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Xinhua Chen - One of the best experts on this subject based on the ideXlab platform.
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development of monoclonal antibody against igt of a perciform fish large yellow croaker Larimichthys crocea and characterization of igt b cells
Developmental and Comparative Immunology, 2021Co-Authors: Zuyun Wei, Yuhong Chen, Jingguang Xie, Xiangyang Zhang, Xinhua ChenAbstract:Abstract Teleost immunoglobulin T (IgT) is considered to be a primitive immunoglobulin class specialized in mucosal immunity. In the present study, a recombinant protein containing the CH2 region of large yellow croaker (Larimichthys crocea) IgT heavy chain was expressed, purified, and used as an immunogen to produce a monoclonal antibody (mAb) against large yellow croaker IgT. Western blotting results indicated that the obtained mouse anti-IgT mAb could specifically recognize a 45 kDa protein in the skin mucus of large yellow croaker, which was identified as the IgT heavy chain by mass spectrometric analysis. Immunofluorescence assay (IFA) analysis further demonstrated that this mouse anti-IgT mAb could recognize membrane-bound IgT (mIgT) molecules on large yellow croaker IgT+ leukocytes. This mAb also could be used for sorting of large yellow croaker IgT+ B cells by flow cytometry sorting technology. Then, flow cytometric immunofluorescence analysis (FCIA) results showed that the percentages of IgT+ B cells in skin, gills, gut, spleen, head kidney and peripheral blood lymphocytes were 27.553% ± 3.312%, 12.588% ± 3.538%, 12.355% ± 3.352%, 13.075 ± 2.258%, 5.552 ± 3.275%, and 2.600 ± 0.521%, respectively, indicating that mucosal tissues (skin, gills, and gut) contained a high ratio of IgT+ B cells. Accordingly, the high protein levels of IgT were also detected in these mucosal tissues, suggesting that IgT may play a role in mucosal immunity in large yellow croaker. Taken together, our data demonstrated that the mouse anti-IgT mAb developed in this study could be used for characterizing IgT+ B cells and studying the functions of IgT in large yellow croaker.
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an improved genome assembly for Larimichthys crocea reveals hepcidin gene expansion with diversified regulation and function
Communications Biology, 2018Co-Authors: Jieying Huo, Xinhua Chen, Dingding Fan, Yanyun Guan, Xiaoqiang Xiao, Jingguang WeiAbstract:Larimichthys crocea (large yellow croaker) is a type of perciform fish well known for its peculiar physiological properties and economic value. Here, we constructed an improved version of the L. crocea genome assembly, which contained 26,100 protein-coding genes. Twenty-four pseudo-chromosomes of L. crocea were also reconstructed, comprising 90% of the genome assembly. This improved assembly revealed several expansions in gene families associated with olfactory detection, detoxification, and innate immunity. Specifically, six hepcidin genes (LcHamps) were identified in L. crocea, possibly resulting from lineage-specific gene duplication. All LcHamps possessed similar genomic structures and functional domains, but varied substantially with respect to expression pattern, transcriptional regulation, and biological function. LcHamp1 was associated specifically with iron metabolism, while LcHamp2s were functionally diverse, involving in antibacterial activity, antiviral activity, and regulation of intracellular iron metabolism. This functional diversity among gene copies may have allowed L. crocea to adapt to diverse environmental conditions. Yinnan Mu and colleagues present an improved yellow croaker genome, constructed using a hybrid assembly method incorporating long-reads and short-reads. With their improved assembly, the authors found several gene family expansions associated with olfactory detection, detoxification, and innate immunity.
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Characterization and function of a group II type I interferon in the perciform fish, large yellow croaker (Larimichthys crocea)
Fish & shellfish immunology, 2018Co-Authors: Yang Ding, Xiaohong Huang, Yanyun Guan, Xinhua ChenAbstract:Teleost fish possess two groups of type I interferons (IFNs) with two (group I IFNs) or four (group II IFNs) conserved cysteines, which are further classified into seven subgroups. In our previous study, two group I type I IFNs, LcIFNd and LcIFNh (a new subgroup member), were identified in the perciform fish, large yellow croaker (Larimichthys crocea). Here, we identified a group II type I IFN, LcIFNc, in this species. The deduced LcIFNc contained six cysteines, four of which are highly conserved (C1: C28, C2:C53, C3: C130, and C4:C159) in the fish group II type I IFNs, and a typical type I IFN signature motif was also found in it. Phylogenetic analysis indicated that LcIFNc belongs to the IFNc subgroup of fish group II type I IFNs. LcIFNc was constitutively expressed in all examined tissues, and was rapidly up-regulated in spleen and head kidney by poly(I:C) and Aeromonas hydrophila. Recombinant LcIFNc protein (rLcIFNc) could increase the expression of antiviral genes, Mx1, PKR and ISG15, in large yellow croaker peripheral blood leukocytes (PBLs). The rLcIFNc also exhibited obvious antiviral activity based on less cytopathic effect (CPE) and decreased expression levels of several viral genes in the rLcIFNc-treated grouper spleen (GS) cells following Singapore grouper iridovirus (SGIV) infection. Additionally, rLcIFNc was able to induce the expression of LcIFNc, as well as LcIFNd and LcIFNh in the PBLs and primary head kidney cells (HKCs) from large yellow croaker. These results therefore indicated that LcIFNc not only had antiviral activity, but also mediated the regulation of type I IFN response.
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Transcriptome Analysis Reveals Comprehensive Insights into the Early Immune Response of Large Yellow Croaker (Larimichthys crocea) Induced by Trivalent Bacterial Vaccine.
PloS one, 2017Co-Authors: Xin Zhang, Xinhua ChenAbstract:Vaccination is an effective and safe strategy for combating bacterial diseases in fish, but the mechanisms underlying the early immune response after vaccination remain to be elucidated. In the present study, we used RNA-seq technology to perform transcriptome analysis of spleens from large yellow croaker (Larimichthys crocea) induced by inactivated trivalent bacterial vaccine (Vibrio parahaemolyticus, Vibrio alginolyticus and Aeromonas hydrophila). A total of 2,789 or 1,511 differentially expressed genes (DEGs) were obtained at 24 or 72 h after vaccination, including 1,132 or 842 remarkably up-regulated genes and 1,657 or 669 remarkably down-regulated genes, respectively. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichments revealed that numerous DEGs belong to immune-relevant genes, involved in many immune-relevant pathways. Most of the strongly up-regulated DEGs are innate defense molecules, such as antimicrobial peptides, complement components, lectins, and transferrins. Trivalent bacterial vaccine affected the expressions of many components associated with bacterial ligand–depending Toll-like receptor signaling pathways and inflammasome formation, indicating that multiple innate immune processes were activated at the early period of vaccination in large yellow croaker. Moreover, the expression levels of genes involved in antigen processing were also up-regulated by bacterial vaccine. However, the expression levels of several T cell receptors and related CD molecules and signal transducers were down-regulated, suggesting that the T cell receptor signaling pathway was rapidly suppressed after vaccination. These results provide the comprehensive insights into the early immune response of large yellow croaker to vaccination and valuable information for developing a highly immunogenic vaccine against bacterial infection in teleosts.
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construction of the high density genetic linkage map and chromosome map of large yellow croaker Larimichthys crocea
International Journal of Molecular Sciences, 2015Co-Authors: Xinxin You, Qiong Shi, Yang Ding, Kaiqiong Mao, Chao Bian, Xinhua ChenAbstract:High-density genetic maps are essential for genome assembly, comparative genomic analysis and fine mapping of complex traits. In this study, 31,191 single nucleotide polymorphisms (SNPs) evenly distributed across the large yellow croaker (Larimichthys crocea) genome were identified using restriction-site associated DNA sequencing (RAD-seq). Among them, 10,150 high-confidence SNPs were assigned to 24 consensus linkage groups (LGs). The total length of the genetic linkage map was 5451.3 cM with an average distance of 0.54 cM between loci. This represents the densest genetic map currently reported for large yellow croaker. Using 2889 SNPs to target specific scaffolds, we assigned 533 scaffolds, comprising 421.44 Mb (62.04%) of the large yellow croaker assembled sequence, to the 24 linkage groups. The mapped assembly scaffolds in large yellow croaker were used for genome synteny analyses against the stickleback (Gasterosteus aculeatus) and medaka (Oryzias latipes). Greater synteny was observed between large yellow croaker and stickleback. This supports the hypothesis that large yellow croaker is more closely related to stickleback than to medaka. Moreover, 1274 immunity-related genes and 195 hypoxia-related genes were mapped to the 24 chromosomes of large yellow croaker. The integration of the high-resolution genetic map and the assembled sequence provides a valuable resource for fine mapping and positional cloning of quantitative trait loci associated with economically important traits in large yellow croaker.
Kangsen Mai - One of the best experts on this subject based on the ideXlab platform.
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comparation of oxylipin profiles as well as their substrates and synthetic enzymes transcriptional expression between marine fish Larimichthys crocea and freshwater fish oncorhynchus mykiss
Aquaculture, 2021Co-Authors: Shengnan Gao, Kun Cui, Yuning Pang, Wei Fang, Kangsen MaiAbstract:Abstract Oxylipins formed from polyunsaturated fatty acids (PUFAs) play an important role in normal physiology and function. Therefore, oxylipin profiles have been revealed in many species such as human, rats and even non-mammals. However, it is rarely studied in fish, a species known to be an excellent source of LC-PUFAs in human diets. In the present study, Larimichthys crocea and Oncorhynchus mykiss were selected as the marine and the freshwater fish model, respectively, used to quantify the oxylipin profiles by liquid chromatography tandem mass spectrometry and further synthesis related enzymes expression of the oxylipins were determined by RNA-seq. A total of 57 oxylipins were quantified and arachidonic acid oxylipins dominated which occupied 42.1%, and oxylipins derived from DHA and EPA ranked the second (17.6%) and third (15.8%). Thirty differential oxylipins were screened and analyzed to compare the differences between L. crocea and O. mykiss. It could be concluded that L. crocea may be better at utilizing substrate fatty acids to synthesize oxylipins than O. mykiss, and the different expression of the synthetic related enzymes probably accounted for the differences. 12-HETE in O. mykiss and PGJ2 in L. crocea were the most representative oxylipins to distinguish the two fishes. In conclusion, our study was the first study comparing the oxylipin profiles between marine fish and freshwater fish, and the representative differential oxylipins may serve as markers, providing a new insight of identifying and distinguishing marine and freshwater fish species.
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Endoplasmic Reticulum Stress Disturbs Lipid Homeostasis and Augments Inflammation in the Intestine and Isolated Intestinal Cells of Large Yellow Croaker (Larimichthys crocea)
'Frontiers Media SA', 2021Co-Authors: Wei Fang, Kangsen Mai, Qiuchi Chen, Yongtao Liu, Zengqi Zhao, Yanan ShenAbstract:The small intestine is crucial for lipid homeostasis and immune regulation of the whole body. Endoplasmic reticulum (ER) stress may affect lipid metabolism and inflammation in the intestine, but the potential mechanism is not completely understood. In the present study, intraperitoneal injection of tunicamycin (TM) induced ER stress in the intestine of large yellow croaker (Larimichthys crocea). ER stress induced excessive accumulation of triglyceride (TG) in the intestine by promoting lipid synthesis. However, it also enhanced lipid secretion and fatty acid β-oxidation. In addition, ER stress augmented inflammation in the intestine by promoting p65 into the nucleus and increasing proinflammatory genes expression. In the isolated intestinal cells, the obtained results showed that TM treatment significantly upregulated the mRNA expression of lipid synthesis and inflammatory response genes, which were consistent with those in vivo. Moreover, overexpression of unfolded protein response (UPR) sensors significantly upregulated promoter activities of lipid synthesis and proinflammatory genes. In conclusion, the results suggested that ER stress disturbed lipid metabolism and augmented inflammation in the intestine and isolated intestinal cells of large yellow croaker, which may contribute to finding novel therapies to tackle lipid dysregulation and inflammation in the intestine of fish and human beings
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Alterations in fatty acid composition and volatile compounds in muscle of large yellow croaker Larimichthys crocea fed different dietary lipid sources
'Elsevier BV', 2021Co-Authors: Xiaoyi Pan, Jiahuan Liu, Jia Chen, Ying Pan, Wenbing Zhang, Kangsen MaiAbstract:A 12-week feeding trial was performed to evaluate the impacts of different dietary lipid sources on the fatty acid composition and volatile compounds in muscle of large yellow croaker Larimichthys crocea (initial body weight: 36.87 ± 0.32 g). The 6.5 % of fish oil, soybean oil, palm oil, vegetable oil blend (soybean oil: palm oil = 1:1), rapeseed oil and linseed oil were added respectively to formulate six isonitrogenous (46 % crude protein) and isolipidic (13 % crude lipid) experimental diets, which were named as FO, SO, PO, BO, RO and LO respectively. Results showed that dietary vegetable oils significantly reduced the contents of arachidonic acid (ARA), eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) in muscle. While the highest levels of linoleic acid (LA), palmitic acid (PA), oleic acid (OA) and linolenic acid (ALA) were found in fillet of fish fed SO, PO, RO and LO respectively. Among the 39 identified volatile compounds in fillet, 23 were significantly affected by replacement of dietary fish oil with vegetable oils. Fish fillets in different treatments were mostly characterized by distinct volatiles and odours. Principal component analysis and Pearson’s correlation analysis indicated that some volatiles had strong positive correlations with main fatty acids in muscle, for example, (E)-2-pentenal, 1-penten-3-ol, etc. In conclusion, replacement of dietary fish oil by vegetable oils changed the volatile compounds in muscle of large yellow croaker, which could be ascribed to the modifications of muscle fatty acids induced by dietary vegetable oils
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Regulation of Free Fatty Acid Receptor 4 on Inflammatory Gene Induced by LPS in Large Yellow Croaker (Larimichthys crocea)
'Frontiers Media SA', 2021Co-Authors: Kangsen MaiAbstract:Free fatty acid receptor 4 (FFAR4) plays a key role in regulating the inflammatory response in mammals. The present study aimed to investigate the function of large yellow croaker FFAR4 on inflammation. In the present study, ffar4 was widely expressed in 10 tissues of large yellow croaker including gill, head kidney and spleen. Further studies showed that treatment of head kidney macrophages with agonists (TUG891 or GSK137647A) or overexpression of ffar4 reduced the mRNA expression of pro-inflammatory genes induced by LPS, and increased the expression of pparγ. Treatment of macrophages with antagonist AH7614 increased the mRNA expression of pro-inflammatory genes induced by LPS, and decreased the mRNA expression of pparγ. In order to verify the immunomodulatory effect of PPARγ, PPARγ was overexpressed in macrophages which significantly reduced the mRNA expression of pro-inflammatory genes il6, il1β, il8, tnfα and cox2. Moreover, results of dual-luciferase assays showed that PPARγ downregulated the transcriptional activity of il6 and il1β promoters. In conclusion, FFAR4 showed anti-inflammatory effects on LPS-induced inflammation in large yellow croaker
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Molecular Cloning, Characterization, and Nutritional Regulation of Elovl6 in Large Yellow Croaker (Larimichthys crocea)
MDPI AG, 2019Co-Authors: Yuning Pang, Xiaojun Xiang, Kangsen MaiAbstract:Elongation of very long chain fatty acids protein 6 (Elovl6) is a key enzyme in fatty acid synthesis, which participates in converting palmitate (C16:0) to stearate (C18:0). Although studies of Elovl6 have been carried out in mammals, the nutritional regulation of elovl6 in fish remains poorly understood. In the present study, the cloning and nutritional regulation of elovl6 were determined in large yellow croaker. Sequence and phylogenetic analysis revealed that the full-length cDNA of elovl6 was 1360 bp, including an open reading frame of 810 bp encoding a putative protein of 269 amino acid that possesses the characteristic features of Elovl proteins. The transcript level of elovl6 was significantly increased in the liver of croaker fed the diets with soybean oil (enriched with 18: 2n-6, LA) or linseed oil (enriched with 18: 3n-3, ALA) than that in croaker fed the diet with fish oil (enriched with 20: 5n-3 and 22: 6n-3). Correspondingly, the elovl6 expression in croaker’s hepatocytes treated with ALA or LA was remarkably increased compared to the controls. Furthermore, the transcription factors including hepatocyte nuclear factor 1α (HNF1α), CCAAT-enhancer-binding protein β (CEBPβ), retinoid X receptor α (RXRα), and cAMP response element-binding protein 1 (CREB1) greatly enhanced promoter activity of elovl6 in large yellow croaker, and the expression of transcription factors is consistent with the changes of elovl6 expression in response to fatty acids in vivo and in vitro. In conclusion, this study revealed that elovl6 expression in large yellow croaker could be upregulated by dietary ALA or LA via the increased transcriptional expression of transcription factors including hnf1α, cebpβ, rxrα, and creb1
Yang Ding - One of the best experts on this subject based on the ideXlab platform.
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Characterization and function of a group II type I interferon in the perciform fish, large yellow croaker (Larimichthys crocea)
Fish & shellfish immunology, 2018Co-Authors: Yang Ding, Xiaohong Huang, Yanyun Guan, Xinhua ChenAbstract:Teleost fish possess two groups of type I interferons (IFNs) with two (group I IFNs) or four (group II IFNs) conserved cysteines, which are further classified into seven subgroups. In our previous study, two group I type I IFNs, LcIFNd and LcIFNh (a new subgroup member), were identified in the perciform fish, large yellow croaker (Larimichthys crocea). Here, we identified a group II type I IFN, LcIFNc, in this species. The deduced LcIFNc contained six cysteines, four of which are highly conserved (C1: C28, C2:C53, C3: C130, and C4:C159) in the fish group II type I IFNs, and a typical type I IFN signature motif was also found in it. Phylogenetic analysis indicated that LcIFNc belongs to the IFNc subgroup of fish group II type I IFNs. LcIFNc was constitutively expressed in all examined tissues, and was rapidly up-regulated in spleen and head kidney by poly(I:C) and Aeromonas hydrophila. Recombinant LcIFNc protein (rLcIFNc) could increase the expression of antiviral genes, Mx1, PKR and ISG15, in large yellow croaker peripheral blood leukocytes (PBLs). The rLcIFNc also exhibited obvious antiviral activity based on less cytopathic effect (CPE) and decreased expression levels of several viral genes in the rLcIFNc-treated grouper spleen (GS) cells following Singapore grouper iridovirus (SGIV) infection. Additionally, rLcIFNc was able to induce the expression of LcIFNc, as well as LcIFNd and LcIFNh in the PBLs and primary head kidney cells (HKCs) from large yellow croaker. These results therefore indicated that LcIFNc not only had antiviral activity, but also mediated the regulation of type I IFN response.
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RESEARCH ARTICLE Genome Sequencing of the Perciform Fish Larimichthys crocea Provides Insights into Molecular and Genetic Mechanisms of Stress Adaptation
2016Co-Authors: Lixin Xiang, Dingding Fan, Mingji Feng, Shicui Zhang, Qiong Shi, Lvyun Zhu, Yang DingAbstract:The large yellow croaker Larimichthys crocea (L. crocea) is one of the most economically important marine fish in China and East Asian countries. It also exhibits peculiar behavioral and physiological characteristics, especially sensitive to various environmental stresses, such as hypoxia and air exposure. These traits may render L. crocea a good model for in-vestigating the response mechanisms to environmental stress. To understand the molecu-lar and genetic mechanisms underlying the adaptation and response of L. crocea to environmental stress, we sequenced and assembled the genome of L. crocea using a bac-terial artificial chromosome and whole-genome shotgun hierarchical strategy. The final ge-nome assembly was 679 Mb, with a contig N50 of 63.11 kb and a scaffold N50 of 1.03 Mb, containing 25,401 protein-coding genes. Gene families underlying adaptive behaviours, such as vision-related crystallins, olfactory receptors, and auditory sense-related genes, were significantly expanded in the genome of L. crocea relative to those of other verte-brates. Transcriptome analyses of the hypoxia-exposed L. crocea brain revealed new as
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construction of the high density genetic linkage map and chromosome map of large yellow croaker Larimichthys crocea
International Journal of Molecular Sciences, 2015Co-Authors: Xinxin You, Qiong Shi, Yang Ding, Kaiqiong Mao, Chao Bian, Xinhua ChenAbstract:High-density genetic maps are essential for genome assembly, comparative genomic analysis and fine mapping of complex traits. In this study, 31,191 single nucleotide polymorphisms (SNPs) evenly distributed across the large yellow croaker (Larimichthys crocea) genome were identified using restriction-site associated DNA sequencing (RAD-seq). Among them, 10,150 high-confidence SNPs were assigned to 24 consensus linkage groups (LGs). The total length of the genetic linkage map was 5451.3 cM with an average distance of 0.54 cM between loci. This represents the densest genetic map currently reported for large yellow croaker. Using 2889 SNPs to target specific scaffolds, we assigned 533 scaffolds, comprising 421.44 Mb (62.04%) of the large yellow croaker assembled sequence, to the 24 linkage groups. The mapped assembly scaffolds in large yellow croaker were used for genome synteny analyses against the stickleback (Gasterosteus aculeatus) and medaka (Oryzias latipes). Greater synteny was observed between large yellow croaker and stickleback. This supports the hypothesis that large yellow croaker is more closely related to stickleback than to medaka. Moreover, 1274 immunity-related genes and 195 hypoxia-related genes were mapped to the 24 chromosomes of large yellow croaker. The integration of the high-resolution genetic map and the assembled sequence provides a valuable resource for fine mapping and positional cloning of quantitative trait loci associated with economically important traits in large yellow croaker.
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genome sequencing of the perciform fish Larimichthys crocea provides insights into molecular and genetic mechanisms of stress adaptation
PLOS Genetics, 2015Co-Authors: Lixin Xiang, Dingding Fan, Mingji Feng, Shicui Zhang, Qiong Shi, Lvyun Zhu, Yang Ding, Li Nie, Weiren Dong, Liang JiangAbstract:The large yellow croaker Larimichthys crocea (L. crocea) is one of the most economically important marine fish in China and East Asian countries. It also exhibits peculiar behavioral and physiological characteristics, especially sensitive to various environmental stresses, such as hypoxia and air exposure. These traits may render L. crocea a good model for investigating the response mechanisms to environmental stress. To understand the molecular and genetic mechanisms underlying the adaptation and response of L. crocea to environmental stress, we sequenced and assembled the genome of L. crocea using a bacterial artificial chromosome and whole-genome shotgun hierarchical strategy. The final genome assembly was 679 Mb, with a contig N50 of 63.11 kb and a scaffold N50 of 1.03 Mb, containing 25,401 protein-coding genes. Gene families underlying adaptive behaviours, such as vision-related crystallins, olfactory receptors, and auditory sense-related genes, were significantly expanded in the genome of L. crocea relative to those of other vertebrates. Transcriptome analyses of the hypoxia-exposed L. crocea brain revealed new aspects of neuro-endocrine-immune/metabolism regulatory networks that may help the fish to avoid cerebral inflammatory injury and maintain energy balance under hypoxia. Proteomics data demonstrate that skin mucus of the air-exposed L. crocea had a complex composition, with an unexpectedly high number of proteins (3,209), suggesting its multiple protective mechanisms involved in antioxidant functions, oxygen transport, immune defence, and osmotic and ionic regulation. Our results reveal the molecular and genetic basis of fish adaptation and response to hypoxia and air exposure. The data generated by this study will provide valuable resources for the genetic improvement of stress resistance and yield potential in L. crocea.
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Summary of the Larimichthys crocea genome
2015Co-Authors: Lixin Xiang, Dingding Fan, Mingji Feng, Shicui Zhang, Qiong Shi, Lvyun Zhu, Yang DingAbstract:BAC = bacterial artificial chromosome; WGS = whole genome shotgun.Summary of the Larimichthys crocea genome
Qinghui Ai - One of the best experts on this subject based on the ideXlab platform.
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high level of dietary olive oil decreased growth increased liver lipid deposition and induced inflammation by activating the p38 mapk and jnk pathways in large yellow croaker Larimichthys crocea
Fish & Shellfish Immunology, 2019Co-Authors: Xueshan Li, Wei Fang, Qiang Chen, Dan Xu, Yanjiao Zhang, Qinghui AiAbstract:Abstract A feeding experiment was conducted to determine the effects of fish oil replaced by olive oil (OO) on growth performance, serum biochemical, antioxidant capacity and inflammatory response in large yellow croaker (Larimichthys crocea). Four iso-nitrogenous and iso-lipidic diets were formulated by replacing fish oil (FO) with 0% (the control group), 33.3%, 66.7% and 100% OO. Fish fed the diet with 100% OO had the lowest growth performance among dietary treatments. However, there were no significant differences in SGR and FI among fish fed diets with 0% (the control group), 33.3% and 66.7% OO (P > 0.05). As to morphological parameters, HSI was significantly increased in fish fed the diet with 100% OO than the control group (P
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effects of dietary chenodeoxycholic acid on growth performance body composition and related gene expression in large yellow croaker Larimichthys crocea fed diets with high replacement of fish oil with soybean oil
Aquaculture, 2017Co-Authors: Jianlong Du, Hanlin Xu, Songlin Li, Qinghui AiAbstract:Abstract An experiment was conducted to determine the effects of dietary chenodeoxycholic acid (CDCA) on the growth performance, body composition and lipid deposition of juvenile large yellow croaker ( Larimichthys crocea ) (initial weight, 10.03 ± 0.02 g) fed a soybean oil diet. The practical diet with 6% soybean oil (SO) was used as the control, and a fish oil (FO) diet was designed with 6% fish oil. On the basis of the soybean oil diet, 300 mg and 900 mg/kg (CDCA) were added, respectively. After 10-week growth trial, results showed that survival rate (SR) and condition factor (CF) were not significantly different among dietary treatments. Compared with the FO group, final weight (FW) and weight gain rates (WGR) in the SO group significantly decreased while the groups with the supplementation of CDCA show significantly better growth performance than the SO group and FO group. The lipid content of liver was significantly increased by the replacement of FO with SO but decreased with the increase of the supplementation of CDCA. The activity of lipoprotein lipase was significantly higher in fish fed the diet with 900 mg/kg CDCA supplementation. The expression of PPARα decreased while the expression of SREBP-1 increased significantly in fish fed the SO diet compared with fish fed the FO diet. Meanwhile, dietary 900 mg/kg CDCA significantly upregulated the expression of PPARα and FXR while the expression of SREBP-1 was decreased by the supplementation of CDCA. The results suggested that the supplementation of CDCA could improve the growth performance and lipid deposition of liver in large yellow croaker which were negatively affected by the replacement of dietary fish oil with soybean oil.
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effects of dietary supplementation of bacillus subtilis and fructooligosaccharide on growth performance survival non specific immune response and disease resistance of juvenile large yellow croaker Larimichthys crocea
Aquaculture, 2011Co-Authors: Qinghui Ai, Jun Wang, Houguo Xu, Wei Xu, Wenbing ZhangAbstract:Abstract A feeding experiment was conducted to examine the effects of dietary administration of Bacillus subtilis and fructooligosaccharide (FOS) on growth performance, survival, immune responses and disease resistance of juvenile large yellow croaker, Larimichthys crocea (mean initial body weight 7.82 g ± 0.68). Nine practical diets were formulated to contain three levels of B. subtilis (0.0, 0.42 × 10 7 cfu g −1 and 1.35 × 10 7 cfu g −1 ), each with three FOS levels (0, 0.2% and 0.4% of dry weight). Each diet was randomly assigned to triplicate groups of 60 juveniles. The experiment was conducted in floating sea cages (1.0 × 1.0 × 1.5 m) for 10 weeks. At the termination of the feeding trial, alternative complement pathway (ACP), superoxide dismutase (SOD) and lysozyme activity of serum and respiratory burst activity of head kidney macrophage were determined and fishes were challenged intraperitoneally with Vibrio harveyi . The results showed that at each dietary FOS level, dietary supplementation of 1.35 × 10 7 cfu g −1 B. subtilis significantly increased the specific growth rate (SGR) ( P P B. subtilis supplementation. The immune assay showed that at each FOS level, compared to the groups without B. subtilis supplementation significantly enhanced serum lysozyme was observed in fish fed the B. subtilis- supplemented diets ( P 7 cfu g −1 B. subtilis ( P B. subtilis supplementation the cumulative mortality after infection with V. harveyi was significantly lower in fish fed the diet with 1.35 × 10 7 cfu g −1 B. subtilis ( P B. subtilis level, addition of FOS in diets did not significantly affect the growth performance, immune response and disease resistance of large yellow croaker. No significant interactions were observed between dietary B. subtilis and FOS. These results showed that dietary supplementation of B. subtilis at a dose of 1.35 × 10 7 cfu g −1 improved growth, feed efficiency ratio, non-specific immune responses and disease resistance of juvenile large yellow croaker, L. crocea .
Qiong Shi - One of the best experts on this subject based on the ideXlab platform.
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Whole-Genome Sequencing and Genome-Wide Studies of Spiny Head Croaker (Collichthys lucidus) Reveals Potential Insights for Well-Developed Otoliths in the Family Sciaenidae
'Frontiers Media SA', 2021Co-Authors: Qiong Shi, Chao Bian, Wu Gan, Chenxi Zhao, Xinran LiuAbstract:Spiny head croaker (Collichthys lucidus), belonging to the family Sciaenidae, is a small economic fish with a main distribution in the coastal waters of Northwestern Pacific. Here, we constructed a nonredundant chromosome-level genome assembly of spiny head croaker and also made genome-wide investigations on genome evolution and gene families related to otolith development. A primary genome assembly of 811.23 Mb, with a contig N50 of 74.92 kb, was generated by a combination of 49.12-Gb Illumina clean reads and 35.24 Gb of PacBio long reads. Contigs of this draft assembly were further anchored into chromosomes by integration with additional 185.33-Gb Hi-C data, resulting in a high-quality chromosome-level genome assembly of 817.24 Mb, with an improved scaffold N50 of 26.58 Mb. Based on our phylogenetic analysis, we observed that C. lucidus is much closer to Larimichthys crocea than Miichthys miiuy. We also predicted that many gene families were significantly expanded (p-value <0.05) in spiny head croaker; among them, some are associated with “calcium signaling pathway” and potential “inner ear functions.” In addition, we identified some otolith-related genes (such as otol1a that encodes Otolin-1a) with critical deletions or mutations, suggesting possible molecular mechanisms for well-developed otoliths in the family Sciaenidae
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RESEARCH ARTICLE Genome Sequencing of the Perciform Fish Larimichthys crocea Provides Insights into Molecular and Genetic Mechanisms of Stress Adaptation
2016Co-Authors: Lixin Xiang, Dingding Fan, Mingji Feng, Shicui Zhang, Qiong Shi, Lvyun Zhu, Yang DingAbstract:The large yellow croaker Larimichthys crocea (L. crocea) is one of the most economically important marine fish in China and East Asian countries. It also exhibits peculiar behavioral and physiological characteristics, especially sensitive to various environmental stresses, such as hypoxia and air exposure. These traits may render L. crocea a good model for in-vestigating the response mechanisms to environmental stress. To understand the molecu-lar and genetic mechanisms underlying the adaptation and response of L. crocea to environmental stress, we sequenced and assembled the genome of L. crocea using a bac-terial artificial chromosome and whole-genome shotgun hierarchical strategy. The final ge-nome assembly was 679 Mb, with a contig N50 of 63.11 kb and a scaffold N50 of 1.03 Mb, containing 25,401 protein-coding genes. Gene families underlying adaptive behaviours, such as vision-related crystallins, olfactory receptors, and auditory sense-related genes, were significantly expanded in the genome of L. crocea relative to those of other verte-brates. Transcriptome analyses of the hypoxia-exposed L. crocea brain revealed new as
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construction of the high density genetic linkage map and chromosome map of large yellow croaker Larimichthys crocea
International Journal of Molecular Sciences, 2015Co-Authors: Xinxin You, Qiong Shi, Yang Ding, Kaiqiong Mao, Chao Bian, Xinhua ChenAbstract:High-density genetic maps are essential for genome assembly, comparative genomic analysis and fine mapping of complex traits. In this study, 31,191 single nucleotide polymorphisms (SNPs) evenly distributed across the large yellow croaker (Larimichthys crocea) genome were identified using restriction-site associated DNA sequencing (RAD-seq). Among them, 10,150 high-confidence SNPs were assigned to 24 consensus linkage groups (LGs). The total length of the genetic linkage map was 5451.3 cM with an average distance of 0.54 cM between loci. This represents the densest genetic map currently reported for large yellow croaker. Using 2889 SNPs to target specific scaffolds, we assigned 533 scaffolds, comprising 421.44 Mb (62.04%) of the large yellow croaker assembled sequence, to the 24 linkage groups. The mapped assembly scaffolds in large yellow croaker were used for genome synteny analyses against the stickleback (Gasterosteus aculeatus) and medaka (Oryzias latipes). Greater synteny was observed between large yellow croaker and stickleback. This supports the hypothesis that large yellow croaker is more closely related to stickleback than to medaka. Moreover, 1274 immunity-related genes and 195 hypoxia-related genes were mapped to the 24 chromosomes of large yellow croaker. The integration of the high-resolution genetic map and the assembled sequence provides a valuable resource for fine mapping and positional cloning of quantitative trait loci associated with economically important traits in large yellow croaker.
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genome sequencing of the perciform fish Larimichthys crocea provides insights into molecular and genetic mechanisms of stress adaptation
PLOS Genetics, 2015Co-Authors: Lixin Xiang, Dingding Fan, Mingji Feng, Shicui Zhang, Qiong Shi, Lvyun Zhu, Yang Ding, Li Nie, Weiren Dong, Liang JiangAbstract:The large yellow croaker Larimichthys crocea (L. crocea) is one of the most economically important marine fish in China and East Asian countries. It also exhibits peculiar behavioral and physiological characteristics, especially sensitive to various environmental stresses, such as hypoxia and air exposure. These traits may render L. crocea a good model for investigating the response mechanisms to environmental stress. To understand the molecular and genetic mechanisms underlying the adaptation and response of L. crocea to environmental stress, we sequenced and assembled the genome of L. crocea using a bacterial artificial chromosome and whole-genome shotgun hierarchical strategy. The final genome assembly was 679 Mb, with a contig N50 of 63.11 kb and a scaffold N50 of 1.03 Mb, containing 25,401 protein-coding genes. Gene families underlying adaptive behaviours, such as vision-related crystallins, olfactory receptors, and auditory sense-related genes, were significantly expanded in the genome of L. crocea relative to those of other vertebrates. Transcriptome analyses of the hypoxia-exposed L. crocea brain revealed new aspects of neuro-endocrine-immune/metabolism regulatory networks that may help the fish to avoid cerebral inflammatory injury and maintain energy balance under hypoxia. Proteomics data demonstrate that skin mucus of the air-exposed L. crocea had a complex composition, with an unexpectedly high number of proteins (3,209), suggesting its multiple protective mechanisms involved in antioxidant functions, oxygen transport, immune defence, and osmotic and ionic regulation. Our results reveal the molecular and genetic basis of fish adaptation and response to hypoxia and air exposure. The data generated by this study will provide valuable resources for the genetic improvement of stress resistance and yield potential in L. crocea.
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Summary of the Larimichthys crocea genome
2015Co-Authors: Lixin Xiang, Dingding Fan, Mingji Feng, Shicui Zhang, Qiong Shi, Lvyun Zhu, Yang DingAbstract:BAC = bacterial artificial chromosome; WGS = whole genome shotgun.Summary of the Larimichthys crocea genome
