1
|
Li Y, Zou X, Jin H, Zhou B, Zhou J, Zhang L, Li Z, Ling L, Liu F, Gao Y, Wang X, Luo H, Chen K, Ye H. Identification of genes related to growth from transcriptome profiles of the muscle and liver of Chinese longsnout catfish (Leiocassis longirostris). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 49:101180. [PMID: 38150989 DOI: 10.1016/j.cbd.2023.101180] [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: 08/14/2023] [Revised: 11/26/2023] [Accepted: 12/13/2023] [Indexed: 12/29/2023]
Abstract
The Chinese longsnout catfish (Leiocassis longirostris) is a commercially important freshwater fish species in China. To understand the molecular mechanisms underlying its growth, we performed a comparative transcriptomic analysis of muscle and liver tissues of fast- and slow-growing L. longirostris. A total of 580 and 511 differentially expressed genes (DEGs) were obtained in the muscle and liver tissues, respectively. We selected 10 DEGs each from muscle and liver tissues by qRT-PCR to verify the reliability of RNA-seq, and it was found that the expression patterns of these genes were consistent with RNA-seq analysis results. According to the differential expression and functional enrichment analysis of genes, we found differences in the expression of several growth-related genes between fast- and slow-growing individuals. These genes may contribute to the differences in the growth of L. longirostris by influencing muscle growth and the metabolism of substances and energy. In particular, the pk and fabp genes were highly expressed in fast-growing individuals, while the cart, leptin, pepck, murf1, trim32, and pparα genes exhibited higher levels in slow-growing individuals. It was speculated that genes related to feeding behavior might be the key genes in regulating the growth of L. longirostris, while glycolytic/gluconeogenic metabolic pathway, lipid metabolism, and ubiquitin-proteasome pathway might be the main pathways involved in regulating body weight of L. longirostris. This study could enrich the available gene resources and provide a valuable basis for further studies on the regulatory mechanisms of growth in L. longirostris.
Collapse
Affiliation(s)
- Yu Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China; Yibin Academy of Southwest University, Yibin 64400, Sichuan, China
| | - Xinxi Zou
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China; Yibin Academy of Southwest University, Yibin 64400, Sichuan, China
| | - Honghao Jin
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China; Yibin Academy of Southwest University, Yibin 64400, Sichuan, China
| | - Bo Zhou
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu 61173, Sichuan, China
| | - Jian Zhou
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu 61173, Sichuan, China
| | - Lu Zhang
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu 61173, Sichuan, China
| | - Zhe Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China; Yibin Academy of Southwest University, Yibin 64400, Sichuan, China
| | - Leyan Ling
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China; Yibin Academy of Southwest University, Yibin 64400, Sichuan, China
| | - Fan Liu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China; Yibin Academy of Southwest University, Yibin 64400, Sichuan, China
| | - Yuan Gao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China; Yibin Academy of Southwest University, Yibin 64400, Sichuan, China
| | - Xinyue Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China; Yibin Academy of Southwest University, Yibin 64400, Sichuan, China
| | - Hui Luo
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China; Yibin Academy of Southwest University, Yibin 64400, Sichuan, China
| | - Kaili Chen
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China; Yibin Academy of Southwest University, Yibin 64400, Sichuan, China.
| | - Hua Ye
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China; Yibin Academy of Southwest University, Yibin 64400, Sichuan, China.
| |
Collapse
|
2
|
Wang B, Zhu F, Shi Z, Huang Z, Sun R, Wang Q, Ouyang G, Ji W. Molecular characteristics, polymorphism and expression analysis of mhc Ⅱ in yellow catfish(pelteobagrus fulvidraco)responding to Flavobacterium columnare infection. FISH & SHELLFISH IMMUNOLOGY 2022; 125:90-100. [PMID: 35483597 DOI: 10.1016/j.fsi.2022.04.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 04/04/2022] [Accepted: 04/21/2022] [Indexed: 06/14/2023]
Abstract
The major histocompatibility complex (MHC) is an important component of the immune system of vertebrates, which plays a vital role in presenting extrinsic antigens. In this study, we cloned and characterized the mhc ⅡA and mhc ⅡB genes of yellow catfish Pelteobagrus fulvidraco. The open reading frames (ORFs) of mhc ⅡA and mhc ⅡB genes were 708 bp and 747bp in length, encoding 235 and 248 amino acids, respectively. The structure of mhc ⅡA and mhc ⅡB includes a signal peptide, an α1/β1 domain, an α2/β2 domain, a transmembrane region and a cytoplasmic region. Homologous identity analysis revealed that both mhc ⅡA and mhc ⅡB shared high protein sequence similarity with that of Chinese longsnout catfish Leiocassis longirostris. mhc ⅡA and mhc ⅡB showed similar expression patterns in different tissues, with the higher expression level in spleen, head kidney and gill and lower expression in liver, stomach, gall bladder and heart. The mRNA expression level of mhc ⅡA and mhc ⅡB in different embryonic development stages also showed the similar trends. The higher expression was detected from fertilized egg to 32 cell stage, low expression from multicellular period to 3 days post hatching (dph), and then the expression increased to a higher level from 4 dph to 14 dph. The mRNA expression levels of mhc ⅡA and mhc ⅡB were significantly up-regulated not only in the body kidney and spleen, but also in the midgut, hindgut, liver and gill after challenge of Flavobacterium columnare. The results suggest that Mhc Ⅱ plays an important role in the anti-infection process of yellow catfish P. fulvidraco.
Collapse
Affiliation(s)
- Bingchao Wang
- Department of Aquatic Animal Medicines, College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fangzheng Zhu
- Department of Aquatic Animal Medicines, College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zechao Shi
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China
| | - Zhenyu Huang
- Department of Aquatic Animal Medicines, College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ruhan Sun
- Department of Aquatic Animal Medicines, College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qingchao Wang
- Department of Aquatic Animal Medicines, College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Gang Ouyang
- Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Wei Ji
- Department of Aquatic Animal Medicines, College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
3
|
Zhao W, Zhou J, Li Z, Jing T, Zhao L, Ye H. Characterization of 55 SNP markers in Chinese longsnout catfish Leriocassis Longirostris. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01137-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
4
|
Development of SNP markers in Leiocassis longirostris Günther using high-throughput sequencing. CONSERV GENET RESOUR 2019. [DOI: 10.1007/s12686-019-01084-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
5
|
Gao FY, Zhang D, Lu MX, Cao JM, Liu ZG, Ke XL, Wang M, Zhang DF, Yi MM. MHC class IIA polymorphisms and their association with resistance-susceptibility to Streptococcus agalactiae in Nile tilapia, Oreochromis niloticus. JOURNAL OF FISH BIOLOGY 2018; 93:1207-1215. [PMID: 30345515 DOI: 10.1111/jfb.13843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/15/2018] [Indexed: 06/08/2023]
Abstract
The association between major histocompatibility complex (MHC) class IIA polymorphisms and the severity of infection by Streptococcus agalactiae was investigated using 40 susceptible and 40 resistant individuals of Nile tilapia Oreochromis niloticus. Twenty-five alleles were identified from 80 individuals, which belong to 22 major allele types. High polymorphism of mhcIIa gene and at least two loci were discovered in O. niloticus. In peptide-binding region (PBR) and non-PBR, the ratio of nonsynonymous substitution (dN) to synonymous substitution (dS) was 1.294 (>1) and 1.240 (>1), suggesting that the loci are evolving under positive balancing selection. Association analysis showed that the allele, orni-daa*0501, was significantly associated with resistance to S. agalactiae, while the alleles, orni-daa*1101, orni-daa*1301, orni-daa*1401 and orni-daa*1201, were associated with susceptibility to S. agalactiae. To confirm these correlations, another independent challenge experiment was performed in the Huizhou population of the O. niloticus. The frequency distribution showed that the orni-daa*1101 allele was significantly more frequent in the Huizhou-Susceptible group (HZ-SG) than in the Huizhou-Resistant group (HZ-RG) (P < 0.05), which was consistent with the first challenge. However, orni-daa*0501 did not present in HZ-SG and HZ-RG and the distribution frequencies of the orni-daa*1201, orni-daa*1301 and orni-daa*1401 alleles were not significantly more frequent in HZ-SG than in HZ-RG. These results indicate that the orni-daa*1101 allele confers susceptibility to S. agalactia infection. These results suggest that the diversity of exon 2 of mcaIIa alleles could be used to explore the association between disease susceptibility or resistance and the multiformity of mcaIIa and to achieve the molecular-assisted selection of O. niloticus with enhanced disease resistance.
Collapse
Affiliation(s)
- Feng-Ying Gao
- Division of Aquaculture and Nutrition, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
- Division of Aquaculture and Nutrition, Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Guangzhou, China
| | - Dong Zhang
- Division of Aquaculture and Nutrition, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
- Division of Aquaculture and Nutrition, Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Guangzhou, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Mai-Xin Lu
- Division of Aquaculture and Nutrition, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
- Division of Aquaculture and Nutrition, Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Guangzhou, China
| | - Jian-Meng Cao
- Division of Aquaculture and Nutrition, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
- Division of Aquaculture and Nutrition, Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Guangzhou, China
| | - Zhi-Gang Liu
- Division of Aquaculture and Nutrition, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
- Division of Aquaculture and Nutrition, Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Guangzhou, China
| | - Xiao-Li Ke
- Division of Aquaculture and Nutrition, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
- Division of Aquaculture and Nutrition, Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Guangzhou, China
| | - Miao Wang
- Division of Aquaculture and Nutrition, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
- Division of Aquaculture and Nutrition, Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Guangzhou, China
| | - De-Feng Zhang
- Division of Aquaculture and Nutrition, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
- Division of Aquaculture and Nutrition, Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Guangzhou, China
| | - Meng-Meng Yi
- Division of Aquaculture and Nutrition, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
- Division of Aquaculture and Nutrition, Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Guangzhou, China
| |
Collapse
|
6
|
Liang H, Guo S, Luo X, Li Z, Zou G. Molecular diagnostic markers of Tachysurus fulvidraco and Leiocassis longirostris and their hybrids. SPRINGERPLUS 2016; 5:2115. [PMID: 28090429 PMCID: PMC5201598 DOI: 10.1186/s40064-016-3766-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 11/30/2016] [Indexed: 11/10/2022]
Abstract
Background Bagridae is an important family of catfishes and has a high market demand. Recently, more cultivable Bagridae fishes are being exploited in China, and hybridization of some species has been carried out to achieve better growth performance, favorable sex ratios and better disease resistance. Yet, these hybrids have further increased the difficulties of taxonomy identification due to morphological indistinguishableness. Results In this study, the molecular identification technologies for Tachysurus fulvidraco, Leiocassis longirostris sand their hybrids were successfully established by using mitochondrial COI and nuclear ITS sequences to identify the maternal and paternal lineage, respectively. Conclusion These molecular diagnostic methods could also be used to manage breeding plans of hybrids, monitor and minimize the negative impacts of hybridization programs in aquaculture. Furthermore, our study could also provide a reference for establishing detection technique for hybrids in other groups of fishes.
Collapse
Affiliation(s)
- Hongwei Liang
- Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences, No. 8, 1st Wudayuan Road, Wuhan East-lake Hi-tech Development Zone, Wuhan, 430223 China ; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070 China
| | - Shanshan Guo
- Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences, No. 8, 1st Wudayuan Road, Wuhan East-lake Hi-tech Development Zone, Wuhan, 430223 China
| | - Xiangzhong Luo
- Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences, No. 8, 1st Wudayuan Road, Wuhan East-lake Hi-tech Development Zone, Wuhan, 430223 China
| | - Zhong Li
- Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences, No. 8, 1st Wudayuan Road, Wuhan East-lake Hi-tech Development Zone, Wuhan, 430223 China
| | - Guiwei Zou
- Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences, No. 8, 1st Wudayuan Road, Wuhan East-lake Hi-tech Development Zone, Wuhan, 430223 China
| |
Collapse
|