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Zheng Q, Liu L, Guo X, Zhu F, Huang Y, Qin Q, Huang X. Fish ELOVL7a is involved in virus replication via lipid metabolic reprogramming. FISH & SHELLFISH IMMUNOLOGY 2024; 149:109530. [PMID: 38570120 DOI: 10.1016/j.fsi.2024.109530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 03/24/2024] [Accepted: 03/27/2024] [Indexed: 04/05/2024]
Abstract
The elongation of very long chain fatty acids (ELOVL) proteins are key rate-limiting enzymes that catalyze fatty acid synthesis to form long chain fatty acids. ELOVLs also play regulatory roles in the lipid metabolic reprogramming induced by mammalian viruses. However, little is known about the roles of fish ELOVLs during virus infection. Here, a homolog of ELOVL7 was cloned from Epinephelus coioides (EcELOVL7a), and its roles in red-spotted grouper nervous necrosis virus (RGNNV) and Singapore grouper iridovirus (SGIV) infection were investigated. The transcription level of EcELOVL7a was significantly increased upon RGNNV and SGIV infection or other pathogen-associated molecular patterns stimulation in grouper spleen (GS) cells. Subcellular localization analysis showed that EcELOVL7a encoded an endoplasmic reticulum (ER) related protein. Overexpression of EcELOVL7a promoted the viral production and virus release during SGIV and RGNNV infection. Furthermore, the lipidome profiling showed that EcELOVL7a overexpression reprogrammed cellular lipid components in vitro, evidenced by the increase of glycerophospholipids, sphingolipids and glycerides components. In addition, VLCFAs including FFA (20:2), FFA (20:4), FFA (22:4), FFA (22:5) and FFA (24:0), were enriched in EcELOVL7a overexpressed cells. Consistently, EcELOVL7a overexpression upregulated the transcription level of the key lipid metabolic enzymes, including fatty acid synthase (FASN), phospholipase A 2α (PLA 2α), and cyclooxygenases -2 (COX-2), LPIN1, and diacylglycerol acyltransferase 1α (DGAT1α). Together, our results firstly provided the evidence that fish ELOVL7a played an essential role in SGIV and RGNNV replication by reprogramming lipid metabolism.
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Affiliation(s)
- Qi Zheng
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Lin Liu
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Xixi Guo
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Fengyi Zhu
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Youhua Huang
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, 511464, China
| | - Qiwei Qin
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, 511464, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, 519082, China.
| | - Xiaohong Huang
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, 511464, China.
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2
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Zhang W, Yang Y, Hua S, Ruan Q, Li D, Wang L, Wang X, Wen X, Liu X, Meng Z. Chromosome-level genome assembly and annotation of the yellow grouper, Epinephelus awoara. Sci Data 2024; 11:151. [PMID: 38296995 PMCID: PMC10830450 DOI: 10.1038/s41597-024-02989-8] [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: 10/23/2023] [Accepted: 01/18/2024] [Indexed: 02/02/2024] Open
Abstract
Epinephelus awoara, as known as yellow grouper, is a significant economic marine fish that has been bred artificially in China. However, the genetic structure and evolutionary history of yellow grouper remains largely unknown. Here, this work presents the high-quality chromosome-level genome assembly of yellow grouper using PacBio single molecule sequencing technique (SMRT) and High-through chromosome conformation capture (Hi-C) technologies. The 984.48 Mb chromosome-level genome of yellow grouper was assembled, with a contig N50 length of 39.77 Mb and scaffold N50 length of 41.39 Mb. Approximately 99.76% of assembled sequences were anchored into 24 pseudo-chromosomes with the assistance of Hi-C reads. Furthermore, approximately 41.17% of the genome was composed of repetitive elements. In total, 24,541 protein-coding genes were predicted, of which 22,509 (91.72%) genes were functionally annotated. The highly accurate, chromosome-level reference genome assembly and annotation are crucial to the understanding of population genetic structure, adaptive evolution and speciation of the yellow grouper.
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Affiliation(s)
- Weiwei Zhang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yang Yang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
- Key Laboratory of Tropical Marine Fish Germplasm Innovation and Utilization, Ministry of Agriculture and Rural Affairs, Sanya, 570000, China
- Hainan Engineering Research Center for Germplasm Innovation and Utilization, Sanya, 570000, China
| | - Sijie Hua
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Qingxin Ruan
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Duo Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Le Wang
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore City, 119077, Singapore
| | - Xi Wang
- Area of Ecology and Biodiversity, School of Biological Sciences, University of Hong Kong, Hong Kong SAR, 999077, China
| | - Xin Wen
- School of Marine Biology and Fisheries, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou, 570228, China
| | - Xiaochun Liu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
- Southern Laboratory of Ocean Science and Engineering (Zhuhai), Zhuhai, 519000, China
| | - Zining Meng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
- Southern Laboratory of Ocean Science and Engineering (Zhuhai), Zhuhai, 519000, China.
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3
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Liang Y, Pan JM, Zhu KC, Xian L, Guo HY, Liu BS, Zhang N, Yang JW, Zhang DC. Genome-Wide Identification of Trachinotus ovatus Antimicrobial Peptides and Their Immune Response against Two Pathogen Challenges. Mar Drugs 2023; 21:505. [PMID: 37888440 PMCID: PMC10608450 DOI: 10.3390/md21100505] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/13/2023] [Accepted: 09/17/2023] [Indexed: 10/28/2023] Open
Abstract
Golden pompano, Trachinotus ovatus, as a highly nutritious commercially valuable marine fish, has become one of the preferred species for many fish farmers due to its rapid growth, wide adaptability, and ease of feeding and management. However, with the expansion of aquaculture scale, bacterial and parasitic diseases have also become major threats to the golden pompano industry. This study, based on comparative genomics, shows the possibility of preferential evolution of freshwater fish over marine fish by analyzing the phylogenetic relationships and divergence times of 14 marine fish and freshwater fish. Furthermore, we identified antimicrobial peptide genes from 14 species at the genomic level and found that the number of putative antimicrobial peptides may be related to species evolution. Subsequently, we classified the 341 identified AMPs from golden pompano into 38 categories based on the classification provided by the APD3. Among them, TCP represented the highest proportion, accounting for 23.2% of the total, followed by scolopendin, lectin, chemokine, BPTI, and histone-derived peptides. At the same time, the distribution of AMPs in chromosomes varied with type, and covariance analysis showed the frequency of its repeat events. Enrichment analysis and PPI indicated that AMP was mainly concentrated in pathways associated with disease immunity. In addition, our transcriptomic data measured the expression of putative AMPs of golden pompano in 12 normal tissues, as well as in the liver, spleen, and kidney infected with Streptococcus agalactiae and skin infected with Cryptocaryon irritans. As the infection with S. agalactiae and C. irritans progressed, we observed tissue specificity in the number and types of responsive AMPs. Positive selection of AMP genes may participate in the immune response through the MAPK signaling pathway. The genome-wide identification of antimicrobial peptides in the golden pompano provided a complete database of potential AMPs that can contribute to further understanding the immune mechanisms in pathogens. AMPs were expected to replace traditional antibiotics and be developed into targeted drugs against specific bacterial and parasitic pathogens for more precise and effective treatment to improve aquaculture production.
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Affiliation(s)
- Yu Liang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (Y.L.); (J.-M.P.); (K.-C.Z.); (L.X.); (H.-Y.G.); (B.-S.L.); (N.Z.); (J.-W.Y.)
- Guangxi Marine Microbial Resources Industrialization Engineering Technology Research Center, Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning 530008, China
| | - Jin-Min Pan
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (Y.L.); (J.-M.P.); (K.-C.Z.); (L.X.); (H.-Y.G.); (B.-S.L.); (N.Z.); (J.-W.Y.)
| | - Ke-Cheng Zhu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (Y.L.); (J.-M.P.); (K.-C.Z.); (L.X.); (H.-Y.G.); (B.-S.L.); (N.Z.); (J.-W.Y.)
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Lin Xian
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (Y.L.); (J.-M.P.); (K.-C.Z.); (L.X.); (H.-Y.G.); (B.-S.L.); (N.Z.); (J.-W.Y.)
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Hua-Yang Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (Y.L.); (J.-M.P.); (K.-C.Z.); (L.X.); (H.-Y.G.); (B.-S.L.); (N.Z.); (J.-W.Y.)
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Bao-Suo Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (Y.L.); (J.-M.P.); (K.-C.Z.); (L.X.); (H.-Y.G.); (B.-S.L.); (N.Z.); (J.-W.Y.)
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Nan Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (Y.L.); (J.-M.P.); (K.-C.Z.); (L.X.); (H.-Y.G.); (B.-S.L.); (N.Z.); (J.-W.Y.)
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Jing-Wen Yang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (Y.L.); (J.-M.P.); (K.-C.Z.); (L.X.); (H.-Y.G.); (B.-S.L.); (N.Z.); (J.-W.Y.)
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Dian-Chang Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (Y.L.); (J.-M.P.); (K.-C.Z.); (L.X.); (H.-Y.G.); (B.-S.L.); (N.Z.); (J.-W.Y.)
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
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Yang Y, Zeng L, Wang T, Wu L, Wu X, Xia J, Meng Z, Liu X. Assembly of Genome and Resequencing Provide Insights into Genetic Differentiation between Parents of Hulong Hybrid Grouper ( Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂). Int J Mol Sci 2023; 24:12007. [PMID: 37569383 PMCID: PMC10418399 DOI: 10.3390/ijms241512007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/22/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
The Hulong hybrid grouper was bred from the brown-marbled grouper (Epinephelus fuscoguttatus) ♀ and the giant grouper (E. lanceolatus) ♂, combining the advantageous traits of both parents. Possessing an excellent performance, this hybrid's cultivation promotes the development of the grouper industry. Its male parent, the giant grouper, possesses the fastest growth and the largest body size among all coral-reef-dwelling fish. This species is not only an economically important species in marine aquaculture, but it is also an ideal male parent in the interspecific crossing of grouper species. In the present study, a high-quality chromosome-level genome of the giant grouper was constructed with a total length of 1.06 Gb, consisting of 24 chromosomes and 69 scaffolds. To analyze the genetic differences between the parents of the Hulong hybrid grouper, the structural variations (SVs) between both parental genomes were detected, and a total of 46,643 SVs were obtained. High-quality SNPs were identified from resequencing data. There were significant differences between the two genomes, and the average FST reached 0.685. A total of 234 highly differentiated regions were detected with an FST > 0.9. The protein-coding genes involved in SVs and highly differentiated regions were significantly enriched in metabolic pathways, including fatty metabolism, carbohydrate metabolism, amino acid metabolism and the TCA cycle. These genes may be related to the differences in feeding preferences and the ability to digest carbohydrates between the two grouper species under natural conditions. In addition, protein-coding genes related to the cell cycle and p53-signaling pathway were also detected. These genes may play important roles in the regulation of body size and growth performance. This research provides genomic resources for further breeding works and evolutionary analyses.
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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 510275, China; (Y.Y.); (L.Z.); (T.W.); (L.W.); (X.W.); (J.X.)
- Key Laboratory of Tropical Marine Fish Germplasm Innovation and Utilization, Ministry of Agriculture, Sanya 572025, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya 572025, China
| | - Leilei Zeng
- 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 510275, China; (Y.Y.); (L.Z.); (T.W.); (L.W.); (X.W.); (J.X.)
| | - Tong Wang
- 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 510275, China; (Y.Y.); (L.Z.); (T.W.); (L.W.); (X.W.); (J.X.)
| | - Lina 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 510275, China; (Y.Y.); (L.Z.); (T.W.); (L.W.); (X.W.); (J.X.)
| | - 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 510275, China; (Y.Y.); (L.Z.); (T.W.); (L.W.); (X.W.); (J.X.)
| | - Junhong 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 510275, China; (Y.Y.); (L.Z.); (T.W.); (L.W.); (X.W.); (J.X.)
- Southern Laboratory of Ocean Science and Engineering, Zhuhai 519000, China
| | - Zining 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 510275, China; (Y.Y.); (L.Z.); (T.W.); (L.W.); (X.W.); (J.X.)
- Southern Laboratory of Ocean Science and Engineering, Zhuhai 519000, China
| | - Xiaochun 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 510275, China; (Y.Y.); (L.Z.); (T.W.); (L.W.); (X.W.); (J.X.)
- Southern Laboratory of Ocean Science and Engineering, Zhuhai 519000, China
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5
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van Gelderen TA, Ladisa C, Salazar-Moscoso M, Folgado C, Habibi HR, Ribas L. Metabolomic and transcriptomic profiles after immune stimulation in the zebrafish testes. Genomics 2023; 115:110581. [PMID: 36796654 DOI: 10.1016/j.ygeno.2023.110581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/09/2023] [Accepted: 02/11/2023] [Indexed: 02/16/2023]
Abstract
Fish farms are prone to disease outbreaks and stress due to high-density rearing conditions in tanks and sea cages, adversely affecting growth, reproduction, and metabolism. To understand the molecular mechanisms affected in the gonads of breeder fish after an immune challenge, we investigated the metabolome and the transcriptome profiles in zebrafish testes after inducing an immune response. After 48 h of the immune challenge, ultra-high-performance liquid chromatography (LC-MS) and transcriptomic analysis by RNA-seq (Illumina) resulted in 20 different released metabolites and 80 differentially expressed genes. Among these, glutamine and succinic acid were the most abundant metabolites released and 27,5% of the genes belong to either the immune or reproduction systems. Pathway analysis based on metabolomic and transcriptomic crosstalk identified cad and iars genes that act simultaneously with succinate metabolite. This study deciphers interactions between reproduction and immune systems and provides a basis to improve protocols in generating more resistant broodstock.
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Affiliation(s)
- T A van Gelderen
- Institut de Ciències del Mar - Consejo Superior de Investigaciones Científicas (ICM-CSIC), Department of Renewable Marine Resources, 08003 Barcelona, Spain
| | - C Ladisa
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - M Salazar-Moscoso
- Institut de Ciències del Mar - Consejo Superior de Investigaciones Científicas (ICM-CSIC), Department of Renewable Marine Resources, 08003 Barcelona, Spain
| | - C Folgado
- Institut de Ciències del Mar - Consejo Superior de Investigaciones Científicas (ICM-CSIC), Department of Renewable Marine Resources, 08003 Barcelona, Spain
| | - H R Habibi
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - L Ribas
- Institut de Ciències del Mar - Consejo Superior de Investigaciones Científicas (ICM-CSIC), Department of Renewable Marine Resources, 08003 Barcelona, Spain.
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6
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Mu X, Liu Y, Liu C, Zhao C, Li R, You X, Yang Y, Wang X, Hu Y, Shi Q, Bian C. Identification of candidate sex-specific genomic regions in male and female Asian arowana genomes. Gigascience 2022; 11:6700067. [PMID: 36106701 PMCID: PMC9475665 DOI: 10.1093/gigascience/giac085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 06/25/2022] [Accepted: 08/10/2022] [Indexed: 11/23/2022] Open
Abstract
Background Asian arowana, Scleropages formosus, is one of the most expensive aquarium fish species worldwide. Its sex, however, cannot be distinguished clearly at any development stage, which impedes captive breeding and species protection for this endangered aquarium fish. Results To discover molecular clues to the sex of Asian arowana, we sequenced 26.5 Gb of PacBio HiFi reads and 179.2 Gb of Hi-C reads for 1 male fish and also sequenced 106.5 Gb of Illumina reads, 36.0 Gb of PacBio Sequel reads, and 80.7 Gb of Hi-C reads for 1 female individual. The final male and female genome assemblies were approximately 756.8 Mb and 781.5 Mb in length and contained 25,262 and 25,328 protein-coding genes, respectively. We also resequenced the genomes of 15 male and 15 female individuals with approximately 722.1 Gb of Illumina reads. A genome-wide association study identified several potentially divergent regions between male and female individuals. In these regions, cd48 and cfap52 could be candidate genes for sex determination of Asian arowana. We also found some structural variations in few chromosomes between male and female individuals. Conclusion We provided an improved reference genome assembly of female arowana and generated the first sequenced genome of 1 male individual. These valuable genetic resources and resequencing data may improve global aquarium fish research.
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Affiliation(s)
- Xidong Mu
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Yi Liu
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Chao Liu
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Chenxi Zhao
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruihan Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinxin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yexin Yang
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.,Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Xuejie Wang
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Yinchang Hu
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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7
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Wang L, Li Z, Liu Y, Chen S, Li L, Duan P, Wang X, Li W, Wang Q, Zhai J, Tian Y. A chromosome-level genome assembly of the potato grouper (Epinephelus tukula). Genomics 2022; 114:110473. [PMID: 36049667 DOI: 10.1016/j.ygeno.2022.110473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/04/2022] [Accepted: 08/29/2022] [Indexed: 12/29/2022]
Abstract
The potato grouper, Epinephelus tukula, is one of the largest coral reef teleost, and it is an important germplasm resource for selection and cross breeding. Here we report a potato grouper genome assembly generated using PacBio long-read sequencing, Illumina sequencing and high-throughput chromatin conformation capture (Hi-C) technology. The genome size was 1.13 Gb, with a total of 508 contigs anchored into 24 chromosomes. The scaffold N50 was 42.65 Mb. For the genome models, our assembled genome contained 98.11% complete BUSCO with the vertebrata_odb9 database. One more copies of Gh and Hsp90b1 were identified in the E. tukula genome, which might contribute to its fast growth and high resistance to stress. In addition, 435 putative antimicrobial peptide (AMP) genes were identified in the potato grouper. This study provides a good reference for whole genome selective breeding of the potato grouper and for future development of novel marine drugs.
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Affiliation(s)
- Linna Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
| | - Zhentong Li
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
| | - Yang Liu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
| | - Shuai Chen
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Linlin Li
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Pengfei Duan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Xinyi Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Wensheng Li
- Mingbo Aquatic Co. Ltd., Laizhou 261400, China
| | | | | | - Yongsheng Tian
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China.
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8
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Jin L, Dong H, Sun D, Wang L, Qu L, Lin S, Yang Q, Zhang X. Biological Functions and Applications of Antimicrobial Peptides. Curr Protein Pept Sci 2022; 23:226-247. [DOI: 10.2174/1389203723666220519155942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/15/2022] [Accepted: 04/01/2022] [Indexed: 11/22/2022]
Abstract
Abstract:
Despite antimicrobial resistance, which is attributed to the misuse of broad-spectrum antibiotics,
antibiotics can indiscriminately kill pathogenic and beneficial microorganisms. These events
disrupt the delicate microbial balance in both humans and animals, leading to secondary infections
and other negative effects. Antimicrobial peptides (AMPs) are functional natural biopolymers in
plants and animals. Due to their excellent antimicrobial activities and absence of microbial resistance,
AMPs have attracted enormous research attention. We reviewed the antibacterial, antifungal, antiviral,
antiparasitic, as well as antitumor properties of AMPs and research progress on AMPs. In addition,
we highlighted various recommendations and potential research areas for their progress and
challenges in practical applications.
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Affiliation(s)
- Libo Jin
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University,
Wenzhou 325035, China
| | - Hao Dong
- College of Life Science and Technology, Jilin Agricultural University, Changchun 130118,
China
| | - Da Sun
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University,
Wenzhou 325035, China
| | - Lei Wang
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University,
Wenzhou 325035, China
| | - Linkai Qu
- College of Life Science and Technology, Jilin Agricultural University, Changchun 130118,
China
| | - Sue Lin
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University,
Wenzhou 325035, China
| | - Qinsi Yang
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Xingxing Zhang
- Department of Endocrinology
and Metabolism, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
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9
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Identification of Antimicrobial Peptide Genes in Black Rockfish Sebastes schlegelii and Their Responsive Mechanisms to Edwardsiella tarda Infection. BIOLOGY 2021; 10:biology10101015. [PMID: 34681113 PMCID: PMC8533284 DOI: 10.3390/biology10101015] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/18/2021] [Accepted: 09/20/2021] [Indexed: 01/01/2023]
Abstract
The black rockfish, Sebastes schlegelii, is a typical viviparous teleost, which belongs to the family Scorpaenidae. Due to its high economic and ecological values, S. schlegelii has been widely cultured in East Asian countries. With the enlargement of cultivation scale, bacterial and viral diseases have become the main threats to the farming industry of S. schlegelii, which have resulted in significant economic losses. In this study, Illumina shotgun sequencing, single-molecule real-time (SMRT) sequencing, 10× genomics and high-throughput chromosome conformation capture (Hi-C) technologies were collectively applied to assemble the genome of S. schlegelii. Then, we identified the antimicrobial peptide genes (AMPs) in the S. schlegelii genome. In total, 214 AMPs were identified in the S. schlegelii genome, which can be divided into 33 classes according to the annotation and cataloging of the Antimicrobial Peptides Database (APD3). Among these AMPs, thrombin-derived C-terminal peptide (TCP) was the dominant type, followed by RegIIIgamma and chemokine. The amino acid sequences of the TCP, cgUbiquitin, RegIIIalpha, RegIIIgamma, chemokine shared 32.55%, 42.63%, 29.87%, 28.09%, and 32.15% similarities among the same type in S. schlegelii. Meanwhile, the expression patterns of these AMPs in nine healthy tissues and at different infection time points in intestine were investigated. The results showed that the numbers and types of AMPs that responded to Edwardsiella tarda infection gradually increased as the infection progressed. In addition, we analyzed the phylogenetic relationships of hepcidins in teleost. The identification of AMPs based on the whole genome could provide a comprehensive database of potential AMPs, and benefit for the understanding of the molecular mechanisms of immune responses to E. tarda infection in S. schlegelii. This would further offer insights into an accurate and effective design and development of AMP for aquaculture therapy in the future.
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10
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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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Genetics of Marine Organisms Associated with Human Health. Mar Drugs 2020; 18:md18110548. [PMID: 33147725 PMCID: PMC7692788 DOI: 10.3390/md18110548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 11/16/2022] Open
Abstract
Marine habitats harbour a large variety of organisms that belong to diverse taxa; from bacteria and unicellular eukaryotes to fungi, animals, and plants. Although we have only started to understand the diversity and structure of marine communities, it is clear that numerous marine species have or might have an impact on human health. Some are a source of natural products with potential or actual medical applications, others are toxic and harmful to humans, and some are used in biomedical research to help understand the molecular basis of human diseases. New molecular genetics and genomic methods provide powerful and ever more indispensable tools for studying marine organisms and all aspects of their influence on human health. Herein, we present work using the latest research, which mostly uses genomics, to tackle the questions related with the topic of the issue.
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12
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Xie Y, Wan H, Zeng X, Zhang Z, Wang Y. Characterization and antimicrobial evaluation of a new Spgly-AMP, glycine-rich antimicrobial peptide from the mud crab Scylla paramamosain. FISH & SHELLFISH IMMUNOLOGY 2020; 106:384-392. [PMID: 32771609 DOI: 10.1016/j.fsi.2020.08.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/30/2020] [Accepted: 08/05/2020] [Indexed: 06/11/2023]
Abstract
Antimicrobial peptide (AMP) is a crucial component of the innate immune system in crustaceans. In mud crab, Scylla paramamosain, a commercially important species, a glycine-rich antimicrobial peptide (Spgly-AMP) gene was newly identified and putatively encoded a 26aa signal peptide and 37aa mature peptide. To understand the function of Spgly-AMP, the expression profile of Spgly-amp gene was characterized, which showed Spgly-amp was expressed widely in most tissues of adult crabs with the highest expression level in hemocytes. After Vibrio parahaemolyticus, PGN, or Poly I:C stimulations, the expression level of Spgly-amp was significantly up-regulated in the hemocytes. In antimicrobial assays, chemically synthesized Spgly-AMP peptides exhibited strong antibacterial activities against both Gram-positive and Gram-negative bacteria and high thermal stability after high-temperature heating. These findings in the present study verified the importance of the Spgly-AMP in defense of pathogenic bacteria infection in the mud crab and provided a promising candidate of antimicrobial agents in the crab aquaculture.
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Affiliation(s)
- Yichao Xie
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Fisheries College, Jimei University, Xiamen, 361021, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, China
| | - Haifu Wan
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Fisheries College, Jimei University, Xiamen, 361021, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, China
| | - Xianyuan Zeng
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Fisheries College, Jimei University, Xiamen, 361021, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, China
| | - Ziping Zhang
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Yilei Wang
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Fisheries College, Jimei University, Xiamen, 361021, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, China.
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13
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Comprehensive transcriptional changes in the liver of Kanglang white minnow ( Anabarilius g rahami) in response to the infection of parasite Ichthyophthirius m ultifiliis. Animals (Basel) 2020; 10:ani10040681. [PMID: 32295151 PMCID: PMC7222788 DOI: 10.3390/ani10040681] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 04/04/2020] [Accepted: 04/09/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Kanglang white minnow (KWM, Anabarilius grahami), is a typical “3E” (Endangered, Endemic and Economic) fish species in Yunnan-Guizhou Plateau. As one of the traditional “Four Famous Fishes” in Yunnan province, it has become the major local aquaculture species with increasing demand after the success of artificial breeding. However, this economically important fish is highly susceptible to the infection of a parasite ciliate, Ichthyophthirius multifiliis (Ich), during the practical procedure of artificial breeding. To examine the host immune responses to Ich, we divided the experimental fishes into three groups (including control, early-infected stage, and late-infected stage) for transcriptome sequencing to analyze the differentially expressed genes (DEGs) and immune response mechanisms. Abstract The notorious parasite Ichthyophthirius multifiliis (Ich) has been recorded worldwide in fish species and causes white spot disease, posing major threats and resulting in severe losses to international fish production. Extensively effective strategies for treating Ich are not available yet, and genetic mechanisms of hosts in response to the parasite are still largely unknown. In this study, we selected Kanglang white minnow (KWM, Anabarilius grahami) to examine its liver transcriptional changes after Ich infection, as white spot disease is one bottleneck problem in exploring this economically important species. We divided the experimental fishes into three groups (control, early-infected, and late-infected) to examine differentially expressed genes (DEGs). A total of 831 DEGs were identified and classified into 128 significantly enriched GO (Gene Ontology) terms and 71 significantly enriched KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways. Most of these terms or pathways were functionally enriched in immunity, inflammatory response, and apoptosis, such as nucleotide-binding oligomerization domain-like (NOD-like) receptor signaling, tumor necrosis factor (TNF) signaling, interleukin-17 (IL-17) signaling, and apoptosis pathways. We also identified 178 putative antimicrobial peptides (AMPs) and AMP precursors based on our previously reported genome assembly of KWM, and revealed that the expressional patterns varied according to different types. In summary, our work reported the first comprehensive transcriptional changes in KWM in response to the exogenous infection of Ich, which would lay a solid foundation for in-depth studies on disease defense or resistant strains selection in this valuable fish.
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Chen HC, Pan CY, Rajanbabu V, Lee YY, Tsai WR, Chen JY. Lack of Acute Toxicity and Mutagenicity from Recombinant Epinephelus lanceolatus Piscidin Expressed in Pichia pastoris. Mar Drugs 2020; 18:md18040206. [PMID: 32290449 PMCID: PMC7230367 DOI: 10.3390/md18040206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/04/2020] [Accepted: 04/08/2020] [Indexed: 12/20/2022] Open
Abstract
The antimicrobial peptide (AMP) piscidin was identified from Epinephelus lanceolatus and demonstrated to possess antimicrobial and immune-related functions. Supplementation of feed with recombinant Epinephelus lanceolatus piscidin (rEP)-expressing yeast pellets may minimize the excessive use of antibiotics and control pathogens in aquaculture or animal husbandry. However, before implementing rEP as a supplement, it is necessary to understand whether it harbors any toxicity. Since toxicological information on the topic is scarce, the present investigation was carried out to test whether rEP exhibits allergenic and/or toxic effects. In an oral acute toxicity test (OECD 425), Sprague Dawley (SD) rats were administered rEP dissolved in reverse osmosis water, yielding an LD50 > 5000 mg/kg (no observed animal death). The compound was therefore classified as non-toxic by oral administration. In an acute respiratory toxicity test (OECD 403), heads and noses of SD rats were exposed to liquid aerosol for 4 h (the highest concentration that could be administered without causing any animal death), and a lethal concentration (LC50) > 0.88 mg/L was obtained. The mass medium aerodynamics diameter (MMAD) of rEP aerosol particles was 8.18 μm and mass medium aerodynamics diameter (GSD) was 3.04, which meant that 25.90% could enter the airway (<4 μm) of a rat, and 58.06% (<10 μm) could be inhaled by humans. An ocular irritation test (OECD 405) with rEP powder was performed on New Zealand White (NZW) rabbits. Signs of irritation included conjunctival swelling and diffuse flushing 1 h after administration. The signs were less apparent after 24 h and disappeared after 72 h. The classification assigned to the powder was mild eye irritation. Skin sensitization was performed for a local lymphoproliferative test (OECD 442B) using BALB/c mice, with the highest soluble concentration of the rEP considered to be 100% test substance; formulations were diluted to 50% and 25%, and bromodeoxyuridine (BrdU) incorporation was used to measure the degree of lymphocyte proliferation. The stimulation indexes (SIs) were 1.06 (100%), 0.44 (50%), and 0.77 (25%), all of which were less than the cutoff value for a positive sensitization result (1.6). Negative response was also seen in the bacterial reverse mutation test (OECD 471), and no chromosomal effects on Chinese hamster ovary (CHO)-K1 cells were observed (OECD 487). Based on these six toxicity tests, rEP showed neither acute toxic effects in experimental animals nor mutagenicity. Thus, rEP can be considered safe for use in subsequent research on its application as a feed additive for poultry, cattle, or aquatic animals.
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Affiliation(s)
- Hsiao-Ching Chen
- Division of Applied Toxicology, Taiwan Agricultural Chemicals and Toxic Substances Research Institute, Council of Agriculture, Taichung City 41358, Taiwan; (H.-C.C.); (Y.-Y.L.)
| | - Chieh-Yu Pan
- Department and Graduate Institute of Aquaculture, National Kaohsiung University of Science and Technology, Kaohsiung 811, Taiwan;
| | - Venugopal Rajanbabu
- Anbil Dharmalingam Agricultural College and Research Institute, Tamil Nadu Agricultural University, Tiruchchirapalli, Tamil Nadu 620027, India;
| | - Yen-Yun Lee
- Division of Applied Toxicology, Taiwan Agricultural Chemicals and Toxic Substances Research Institute, Council of Agriculture, Taichung City 41358, Taiwan; (H.-C.C.); (Y.-Y.L.)
| | - Wei-Ren Tsai
- Division of Applied Toxicology, Taiwan Agricultural Chemicals and Toxic Substances Research Institute, Council of Agriculture, Taichung City 41358, Taiwan; (H.-C.C.); (Y.-Y.L.)
- Correspondence: (W.-R.T.); (J.-Y.C.); Tel.: +886-988105706 (W.-R.T.); +886-920802111 (J.-Y.C.)
| | - Jyh-Yih Chen
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, 23-10 Dahuen Road, Jiaushi, Ilan 262, Taiwan
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
- Correspondence: (W.-R.T.); (J.-Y.C.); Tel.: +886-988105706 (W.-R.T.); +886-920802111 (J.-Y.C.)
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15
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Heras J, Chakraborty M, Emerson JJ, German DP. Genomic and biochemical evidence of dietary adaptation in a marine herbivorous fish. Proc Biol Sci 2020; 287:20192327. [PMID: 32070255 PMCID: PMC7062031 DOI: 10.1098/rspb.2019.2327] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 01/26/2020] [Indexed: 01/30/2023] Open
Abstract
Adopting a new diet is a significant evolutionary change, and can profoundly affect an animal's physiology, biochemistry, ecology and genome. To study this evolutionary transition, we investigated the physiology and genomics of digestion of a derived herbivorous fish, Cebidichthys violaceus. We sequenced and assembled its genome (N50 = 6.7 Mb) and digestive transcriptome, and revealed the molecular changes related to digestive enzymes (carbohydrases, proteases and lipases), finding abundant evidence of molecular adaptation. Specifically, two gene families experienced expansion in copy number and adaptive amino acid substitutions: amylase and carboxyl ester lipase (cel), which are involved in the digestion of carbohydrates and lipids, respectively. Both show elevated levels of gene expression and increased enzyme activity. Because carbohydrates are abundant in the prickleback's diet and lipids are rare, these findings suggest that such dietary specialization involves both exploiting abundant resources and scavenging rare ones, especially essential nutrients, like essential fatty acids.
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Affiliation(s)
- Joseph Heras
- Department of Ecology & Evolutionary Biology, University of California, Irvine, CA 92697-2525, USA
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