.13551] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/02/2023] [Accepted: 04/12/2023] [Indexed: 05/24/2023] Open
Abstract
Consideration of the thermal adaptation of species is essential in both evolutionary biology and climate-change biology because it frequently leads to latitudinal gradients of various phenotypes among populations. The spotted sea bass (Lateolabrax maculatus) has a broad latitudinal distribution range along the marginal seas of the Northwest Pacific and thus provides an excellent teleost model for population genetic and climate adaptation studies. We generated over 8.57 million SNP loci using whole-genome resequencing from 100 samples collected at 14 geographic sites (five or ten samples per site). We estimated the genetic structure of the sampled fish and clustered them into three highly differentiated populations. The genetic differentiation pattern estimated by multivariable models combining geographic distance and sea surface temperature differences suggests that isolation by distance and isolation by environment both have significant effects on this species. Further investigation of genome-wide evolutionary signatures of climate adaptation identified many genes related to growth, muscle contraction, and vision that are under positive natural selection. Moreover, the contrasting patterns of natural selection in high-latitude and low-latitude populations prompted different strategies of trade-offs between growth rate and other traits that may play an essential role in adaptation to different local climates. Our results offer an opportunity to better understand the genetic basis of the phenotypic variation in eurythermal fishes inhabiting different climatic regions.
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Affiliation(s)
- Baohua Chen
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth SciencesXiamen UniversityXiamenChina
- Shenzhen Research Institute of Xiamen UniversityShenzhenChina
| | - Zhixiong Zhou
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth SciencesXiamen UniversityXiamenChina
- Shenzhen Research Institute of Xiamen UniversityShenzhenChina
| | - Yue Shi
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth SciencesXiamen UniversityXiamenChina
- Shenzhen Research Institute of Xiamen UniversityShenzhenChina
| | - Jie Gong
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth SciencesXiamen UniversityXiamenChina
- Shenzhen Research Institute of Xiamen UniversityShenzhenChina
| | - Chengyu Li
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth SciencesXiamen UniversityXiamenChina
- Shenzhen Research Institute of Xiamen UniversityShenzhenChina
| | - Tao Zhou
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth SciencesXiamen UniversityXiamenChina
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth SciencesXiamen UniversityXiamenChina
| | - Yun Li
- The Key Laboratory of Mariculture, Ministry of EducationOcean University of ChinaQingdaoChina
| | - Dianchang Zhang
- South China Sea Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouChina
| | - Peng Xu
- Shenzhen Research Institute of Xiamen UniversityShenzhenChina
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth SciencesXiamen UniversityXiamenChina
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6
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Cai M, Cheng W, Bai Y, Mu C, Zheng H, Cheng Z, Gao J. PheGRF4e initiated auxin signaling during moso bamboo shoot development. Mol Biol Rep 2022; 49:8815-8825. [PMID: 35867290 DOI: 10.1007/s11033-022-07731-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/20/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND As a ubiquitous acid-regulating protein family in eukaryotes, general regulatory factors (GRFs) are active in various life activities of plants. However, detailed investigations of the GRFs gene family in moso bamboo are scarce. METHODS AND RESULTS Genome-wide characteristics of the GRF gene family in moso bamboo were analyzed using the moso bamboo genome. GRF phylogeny, gene structure, conserved domains, cis-element promoters, and gene expression were systematically analyzed. A total of 20 GRF gene family members were identified in the moso bamboo genome. These genes were divided into ε and non-ε groups. qRT-PCR (real-time quantitative reverse transcription polymerase chain reaction) showed that PheGRF genes responded to auxin and gibberellin treatment. To further study PheGRF gene functions, a yeast two-hybrid experiment was performed and verified by a bimolecular fluorescence complementation experiment. The results showed that PheGRF4e could interact with PheIAA30 (auxin/indole-3-acetic acid, an Aux/IAA family gene), and both were found to act mainly on the root tip meristem and vascular bundle cells of developing shoots by in situ hybridization assay. CONCLUSIONS This study revealed that PheGRF genes were involved in hormone response during moso bamboo shoot development, and the possible regulatory functions of PheGRF genes were enriched by the fact that PheGRF4e initiated auxin signaling by binding to PheIAA30.
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Affiliation(s)
- Miaomiao Cai
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing, 100102, China
| | - Wenlong Cheng
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing, 100102, China
| | - Yucong Bai
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing, 100102, China
| | - Changhong Mu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing, 100102, China
| | - Huifang Zheng
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing, 100102, China
| | - Zhanchao Cheng
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing, 100102, China
| | - Jian Gao
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing, 100102, China.
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Xie Z, Wang D, Jiang S, Peng C, Wang Q, Huang C, Li S, Lin H, Zhang Y. Chromosome-Level Genome Assembly and Transcriptome Comparison Analysis of Cephalopholis sonnerati and Its Related Grouper Species. BIOLOGY 2022; 11:biology11071053. [PMID: 36101431 PMCID: PMC9312885 DOI: 10.3390/biology11071053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 11/16/2022]
Abstract
The tomato hind, Cephalopholis sonnerati, is a bottom-dwelling coral reef fish, which is widely distributed in the Indo-Pacific and Red Sea. C. sonnerati also features complex social structures and behaviour mechanisms. Here, we present a high-quality, chromosome-level genome assembly for C. sonnerati that was derived using PacBio sequencing and Hi-C technologies. A 1043.66 Mb genome with an N50 length of 2.49 Mb was assembled, produced containing 795 contigs assembled into 24 chromosomes. Overall, 97.2% of the complete BUSCOs were identified in the genome. A total of 26,130 protein-coding genes were predicted, of which 94.26% were functionally annotated. Evolutionary analysis revealed that C. sonnerati diverged from its common ancestor with E. lanceolatus and E. akaara approximately 41.7 million years ago. In addition, comparative genome analyses indicated that the expanded gene families were highly enriched in the sensory system. Finally, we found the tissue-specific expression of 8108 genes. We found that these tissue-specific genes were highly enriched in the brain. In brief, the high-quality, chromosome-level reference genome will provide a valuable genome resource for studies of the genetic conservation, resistance breeding, and evolution of C. sonnerati.
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Affiliation(s)
- Zhenzhen Xie
- College of Basic Medicine, Nanchang University, Nanchang 330031, China;
| | - Dengdong Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (D.W.); (S.J.); (S.L.); (H.L.)
| | - Shoujia Jiang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (D.W.); (S.J.); (S.L.); (H.L.)
| | - Cheng Peng
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China;
| | - Qing Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China;
| | - Chunren Huang
- Hainan Chenhai Aquatic Products Co., Ltd., Sanya 572000, China;
| | - Shuisheng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (D.W.); (S.J.); (S.L.); (H.L.)
| | - Haoran Lin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (D.W.); (S.J.); (S.L.); (H.L.)
| | - Yong Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (D.W.); (S.J.); (S.L.); (H.L.)
- Correspondence:
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Li M, Xu X, Liu S, Fan G, Zhou Q, Chen S. The chromosome-level genome assembly of the Japanese yellowtail jack Seriola aureovittata provides insights into genome evolution and efficient oxygen transport. Mol Ecol Resour 2022; 22:2701-2712. [PMID: 35593537 DOI: 10.1111/1755-0998.13648] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 04/16/2022] [Accepted: 05/11/2022] [Indexed: 11/27/2022]
Abstract
Fishes of the genus Seriola are widely farmed and highly valued in global aquaculture production. To further understand their economically important traits and help improve aquaculture product quality and sustainability, we performed a chromosome-level genome construction for Seriola aureovittata. Combining two technologies, PacBio and BGISEQ-500, we assembled 649.86 Mb S. aureovittata genome sequences with a contig N50 of 22.21 Mb, and 98% of BUSCO genes were detected in total. The initial assembly was then further scaffolded into 24 pseudochromosomes using Hi-C data, indicating the high quality of the genome. Genome evolution analysis showed that many genes related to fatty acid metabolism and oxygen binding, or transport were expanded, which provided insights into the metabolic characteristics of fatty acids and efficient oxygen transport. Based on the genome data, we confirmed the evolutionary relationship of S. aureovittata, S. dorsalis and S. lalandi and identified chr12 as the putative sex chromosome of S. aureovittata. Our chromosome-level genome assembly provides a genetic foundation for the phylogenetic and taxonomic investigation of different Seriola species. Moreover, the genome will provide an important genomic resource for further biological and aquaculture studies of S. aureovittata.
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Affiliation(s)
- Ming Li
- Yellow Sea Fisheries Research Institute, CAFS, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,Shandong Provincial Key Laboratory of Marine Fishery Biotechnology and Genetic Breeding, Qingdao, China
| | - Xiwen Xu
- Yellow Sea Fisheries Research Institute, CAFS, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,Shandong Provincial Key Laboratory of Marine Fishery Biotechnology and Genetic Breeding, Qingdao, China
| | | | | | - Qian Zhou
- Yellow Sea Fisheries Research Institute, CAFS, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,Shandong Provincial Key Laboratory of Marine Fishery Biotechnology and Genetic Breeding, Qingdao, China
| | - Songlin Chen
- Yellow Sea Fisheries Research Institute, CAFS, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,Shandong Provincial Key Laboratory of Marine Fishery Biotechnology and Genetic Breeding, Qingdao, China
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Yang T, Huang X, Ning Z, Gao T. Genome-Wide Survey Reveals the Microsatellite Characteristics and Phylogenetic Relationships of Harpadon nehereus. Curr Issues Mol Biol 2021; 43:1282-1292. [PMID: 34698106 PMCID: PMC8928995 DOI: 10.3390/cimb43030091] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/19/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022] Open
Abstract
Harpadon nehereus forms one of the most important commercial fisheries along the Bay of Bengal and the southeast coast of China. In this study, the genome-wide survey dataset first produced using next-generation sequencing (NGS) was used to provide general information on the genome size, heterozygosity and repeat sequence ratio of H. nehereus. About 68.74 GB of high-quality sequence data were obtained in total and the genome size was estimated to be 1315 Mb with the 17-mer frequency distribution. The sequence repeat ratio and heterozygosity were calculated to be 52.49% and 0.67%, respectively. A total of 1,027,651 microsatellite motifs were identified and dinucleotide repeat was the most dominant simple sequence repeat (SSR) motif with a frequency of 54.35%. As a by-product of whole genome sequencing, the mitochondrial genome is a powerful tool to investigate the evolutionary relationships between H. nehereus and its relatives. The maximum likelihood (ML) phylogenetic tree was constructed according to the concatenated matrix of amino acids translated from the 13 protein-coding genes (PCGs). Monophyly of two species of the genus Harpadon was revealed in the present study and they formed a monophyletic clade with Saurida with a high bootstrap value of 100%. The results would help to push back the frontiers of genomics and open the doors of molecular diversity as well as conservation genetics studies on this species.
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Yang Y, Wang T, Chen J, Wu L, Wu X, Zhang W, Luo J, Xia J, Meng Z, Liu X. Whole-genome sequencing of brown-marbled grouper (Epinephelus fuscoguttatus) provides insights into adaptive evolution and growth differences. Mol Ecol Resour 2021; 22:711-723. [PMID: 34455708 DOI: 10.1111/1755-0998.13494] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 07/29/2021] [Accepted: 08/23/2021] [Indexed: 11/27/2022]
Abstract
The brown-marbled grouper (Epinephelus fuscoguttatus) is an important species of fish in the coral reef ecosystem and marine aquaculture industry. In this study, a high-quality chromosome-level genome of brown-marbled grouper was assembled using Oxford Nanopore technology and Hi-C technology. The GC content and heterozygosity were approximately 42% and 0.35%, respectively. A total of 230 contigs with a total length of 1047 Mb and contig N50 of 13.8 Mb were assembled, and 228 contigs (99.13%) were anchored into 24 chromosomes. A total of 24,005 protein-coding genes were predicted, among which 23,862 (99.4%) predicted genes were annotated. Phylogenetic analysis showed that brown-marbled grouper and humpback grouper were clustered into one clade that separated approximately 11-23 million years ago. Collinearity analyses showed that there was no obvious duplication of large fragments between chromosomes in the brown-marbled grouper. Genomes of the humpback grouper and giant grouper showed a high collinearity with that of the brown-marbled grouper. A total of 305 expanded gene families were detected in the brown-marbled grouper genome, which is mainly involved in disease resistance. In addition, a genetic linkage map with 3061.88 cM was constructed. Based on the physical and genetic map, one growth-related quantitative trait loci was detected in 32,332,447 bp of chromosome 20, and meox1 and etv4 were considered candidate growth-related genes. This study provides pivotal genetic resources for further evolutionary analyses and artificial breeding of groupers.
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Affiliation(s)
- Yang Yang
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou, China
| | - Tong Wang
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou, China
| | - Jingfang Chen
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou, China
| | - Lina Wu
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou, China
| | - Xi Wu
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou, China
| | - Weiwei Zhang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Key Laboratory of Tropical Biological Resources of Education, Marine Sciences College of Hainan University, Haikou, China
| | - Jian Luo
- State Key Laboratory of Marine Resource Utilization in South China Sea, Key Laboratory of Tropical Biological Resources of Education, Marine Sciences College of Hainan University, Haikou, China
| | - Junhong Xia
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou, China.,Southern Laboratory of Ocean Science and Engineering, Zhuhai, China
| | - Zining Meng
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou, China.,Southern Laboratory of Ocean Science and Engineering, Zhuhai, China
| | - Xiaochun Liu
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou, China.,Southern Laboratory of Ocean Science and Engineering, Zhuhai, China
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11
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Merlo MA, Portela-Bens S, Rodríguez ME, García-Angulo A, Cross I, Arias-Pérez A, García E, Rebordinos L. A Comprehensive Integrated Genetic Map of the Complete Karyotype of Solea senegalensis (Kaup 1858). Genes (Basel) 2020; 12:genes12010049. [PMID: 33396249 PMCID: PMC7824234 DOI: 10.3390/genes12010049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/24/2020] [Accepted: 12/28/2020] [Indexed: 12/23/2022] Open
Abstract
Solea senegalensis aquaculture production has experienced a great increase in the last decade and, consequently, the genome knowledge of the species is gaining attention. In this sense, obtaining a high-density genome mapping of the species could offer clues to the aquaculture improvement in those aspects not resolved so far. In the present article, a review and new processed data have allowed to obtain a high-density BAC-based cytogenetic map of S. senegalensis beside the analysis of the sequences of such BAC clones to achieve integrative data. A total of 93 BAC clones were used to localize the chromosome complement of the species and 588 genes were annotated, thus almost reaching the 2.5% of the S. senegalensis genome sequences. As a result, important data about its genome organization and evolution were obtained, such as the lesser gene density of the large metacentric pair compared with the other metacentric chromosomes, which supports the theory of a sex proto-chromosome pair. In addition, chromosomes with a high number of linked genes that are conserved, even in distant species, were detected. This kind of result widens the knowledge of this species’ chromosome dynamics and evolution.
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12
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Lv M, Zhang Y, Liu K, Li C, Wang J, Fan G, Liu X, Yang H, Liu C, Mahboob S, Liu J, Shao C. A Chromosome-Level Genome Assembly of the Anglerfish Lophius litulon. Front Genet 2020; 11:581161. [PMID: 33329719 PMCID: PMC7729161 DOI: 10.3389/fgene.2020.581161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/15/2020] [Indexed: 11/13/2022] Open
Abstract
Anglerfishes are a highly diverse group of species with unique characteristics. Here, we report the first chromosome-level genome of a species in the order Lophiiformes, the yellow goosefish (Lophius litulon), obtained by whole genome shotgun sequencing and high-throughput chromatin conformation capture. Approximately 97.20% of the assembly spanning 709.23 Mb could be anchored to 23 chromosomes with a contig N50 of 164.91 kb. The BUSCO value was 95.4%, suggesting that the quality of the assembly was high. A comparative gene family analysis identified expanded and contracted gene families, and these may be associated with adaptation to the benthic environment and the lack of scales in the species. A majority of positively selected genes were related to metabolic processes, suggesting that digestive and metabolic system evolution expanded the diversity of yellow goosefish prey. Our study provides a valuable genetic resource for understanding the mechanisms underlying the unique features of the yellow goosefish and for investigating anglerfish evolution.
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Affiliation(s)
- Meiqi Lv
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China.,BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Yaolei Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.,Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Kaiqiang Liu
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Chang Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | | | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Xin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Huanming Yang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Changlin Liu
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shahid Mahboob
- Department of Zoology, College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Junnian Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China.,Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China
| | - Changwei Shao
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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13
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Jung H, Ventura T, Chung JS, Kim WJ, Nam BH, Kong HJ, Kim YO, Jeon MS, Eyun SI. Twelve quick steps for genome assembly and annotation in the classroom. PLoS Comput Biol 2020; 16:e1008325. [PMID: 33180771 PMCID: PMC7660529 DOI: 10.1371/journal.pcbi.1008325] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Eukaryotic genome sequencing and de novo assembly, once the exclusive domain of well-funded international consortia, have become increasingly affordable, thus fitting the budgets of individual research groups. Third-generation long-read DNA sequencing technologies are increasingly used, providing extensive genomic toolkits that were once reserved for a few select model organisms. Generating high-quality genome assemblies and annotations for many aquatic species still presents significant challenges due to their large genome sizes, complexity, and high chromosome numbers. Indeed, selecting the most appropriate sequencing and software platforms and annotation pipelines for a new genome project can be daunting because tools often only work in limited contexts. In genomics, generating a high-quality genome assembly/annotation has become an indispensable tool for better understanding the biology of any species. Herein, we state 12 steps to help researchers get started in genome projects by presenting guidelines that are broadly applicable (to any species), sustainable over time, and cover all aspects of genome assembly and annotation projects from start to finish. We review some commonly used approaches, including practical methods to extract high-quality DNA and choices for the best sequencing platforms and library preparations. In addition, we discuss the range of potential bioinformatics pipelines, including structural and functional annotations (e.g., transposable elements and repetitive sequences). This paper also includes information on how to build a wide community for a genome project, the importance of data management, and how to make the data and results Findable, Accessible, Interoperable, and Reusable (FAIR) by submitting them to a public repository and sharing them with the research community.
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Affiliation(s)
- Hyungtaek Jung
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Centre for Agriculture and Bioeconomy, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Tomer Ventura
- Genecology Research Centre, School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - J. Sook Chung
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, United States of America
| | - Woo-Jin Kim
- Genetics and Breeding Research Center, National Institute of Fisheries Science, Geoje, Korea
| | - Bo-Hye Nam
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Korea
| | - Hee Jeong Kong
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Korea
| | - Young-Ok Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Korea
| | - Min-Seung Jeon
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Seong-il Eyun
- Department of Life Science, Chung-Ang University, Seoul, Korea
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14
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Liu Y, Wang H, Wen H, Shi Y, Zhang M, Qi X, Zhang K, Gong Q, Li J, He F, Hu Y, Li Y. First High-Density Linkage Map and QTL Fine Mapping for Growth-Related Traits of Spotted Sea bass (Lateolabrax maculatus). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:526-538. [PMID: 32424479 DOI: 10.1007/s10126-020-09973-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/28/2020] [Indexed: 06/11/2023]
Abstract
Possessing powerful adaptive capacity and a pleasant taste, spotted sea bass (Lateolabrax maculatus) has a broad natural distribution and is one of the most popular mariculture fish in China. However, the genetic improvement program for this fish is still in its infancy. Growth is the most economically important trait and is controlled by quantitative trait loci (QTL); thus, the identification of QTLs and genetic markers for growth-related traits is an essential step for the establishment of marker-assisted selection (MAS) breeding programs. In this study, we report the first high-density linkage map of spotted sea bass constructed by sequencing 333 F1 generation individuals in a full-sib family using 2b-RAD technology. A total of 6883 SNP markers were anchored onto 24 linkage groups, spanning 2189.96 cM with an average marker interval of 0.33 cM. Twenty-four growth-related QTLs, including 13 QTLs for body weight and 11 QTLs for body length, were successfully detected, with phenotypic variance explained (PVE) ranging from 5.1 to 8.6%. Thirty potential candidate growth-related genes surrounding the associated SNPs were involved in cell adhesion, cell proliferation, cytoskeleton reorganization, calcium channels, and neuromodulation. Notably, the fgfr4 gene was detected in the most significant QTL; this gene plays a pivotal role in myogenesis and bone growth. The results of this study may facilitate marker-assisted selection for breeding populations and establish the foundation for further genomic and genetic studies investigating spotted sea bass.
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Affiliation(s)
- Yang Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Haolong Wang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Haishen Wen
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yue Shi
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Meizhao Zhang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Xin Qi
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Kaiqiang Zhang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qingli Gong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Jifang Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Feng He
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yanbo Hu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yun Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
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15
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Yang Y, Wu LN, Chen JF, Wu X, Xia JH, Meng ZN, Liu XC, Lin HR. Whole-genome sequencing of leopard coral grouper ( Plectropomus leopardus) and exploration of regulation mechanism of skin color and adaptive evolution. Zool Res 2020; 41:328-340. [PMID: 32212431 PMCID: PMC7231471 DOI: 10.24272/j.issn.2095-8137.2020.038] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/25/2020] [Indexed: 01/09/2023] Open
Abstract
Leopard coral groupers belong to the Plectropomus genus of the Epinephelidae family and are important fish for coral reef ecosystems and the marine aquaculture industry. To promote future research of this species, a high-quality chromosome-level genome was assembled using PacBio sequencing and Hi-C technology. A 787.06 Mb genome was assembled, with 99.7% (784.57 Mb) of bases anchored to 24 chromosomes. The leopard coral grouper genome size was smaller than that of other groupers, which may be related to its ancient status among grouper species. A total of 22 317 protein-coding genes were predicted. This high-quality genome of the leopard coral grouper is the first genomic resource for Plectropomus and should provide a pivotal genetic foundation for further research. Phylogenetic analysis of the leopard coral grouper and 12 other fish species showed that this fish is closely related to the brown-marbled grouper. Expanded genes in the leopard coral grouper genome were mainly associated with immune response and movement ability, which may be related to the adaptive evolution of this species to its habitat. In addition, we also identified differentially expressed genes (DEGs) associated with carotenoid metabolism between red and brown-colored leopard coral groupers. These genes may play roles in skin color decision by regulating carotenoid content in these groupers.
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Affiliation(s)
- Yang Yang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Sciences School, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China
| | - Li-Na Wu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Sciences School, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China
| | - Jing-Fang Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China
| | - Xi Wu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Sciences School, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China
| | - Jun-Hong Xia
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Sciences School, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, Guangdong 519000, China
| | - Zi-Ning Meng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Sciences School, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, Guangdong 519000, China. E-mail:
| | - Xiao-Chun Liu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Sciences School, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, Guangdong 519000, China. E-mail:
| | - Hao-Ran Lin
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Sciences School, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, Guangdong 519000, China
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16
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Genome Survey of Male and Female Spotted Scat ( Scatophagus argus). Animals (Basel) 2019; 9:ani9121117. [PMID: 31835725 PMCID: PMC6940847 DOI: 10.3390/ani9121117] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/07/2019] [Accepted: 12/09/2019] [Indexed: 12/17/2022] Open
Abstract
Simple Summary The spotted scat, Scatophagus argus, is a marine aquaculture fish species that is economically important in Asia. As the spotted scat exhibits notable sexual dimorphism with respect to growth, aquaculture efficiency can be increased through the practice of sex control breeding. However, genomic data from S. argus is lacking. In the present study, a genomic survey was conducted using next-generation sequencing technologies. Data, including the size of the genome, sequence repeat ratio, heterozygosity ratio, whole genome sequence and gene annotation were obtained. This information will serve to support the breeding and aquaculture of S. argus. Abstract The spotted scat, Scatophagus argus, is a species of fish that is widely propagated within the Chinese aquaculture industry and therefore has significant economic value. Despite this, studies of its genome are severely lacking. In the present study, a genomic survey of S. argus was conducted using next-generation sequencing (NGS). In total, 55.699 GB (female) and 51.047 GB (male) of high-quality sequence data were obtained. Genome sizes were estimated to be 598.73 (female) and 597.60 (male) Mbp. The sequence repeat ratios were calculated to be 27.06% (female) and 26.99% (male). Heterozygosity ratios were 0.37% for females and 0.38% for males. Reads were assembled into 444,961 (female) and 453,459 (male) contigs with N50 lengths of 5,747 and 5,745 bp for females and males, respectively. The average guanine-cytosine (GC) content of the female genome was 41.78%, and 41.82% for the male. A total of 42,869 (female) and 43,283 (male) genes were annotated to the non-redundant (NR) and SwissProt databases. The female and male genomes contained 66.6% and 67.8% BUSCO core genes, respectively. Dinucleotide repeats were the dominant form of simple sequence repeats (SSR) observed in females (68.69%) and males (68.56%). Additionally, gene fragments of Dmrt1 were only observed in the male genome. This is the first report of a genome-wide characterization of S. argus.
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17
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Tian Y, Wen H, Qi X, Zhang X, Liu S, Li B, Sun Y, Li J, He F, Yang W, Li Y. Characterization of Full-Length Transcriptome Sequences and Splice Variants of Lateolabrax maculatus by Single-Molecule Long-Read Sequencing and Their Involvement in Salinity Regulation. Front Genet 2019; 10:1126. [PMID: 31803231 PMCID: PMC6873903 DOI: 10.3389/fgene.2019.01126] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 10/17/2019] [Indexed: 12/17/2022] Open
Abstract
Transcriptome complexity plays crucial roles in regulating the biological functions of eukaryotes. Except for functional genes, alternative splicing and fusion transcripts produce a vast expansion of transcriptome diversity. In this study, we applied PacBio single-molecule long-read sequencing technology to unveil the whole transcriptome landscape of Lateolabrax maculatus. We obtained 28,809 high-quality non-redundant transcripts, including 18,280 novel isoforms covering 8,961 annotated gene loci within the current reference genome and 3,172 novel isoforms. A total of 10,249 AS events were detected, and intron retention was the predominant AS event. In addition, 1,359 alternative polyadenylation events, 3,112 lncRNAs, 29,609 SSRs, 365 fusion transcripts, and 1,194 transcription factors were identified in this study. Furthermore, we performed RNA-Seq analysis combined with Iso-Seq results to investigate salinity regulation mechanism at the transcripts level. A total of 518 transcripts were differentially expressed, which were further divided into 8 functional groups. Notably, transcripts from the same genes exhibited similar or opposite expression patterns. Our study provides a comprehensive view of the transcriptome complexity in L. maculatus, which significantly improves current gene models. Moreover, the diversity of the expression patterns of transcripts may enhance the understanding of salinity regulatory mechanism in L. maculatus and other euryhaline teleosts.
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Affiliation(s)
- Yuan Tian
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Haishen Wen
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Xin Qi
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Xiaoyan Zhang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Bingyu Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Yalong Sun
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Jifang Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Feng He
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Wenzhao Yang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Yun Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
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18
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Chromosome-level genome assembly of golden pompano (Trachinotus ovatus) in the family Carangidae. Sci Data 2019; 6:216. [PMID: 31641137 PMCID: PMC6805935 DOI: 10.1038/s41597-019-0238-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 09/11/2019] [Indexed: 12/20/2022] Open
Abstract
Golden pompano (Trachinotus ovatus), a marine fish in the Carangidae family, has a wide geographical distribution and adapts to severe environmental rigours. It is also an economically valuable aquaculture fish. To understand the genetic mechanism of adaption to environmental rigours and improve the production in aquaculture, we assembled its genome. By combination of Illumina and Pacbio reads, the obtained genome sequence is 647.5 Mb with the contig N50 of 1.80 Mb and the scaffold N50 of 5.05 Mb. The assembly covers 98.9% of the estimated genome size (655 Mb). Based on Hi-C data, 99.4% of the assembled bases are anchored into 24 pseudo-chromosomes. The annotation includes 21,915 protein-coding genes, in which 95.7% of 2,586 BUSCO vertebrate conserved genes are complete. This genome is expected to contribute to the comparative analysis of the Carangidae family. Measurement(s) | DNA • chromosome conformation capture assay • transcription profiling assay | Technology Type(s) | DNA sequencing • Hi-C • RNA sequencing | Factor Type(s) | organism part | Sample Characteristic - Organism | Trachinotus ovatus | Sample Characteristic - Environment | ocean biome |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.9933515
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19
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Nguinkal JA, Brunner RM, Verleih M, Rebl A, de Los Ríos-Pérez L, Schäfer N, Hadlich F, Stüeken M, Wittenburg D, Goldammer T. The First Highly Contiguous Genome Assembly of Pikeperch ( Sander lucioperca), an Emerging Aquaculture Species in Europe. Genes (Basel) 2019; 10:E708. [PMID: 31540274 PMCID: PMC6770990 DOI: 10.3390/genes10090708] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/27/2019] [Accepted: 09/08/2019] [Indexed: 01/14/2023] Open
Abstract
The pikeperch (Sander lucioperca) is a fresh and brackish water Percid fish natively inhabiting the northern hemisphere. This species is emerging as a promising candidate for intensive aquaculture production in Europe. Specific traits like cannibalism, growth rate and meat quality require genomics based understanding, for an optimal husbandry and domestication process. Still, the aquaculture community is lacking an annotated genome sequence to facilitate genome-wide studies on pikeperch. Here, we report the first highly contiguous draft genome assembly of Sander lucioperca. In total, 413 and 66 giga base pairs of DNA sequencing raw data were generated with the Illumina platform and PacBio Sequel System, respectively. The PacBio data were assembled into a final assembly size of ~900 Mb covering 89% of the 1,014 Mb estimated genome size. The draft genome consisted of 1966 contigs ordered into 1,313 scaffolds. The contig and scaffold N50 lengths are 3.0 Mb and 4.9 Mb, respectively. The identified repetitive structures accounted for 39% of the genome. We utilized homologies to other ray-finned fishes, and ab initio gene prediction methods to predict 21,249 protein-coding genes in the Sander lucioperca genome, of which 88% were functionally annotated by either sequence homology or protein domains and signatures search. The assembled genome spans 97.6% and 96.3% of Vertebrate and Actinopterygii single-copy orthologs, respectively. The outstanding mapping rate (99.9%) of genomic PE-reads on the assembly suggests an accurate and nearly complete genome reconstruction. This draft genome sequence is the first genomic resource for this promising aquaculture species. It will provide an impetus for genomic-based breeding studies targeting phenotypic and performance traits of captive pikeperch.
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Affiliation(s)
- Julien Alban Nguinkal
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Ronald Marco Brunner
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Marieke Verleih
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Alexander Rebl
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Lidia de Los Ríos-Pérez
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Nadine Schäfer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Frieder Hadlich
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Marcus Stüeken
- State Research Center of Agriculture and Fisheries M-V, 17194 Hohen Wangelin, Germany.
| | - Dörte Wittenburg
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Tom Goldammer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
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20
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Chen B, Li Y, Peng W, Zhou Z, Shi Y, Pu F, Luo X, Chen L, Xu P. Chromosome-Level Assembly of the Chinese Seabass ( Lateolabrax maculatus) Genome. Front Genet 2019; 10:275. [PMID: 31019525 PMCID: PMC6459032 DOI: 10.3389/fgene.2019.00275] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/12/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Baohua Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Shenzhen Research Institute of Xiamen University, Shenzhen, China
| | - Yun Li
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Wenzhu Peng
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,State-Province Joint Engineer Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Zhixiong Zhou
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,State-Province Joint Engineer Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yue Shi
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,State-Province Joint Engineer Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Fei Pu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Shenzhen Research Institute of Xiamen University, Shenzhen, China
| | - Xuan Luo
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,State-Province Joint Engineer Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Lin Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,State-Province Joint Engineer Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Peng Xu
- Shenzhen Research Institute of Xiamen University, Shenzhen, China.,State-Province Joint Engineer Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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21
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Shao C, Li C, Wang N, Qin Y, Xu W, Liu Q, Zhou Q, Zhao Y, Li X, Liu S, Chen X, Mahboob S, Liu X, Chen S. Chromosome-level genome assembly of the spotted sea bass, Lateolabrax maculatus. Gigascience 2018; 7:5099471. [PMID: 30239684 PMCID: PMC6240815 DOI: 10.1093/gigascience/giy114] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 08/31/2018] [Indexed: 11/16/2022] Open
Abstract
Background The spotted sea bass (Lateolabrax maculatus) is a valuable commercial fish that is widely cultured in China. While analyses using molecular markers and population genetics have been conducted, genomic resources are lacking. Findings Here, we report a chromosome-scale assembly of the spotted sea bass genome by high-depth genome sequencing, assembly, and annotation. The genome scale was 0.67 Gb with contig and scaffold N50 length of 31 Kb and 1,040 Kb, respectively. Hi-C scaffolding of the genome resulted in 24 pseudochromosomes containing 77.68% of the total assembled sequences. A total of 132.38 Mb repeat sequences were detected, accounting for 20.73% of the assembled genome. A total of 22, 015 protein-coding genes were predicted, of which 96.52% were homologous to proteins in various databases. In addition, we constructed a phylogenetic tree using 1,586 single-copy gene families and identified 125 unique gene families in the spotted sea bass genome. Conclusions We assembled a spotted sea bass genome that will be a valuable genomic resource to understanding the biology of the spotted sea bass and will also lead to the development of molecular breeding techniques to generate spotted sea bass with better economic traits.
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Affiliation(s)
- Changwei Shao
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao, 266071, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Wenhai Road 1, Qingdao, 266237, China
| | - Chang Li
- BGI Education Center, University of Chinese Academy of Sciences, Beishan Road, Shenzhen, 518083, China.,BGI-Qingdao, BGI-Shenzhen, Hengyun Mountain Road, Qingdao, 266555, China.,BGI-Shenzhen, Beishan Road, Shenzhen, 518083, China
| | - Na Wang
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao, 266071, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Wenhai Road 1, Qingdao, 266237, China
| | - Yating Qin
- BGI-Qingdao, BGI-Shenzhen, Hengyun Mountain Road, Qingdao, 266555, China.,BGI-Shenzhen, Beishan Road, Shenzhen, 518083, China
| | - Wenteng Xu
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao, 266071, China
| | - Qun Liu
- BGI-Qingdao, BGI-Shenzhen, Hengyun Mountain Road, Qingdao, 266555, China
| | - Qian Zhou
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao, 266071, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Wenhai Road 1, Qingdao, 266237, China
| | - Yong Zhao
- BGI-Qingdao, BGI-Shenzhen, Hengyun Mountain Road, Qingdao, 266555, China
| | - Xihong Li
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao, 266071, China
| | - Shanshan Liu
- BGI-Qingdao, BGI-Shenzhen, Hengyun Mountain Road, Qingdao, 266555, China.,BGI-Shenzhen, Beishan Road, Shenzhen, 518083, China
| | - Xiaowu Chen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Huchenghuan Road 999, Shanghai, 201306, China
| | - Shahid Mahboob
- Department of Zoology, College of Science, King Saud University, P.O.Box 2455, Riyadh, 11451, Saudi Arabia.,Department of Zoology, Government College University, Allama Iqbal Road, Faisalabad, 38000, Pakistan
| | - Xin Liu
- BGI-Qingdao, BGI-Shenzhen, Hengyun Mountain Road, Qingdao, 266555, China.,BGI-Shenzhen, Beishan Road, Shenzhen, 518083, China
| | - Songlin Chen
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao, 266071, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Wenhai Road 1, Qingdao, 266237, China
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