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Li X, Bai Y, Xu C, Liu S, Yu H, Kong L, Du S, Li Q. OysterDB: A Genome Database for Ostreidae. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024:10.1007/s10126-024-10327-7. [PMID: 38822152 DOI: 10.1007/s10126-024-10327-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/23/2024] [Indexed: 06/02/2024]
Abstract
The molluscan family Ostreidae, commonly known as oysters, is an important molluscan group due to its economic and ecological importance. In recent years, an abundance of genomic data of Ostreidae species has been generated and available in public domain. However, there is still a lack of a high-efficiency database platform to store and distribute these data with comprehensive tools. In this study, we developed an oyster genome database (OysterDB) to consolidate oyster genomic data. This database includes eight oyster genomes and 208,923 protein-coding gene annotations. Bioinformatic tools, such as BLAST and JBrowse, are integrated into the database to provide a user-friendly platform for homologous sequence searching, visualization of genomes, and screen for candidate gene information. Moreover, OysterDB will be continuously updated with ever-growing oyster genomic resources and facilitate future studies for comparative and functional genomic analysis of oysters ( http://oysterdb.com.cn/ ).
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Affiliation(s)
- Xinchun Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Yitian Bai
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Chengxun Xu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Shaojun Du
- Institute of Marine and Environmental Technology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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Zhang X, Guan J, Zou M, He P, Zhang L, Chen Y, Li W, Wang D, Yu E, Zhong F, Zhu P, Yan X, Xu Y, Luo B, Huang T, Jiang L, Wei P, Peng J. Whole genome sequencing of Crassostrea ariakensis (Mollusca: Ostreidae) and C. hongkongensis expands understandings of stress resistance in sessile oysters. Genomics 2024; 116:110757. [PMID: 38061482 DOI: 10.1016/j.ygeno.2023.110757] [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: 09/06/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 12/17/2023]
Abstract
To understand the environmental adaptations among sessile bivalves lacking adaptive immunity, a series of analyses were conducted, with special emphasis on the widely distributed C. ariakensis. Employing Pacbio sequencing and Hi-C technologies, whole genome for each of a C. ariakensis (southern China) and C. hongkongensis individual was generated, with the contig N50 reaching 6.2 and 13.0 Mb, respectively. Each genome harbored over 30,000 protein-coding genes, with approximately half of each genome consisting of repeats. Genome alignment suggested possible introgression between C. gigas and C. ariakensis (northern China), and re-sequencing data corroborated this result and indicated significant gene flow between C. gigas and C. ariakensis. These introgressed candidates, well-represented by genes related to immunity and osmotic pressure, may be associated with environmental stresses. Gene family dynamics modeling suggested immune-related genes were well represented among the expanded genes in C. ariakensis. These outcomes could be attributed to the spread of C. ariakensis.
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Affiliation(s)
- Xingzhi Zhang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China
| | - Junliang Guan
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China
| | - Ming Zou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Pingping He
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China
| | - Li Zhang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China
| | - Yongxian Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China.
| | - Wei Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China
| | - Dapeng Wang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China
| | - Ermeng Yu
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China.
| | | | - Peng Zhu
- Beibu Gulf University, Qinzhou 535000, China
| | - Xueyu Yan
- Beibu Gulf University, Qinzhou 535000, China.
| | - Youhou Xu
- Beibu Gulf University, Qinzhou 535000, China
| | - Bang Luo
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China
| | - Ting Huang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China
| | - Linyuan Jiang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China.
| | - Pinyuan Wei
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China.
| | - Jinxia Peng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Key Laboratory of Comprehensive Development and Utilization of Aquatic Germplasm Resources of China (Guangxi) and ASEAN (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fisheries Sciences, Nanning 530021, China.
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Du M, Jiang Z, Wang C, Wei C, Li Q, Cong R, Wang W, Zhang G, Li L. Genome-Wide Association Analysis of Heat Tolerance in F 2 Progeny from the Hybridization between Two Congeneric Oyster Species. Int J Mol Sci 2023; 25:125. [PMID: 38203295 PMCID: PMC10778899 DOI: 10.3390/ijms25010125] [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: 11/23/2023] [Revised: 12/13/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024] Open
Abstract
As the world's largest farmed marine animal, oysters have enormous economic and ecological value. However, mass summer mortality caused by high temperature poses a significant threat to the oyster industry. To investigate the molecular mechanisms underlying heat adaptation and improve the heat tolerance ability in the oyster, we conducted genome-wide association analysis (GWAS) analysis on the F2 generation derived from the hybridization of relatively heat-tolerant Crassostrea angulata ♀ and heat-sensitive Crassostrea gigas ♂, which are the dominant cultured species in southern and northern China, respectively. Acute heat stress experiment (semi-lethal temperature 42 °C) demonstrated that the F2 population showed differentiation in heat tolerance, leading to extremely differentiated individuals (approximately 20% of individuals die within the first four days with 10% survival after 14 days). Genome resequencing and GWAS of the two divergent groups had identified 18 significant SNPs associated with heat tolerance, with 26 candidate genes located near these SNPs. Eleven candidate genes that may associate with the thermal resistance were identified, which were classified into five categories: temperature sensor (Trpm2), transcriptional factor (Gata3), protein ubiquitination (Ube2h, Usp50, Uchl3), heat shock subfamily (Dnajc17, Dnaja1), and transporters (Slc16a9, Slc16a14, Slc16a9, Slc16a2). The expressional differentiation of the above genes between C. gigas and C. angulata under sublethal temperature (37 °C) further supports their crucial role in coping with high temperature. Our results will contribute to understanding the molecular mechanisms underlying heat tolerance, and provide genetic markers for heat-resistance breeding in the oyster industry.
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Affiliation(s)
- Mingyang Du
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.D.); (Z.J.); (C.W.); (C.W.); (Q.L.); (R.C.); (W.W.); (G.Z.)
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266100, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Zhuxiang Jiang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.D.); (Z.J.); (C.W.); (C.W.); (Q.L.); (R.C.); (W.W.); (G.Z.)
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266100, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Chaogang Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.D.); (Z.J.); (C.W.); (C.W.); (Q.L.); (R.C.); (W.W.); (G.Z.)
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266100, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Chenchen Wei
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.D.); (Z.J.); (C.W.); (C.W.); (Q.L.); (R.C.); (W.W.); (G.Z.)
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266100, China
| | - Qingyuan Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.D.); (Z.J.); (C.W.); (C.W.); (Q.L.); (R.C.); (W.W.); (G.Z.)
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266100, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Rihao Cong
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.D.); (Z.J.); (C.W.); (C.W.); (Q.L.); (R.C.); (W.W.); (G.Z.)
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266100, China
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Wei Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.D.); (Z.J.); (C.W.); (C.W.); (Q.L.); (R.C.); (W.W.); (G.Z.)
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266100, China
| | - Guofan Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.D.); (Z.J.); (C.W.); (C.W.); (Q.L.); (R.C.); (W.W.); (G.Z.)
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266100, China
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Wuhan 430072, China
| | - Li Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.D.); (Z.J.); (C.W.); (C.W.); (Q.L.); (R.C.); (W.W.); (G.Z.)
- University of Chinese Academy of Sciences, Beijing 101408, China
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266100, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Wuhan 430072, China
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