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Samarin AM, Samarin AM, Waghmare SG, Danielsen M, Møller HS, Policar T, Linhart O, Dalsgaard TK. In vitro post-ovulatory oocyte ageing in grass carp Ctenopharyngodon idella affects H4K12 acetylation pattern and histone acetyltransferase activity. FISH PHYSIOLOGY AND BIOCHEMISTRY 2023:10.1007/s10695-023-01273-7. [PMID: 38019384 DOI: 10.1007/s10695-023-01273-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 11/12/2023] [Indexed: 11/30/2023]
Abstract
Delayed fertilization leads to the ageing of post-ovulatory oocytes and reduces the developmental competence of arising embryos. Little information is available about the molecular processes during fish oocyte ageing. The current study investigated the functional consequences of oocyte ageing in grass carp Ctenopharyngodon idella embryos. In addition, the dynamics of selected post-transcriptionally modified histones (acetylation of H3K9, H3K14, H4K5, H4K8, H4K12, and H4K16) were analyzed during oocyte ageing. Ovulated oocytes were aged in vitro for 4 h in the laboratory incubator at 20 °C and studied for selected post-translational modification of histones. In addition, histone acetyltransferase activity was investigated as an important regulator of histone acetylation modification. The results indicated a significant decrease in oocyte fertilizing ability through 1 h of post-ovulatory ageing, and a complete loss of egg fertilizing abilities was detected at 4-h aged oocytes. Furthermore, post-ovulatory oocyte ageing for 1 and 4 h led to decreased levels of H4K12 acetylation. The activity of histone acetyltransferases increased significantly after ageing of the oocytes for 30 h in vitro. This modification may partly contribute to explaining the failures of egg viability and embryo development in the offspring from the aged oocytes. The results are the first to report histone modifications as a crucial epigenetic regulator during oocyte ageing in fish and might also benefit other vertebrates.
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Affiliation(s)
- Azin Mohagheghi Samarin
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, 389 25 Vodňany, České Budějovice, Czech Republic.
| | - Azadeh Mohagheghi Samarin
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, 389 25 Vodňany, České Budějovice, Czech Republic
| | - Swapnil Gorakh Waghmare
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, 389 25 Vodňany, České Budějovice, Czech Republic
| | - Marianne Danielsen
- Department of Food Science, Aarhus University, Agro Food Park 48, 8200, Aarhus, Denmark
- CiFood Centre of Innovative Food Research, Aarhus University, 8200, Aarhus, Denmark
- CBIO, Aarhus University Centre for Circular Bioeconomy, 8830, Tjele, Denmark
| | | | - Tomáš Policar
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, 389 25 Vodňany, České Budějovice, Czech Republic
| | - Otomar Linhart
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, 389 25 Vodňany, České Budějovice, Czech Republic
| | - Trine Kastrup Dalsgaard
- Department of Food Science, Aarhus University, Agro Food Park 48, 8200, Aarhus, Denmark
- CiFood Centre of Innovative Food Research, Aarhus University, 8200, Aarhus, Denmark
- CBIO, Aarhus University Centre for Circular Bioeconomy, 8830, Tjele, Denmark
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2
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Li Y, Song WJ, Yi SK, Yu HX, Mo HL, Yao MX, Tao YX, Wang LX. Molecular Cloning, Tissue Distribution, and Pharmacological Characterization of GPR84 in Grass Carp ( Ctenopharyngodon Idella). Animals (Basel) 2023; 13:3001. [PMID: 37835607 PMCID: PMC10571743 DOI: 10.3390/ani13193001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 09/09/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
The G-protein-coupled receptor GPR84, activated by medium-chain fatty acids, primarily expressed in macrophages and microglia, is involved in inflammatory responses and retinal development in mammals and amphibians. However, our understanding of its structure, function, tissue expression, and signaling pathways in fish is limited. In this study, we cloned and characterized the coding sequence of GPR84 (ciGPR84) in grass carp. A phylogenetic analysis revealed its close relationship with bony fishes. High expression levels of GPR84 were observed in the liver and spleen. The transfection of HEK293T cells with ciGPR84 demonstrated its responsiveness to medium-chain fatty acids and diindolylmethane (DIM). Capric acid, undecanoic acid, and lauric acid activated ERK and inhibited cAMP signaling. Lauric acid showed the highest efficiency in activating the ERK pathway, while capric acid was the most effective in inhibiting cAMP signaling. Notably, DIM did not activate GPR84 in grass carp, unlike in mammals. These findings provide valuable insights for mitigating chronic inflammation in grass carp farming and warrant further exploration of the role of medium-chain fatty acids in inflammation regulation in this species.
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Affiliation(s)
- Yang Li
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (W.-J.S.); (H.-X.Y.); (H.-L.M.); (M.-X.Y.); (L.-X.W.)
| | - Wei-Jia Song
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (W.-J.S.); (H.-X.Y.); (H.-L.M.); (M.-X.Y.); (L.-X.W.)
| | - Shao-Kui Yi
- College of Life Sciences, Huzhou University, Huzhou 313000, China;
| | - Hui-Xia Yu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (W.-J.S.); (H.-X.Y.); (H.-L.M.); (M.-X.Y.); (L.-X.W.)
| | - Hao-Lin Mo
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (W.-J.S.); (H.-X.Y.); (H.-L.M.); (M.-X.Y.); (L.-X.W.)
| | - Ming-Xing Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (W.-J.S.); (H.-X.Y.); (H.-L.M.); (M.-X.Y.); (L.-X.W.)
| | - Ya-Xiong Tao
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA;
| | - Li-Xin Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (W.-J.S.); (H.-X.Y.); (H.-L.M.); (M.-X.Y.); (L.-X.W.)
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3
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Li Y, Chen L, Li Y, Deng P, Yang C, Li Y, Liao L, Zhu Z, Wang Y, Huang R. miR-2188-5p promotes GCRV replication by the targeted degradation of klf2a in Ctenopharyngodon idellus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 138:104516. [PMID: 36084755 DOI: 10.1016/j.dci.2022.104516] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
Studies on host immunity evasion by aquatic viruses have largely focused on coding genes. There is accumulating evidence for the important biological functions of non-coding miRNAs in virus-host interactions. The regulatory functions of non-coding miRNAs in fish reovirus-host interactions remain unknown. Here, miR-2188-5p in grass carp (Ctenopharyngodon idellus), a miRNA specific to teleosts, was predicted to target the 3' UTR of the transcription factor klf2a. A correlation analysis and dual-luciferase reporter assay revealed that miR-2188-5p could induce the degradation of klf2a. The expression of miR-2188-5p induced the degradation of klf2a in a dose-dependent manner, suppressing the type I interferon response and promoting grass carp reovirus (GCRV) replication. As determined by a co-expression analysis, klf2a inhibited viral infection when miR-2188-5p was overexpressed. The targeted degradation of klf2a by miR-2188-5p could inhibit the type I interferon response and promote the replication of GCRV; however, this targeted degradation ability was insufficient to fully inhibit GCRV infection. These results provide novel insights into the regulatory effects and biological functions of non-coding miRNAs in fish-virus interactions.
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Affiliation(s)
- Yangyu Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liangming Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yangyang Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ping Deng
- Wuhan Academy of Agricultural Sciences, Wuhan, 430207, China
| | - Cheng Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yongming Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Lanjie Liao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zuoyan Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yaping Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Rong Huang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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4
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Yang L, Xu Z, Zeng H, Sun N, Wu B, Wang C, Bo J, Li L, Dong Y, He S. FishDB: an integrated functional genomics database for fishes. BMC Genomics 2020; 21:801. [PMID: 33203359 PMCID: PMC7670658 DOI: 10.1186/s12864-020-07159-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 10/19/2020] [Indexed: 11/29/2022] Open
Abstract
Background Hundreds of genomes and transcriptomes of fish species have been sequenced in recent years. However, fish scholarship currently lacks a comprehensive, integrated, and up-to-date collection of fish genomic data. Results Here we present FishDB, the first database for fish multi-level omics data, available online at http://fishdb.ihb.ac.cn. The database contains 233 fish genomes, 201 fish transcriptomes, 5841 fish mitochondrial genomes, 88 fish gene sets, 16,239 miRNAs of 65 fishes, 1,330,692 piRNAs and 4852 lncRNAs of Danio rerio, 59,040 Mb untranslated regions (UTR) of 230 fishes, and 31,918 Mb coding sequences (CDS) of 230 fishes. Among these, we newly generated a total of 11 fish genomes and 53 fish transcriptomes. Conclusions This release contains over 410,721.67 Mb sequences and provides search functionality, a BLAST server, JBrowse, and PrimerServer modules. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07159-9.
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Affiliation(s)
- Liandong Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zetan Xu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Honghui Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Ning Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baosheng Wu
- University of Chinese Academy of Sciences, Beijing, 100049, China.,Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Cheng Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Bo
- University of Chinese Academy of Sciences, Beijing, 100049, China.,Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Lin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China. .,Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
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5
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Shi M, Zhang Q, Li Y, Zhang W, Liao L, Cheng Y, Jiang Y, Huang X, Duan Y, Xia L, Ye W, Wang Y, Xia XQ. Global gene expression profile under low-temperature conditions in the brain of the grass carp (Ctenopharyngodon idellus). PLoS One 2020; 15:e0239730. [PMID: 32976524 PMCID: PMC7518592 DOI: 10.1371/journal.pone.0239730] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 09/13/2020] [Indexed: 01/29/2023] Open
Abstract
Grass carp is an important commercial fish widely cultivated in China. A wide range of temperatures, particularly extremely low temperatures, have dramatic effects on the aquaculture of this teleost. However, relatively few studies have characterized the molecular responses of grass carp exposed to acute cooling in natural environment. Here, we investigated the transcriptome profiles of the grass carp brain in response to cooling. Through regulation pattern analyses, we identified 2,513 differentially expressed genes (DEGs) that responded to moderate cold stress (12°C), while 99 DEGs were induced by severe low temperature (4°C).The pathway analyses revealed that the DEGs sensitive to moderate cold were largely enriched in steroid biosynthesis, spliceosome, translation, protein metabolism, phagosome, gap junction and estrogen signaling pathways. Additionally, we discerned genes most likely involved in low temperature tolerance, of which the MAPK signaling pathway was dominantly enriched. Further examination and characterization of the candidate genes may help to elucidate the mechanisms underpinning extreme plasticity to severe cold stress in grass carp.
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Affiliation(s)
- Mijuan Shi
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Qiangxiang Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yongming Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Wanting Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Lanjie Liao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Yingyin Cheng
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Yanxin Jiang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoli Huang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - You Duan
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lei Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Weidong Ye
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yaping Wang
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- * E-mail: (XQX); (YW)
| | - Xiao-Qin Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- * E-mail: (XQX); (YW)
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6
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Huang X, Jiang Y, Zhang W, Cheng Y, Wang Y, Ma X, Duan Y, Xia L, Chen Y, Wu N, Shi M, Xia XQ. Construction of a high-density genetic map and mapping of growth related QTLs in the grass carp (Ctenopharyngodon idellus). BMC Genomics 2020; 21:313. [PMID: 32306899 PMCID: PMC7168995 DOI: 10.1186/s12864-020-6730-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 04/14/2020] [Indexed: 12/25/2022] Open
Abstract
Background Grass carp (Ctenopharyngodon idellus) are important species in Asian aquaculture. A draft genome for grass carp has already been published in 2015. However, there is still a requirement for a suitable genetic linkage map to arrange scaffolds on chromosomal frameworks. QTL analysis is a powerful tool to detect key locations for quantitative traits, especially in aquaculture. There no growth related QTLs of grass carp have been published yet. Even the growth trait is one of the focuses in grass carp culture. Results In this study, a pair of distantly related parent grass carps and their 100 six-month-old full-sib offspring were used to construct a high-density genetic map with 6429 single nucleotide polymorphisms (SNPs) by 2b-RAD technology. The total length of the consensus map is 5553.43 cM with the average marker interval of 1.92 cM. The map has a good collinearity with both the grass carp draft genome and the zebrafish genome, and it assembled 89.91% of the draft genome to a chromosomal level. Additionally, according to the growth-related traits of progenies, 30 quantitative trait loci (QTLs), including 7 for body weight, 9 for body length, 5 for body height and 9 for total length, were identified in 16 locations on 5 linkage groups. The phenotypic variance explained for these QTLs varies from 13.4 to 21.6%. Finally, 17 genes located in these regions were considered to be growth-related because they either had functional mutations predicted from the resequencing data of the parents. Conclusion A high density genetic linkage map of grass carp was built and it assembled the draft genome to a chromosomal level. Thirty growth related QTLs were detected. After the cross analysis of Parents resequencing data, 17 candidate genes were obtained for further researches.
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Affiliation(s)
- Xiaoli Huang
- Institute of Hydrobiology, the Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yanxin Jiang
- Institute of Hydrobiology, the Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wanting Zhang
- Institute of Hydrobiology, the Chinese Academy of Sciences, Wuhan, China
| | - Yingyin Cheng
- Institute of Hydrobiology, the Chinese Academy of Sciences, Wuhan, China
| | - Yaping Wang
- Institute of Hydrobiology, the Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaocui Ma
- Institute of Hydrobiology, the Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - You Duan
- Institute of Hydrobiology, the Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Lei Xia
- Institute of Hydrobiology, the Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yaxin Chen
- Institute of Hydrobiology, the Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Nan Wu
- Institute of Hydrobiology, the Chinese Academy of Sciences, Wuhan, China
| | - Mijuan Shi
- Institute of Hydrobiology, the Chinese Academy of Sciences, Wuhan, China.
| | - Xiao-Qin Xia
- Institute of Hydrobiology, the Chinese Academy of Sciences, Wuhan, China. .,University of Chinese Academy of Sciences, Beijing, China.
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7
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Tang M, Lu Y, Xiong Z, Chen M, Qin Y. The Grass Carp Genomic Visualization Database (GCGVD): an informational platform for genome biology of grass carp. Int J Biol Sci 2019; 15:2119-2127. [PMID: 31592084 PMCID: PMC6775296 DOI: 10.7150/ijbs.32860] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 05/27/2019] [Indexed: 11/25/2022] Open
Abstract
With the release of the draft genome of the grass carp, researches on the grass carp from the genetic level and the further molecular mechanisms of economically valuable physiological behaviors have gained great attention. In this paper, we integrated a large number of genomic, genetic and some other data resources and established a web-based grass carp genomic visualization database (GCGVD). To view these data more effectively, we visualized grass carp and zebrafish gene collinearity and genetic linkage map using Scalable Vector Graphics (SVG) format in the browser, and genomic annotations by JBrowse. Furthermore, we carried out some preliminary study on a whole-genome alternative splicing (AS)of the grass carp. The RNA-seq reads of 15 samples were aligned to the reference genome of the grass carp by Bowtie2 software. RNA-seq reads of each sample and density map of reads were also exhibited in JBrowse. Additionally, we designed a universal grass carp genome annotation data model to improve the retrieval speed and scalability. Compared with the published database GCGD previously, we newly added the visualization of some more genomic annotations, conserved domain and RNA-seq reads aligned to the reference genome. GCGVD can be accessed at http://122.112.216.104.
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Affiliation(s)
- Min Tang
- College of Information Technology, Shanghai Ocean University, Shanghai, 201306, China.,Key Laboratory of Fisheries Information Ministry of Agriculture, Shanghai, 201306, China
| | - Ying Lu
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Zhongmin Xiong
- College of Information Technology, Shanghai Ocean University, Shanghai, 201306, China.,Key Laboratory of Fisheries Information Ministry of Agriculture, Shanghai, 201306, China
| | - Ming Chen
- College of Information Technology, Shanghai Ocean University, Shanghai, 201306, China.,Key Laboratory of Fisheries Information Ministry of Agriculture, Shanghai, 201306, China
| | - Yufang Qin
- College of Information Technology, Shanghai Ocean University, Shanghai, 201306, China.,Key Laboratory of Fisheries Information Ministry of Agriculture, Shanghai, 201306, China
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8
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Chen Z, Omori Y, Koren S, Shirokiya T, Kuroda T, Miyamoto A, Wada H, Fujiyama A, Toyoda A, Zhang S, Wolfsberg TG, Kawakami K, Phillippy AM, Mullikin JC, Burgess SM. De novo assembly of the goldfish ( Carassius auratus) genome and the evolution of genes after whole-genome duplication. SCIENCE ADVANCES 2019; 5:eaav0547. [PMID: 31249862 PMCID: PMC6594761 DOI: 10.1126/sciadv.aav0547] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 05/21/2019] [Indexed: 05/20/2023]
Abstract
For over a thousand years, the common goldfish (Carassius auratus) was raised throughout Asia for food and as an ornamental pet. As a very close relative of the common carp (Cyprinus carpio), goldfish share the recent genome duplication that occurred approximately 14 million years ago in their common ancestor. The combination of centuries of breeding and a wide array of interesting body morphologies provides an exciting opportunity to link genotype to phenotype and to understand the dynamics of genome evolution and speciation. We generated a high-quality draft sequence and gene annotations of a "Wakin" goldfish using 71X PacBio long reads. The two subgenomes in goldfish retained extensive synteny and collinearity between goldfish and zebrafish. However, genes were lost quickly after the carp whole-genome duplication, and the expression of 30% of the retained duplicated gene diverged substantially across seven tissues sampled. Loss of sequence identity and/or exons determined the divergence of the expression levels across all tissues, while loss of conserved noncoding elements determined expression variance between different tissues. This assembly provides an important resource for comparative genomics and understanding the causes of goldfish variants.
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Affiliation(s)
- Zelin Chen
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Yoshihiro Omori
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Sergey Koren
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Takuya Shirokiya
- Yatomi Station, Aichi Fisheries Research Institute, Yatomi, Aichi, Japan
| | - Takuo Kuroda
- Yatomi Station, Aichi Fisheries Research Institute, Yatomi, Aichi, Japan
| | - Atsushi Miyamoto
- Yatomi Station, Aichi Fisheries Research Institute, Yatomi, Aichi, Japan
| | - Hironori Wada
- Laboratory of Molecular and Developmental Biology, National Institute of Genetics, and Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Mishima, Shizuoka, Japan
| | - Asao Fujiyama
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Suiyuan Zhang
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Tyra G. Wolfsberg
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Koichi Kawakami
- Laboratory of Molecular and Developmental Biology, National Institute of Genetics, and Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Mishima, Shizuoka, Japan
| | - Adam M. Phillippy
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | | | - James C. Mullikin
- NIH Intramural Sequencing Center, National Human Genome Research Institute, Bethesda, MD, USA
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Shawn M. Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
- Corresponding author.
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