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Liu Q, Liu Y, Zhang X, Huang W, Shu G, Zhao H, Dai L, Dai L. Comparative transcriptome profile reveals insight into the antibacterial immunity mechanism of the loach (Misgurnus anguillicaudatus) fed with soybean fermented broth during lipopolysaccharide (LPS) exposure. Int J Biol Macromol 2024; 259:129239. [PMID: 38184041 DOI: 10.1016/j.ijbiomac.2024.129239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 01/02/2024] [Accepted: 01/02/2024] [Indexed: 01/08/2024]
Abstract
Loach (Misgurnus anguillicaudatus) is a common freshwater commercial fish species in China. The meat of this fish is a good source of protein and other nutrients that are needed for human health. Aquaculture challenges such as diseases and pest susceptibility, excessive density, and nutritional deficiency result in low production of loach rather than increased demand. Due to a lack of knowledge about the immune system of loaches, we carried out this study to better understand its antibacterial molecular mechanism. Here, we performed RNA sequencing from liver tissue obtained from soya bean-fermented fed loach after subjecting it to the LPS challenge. The results revealed a total of 18,399 differentially expressed genes (DEGs) in the LPS-treated and control groups. There were 7482 DEGs that were upregulated and 10,917 DEGs were downregulated. The enrichment analysis of DEGs revealed that the majority of DEGs were found to be abundant in the pathways of DNA replication, spliceosome, nucleotide exception repair, cell cycle, and Herpes simplex virus 1 infection. Furthermore, qRT-PCR analysis of 21 selected DEGs demonstrated that the transcriptomic data is extremely reliable. Overall, this study provides insight into the molecular features and control mechanisms of genes that affect loach growth. The availability of this information will also contribute to the enhancement of the breeding and protection of loach resources.
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Affiliation(s)
- Qiuning Liu
- College of Wetland, Yancheng Teachers University, Yancheng 224007, PR China; School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, PR China
| | - Yu Liu
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, PR China
| | - Xinxin Zhang
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, PR China
| | - Wentian Huang
- College of Basic Medicine, Chinese People's Liberation Army Naval Medical University, Shanghai 200433, PR China; Cardiology Department, General Hospital of Eastern Theater Command, Shanghai 201101, PR China
| | - Guixia Shu
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, PR China
| | - Haiyang Zhao
- Institute of Life Sciences, Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou 325035, PR China.
| | - Lu Dai
- Department of Oral and Maxillofacial Surgery, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing 210029, PR China; The Fourth Outpatient Department, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing 210029, PR China.
| | - Lishang Dai
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, PR China.
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Ke Z, Zhou K, Hou M, Luo H, Li Z, Pan X, Zhou J, Jing T, Ye H. Characterization of the Complete Mitochondrial Genome of the Elongate Loach and Its Phylogenetic Implications in Cobitidae. Animals (Basel) 2023; 13:3841. [PMID: 38136877 PMCID: PMC10740543 DOI: 10.3390/ani13243841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 12/24/2023] Open
Abstract
The elongate loach is an endemic fish in China. Previous studies have provided some insights into the mitochondrial genome composition and the phylogenetic relationships of the elongate loach inferred using protein-coding genes (PCGs), yet detailed information about it remains limited. Therefore, in this study we sequenced the complete mitochondrial genome of the elongate loach and analyzed its structural characteristics. The PCGs and mitochondrial genome were used for selective stress analysis and genomic comparative analysis. The complete mitochondrial genome of the elongate loach, together with those of 35 Cyprinidae species, was used to infer the phylogenetic relationships of the Cobitidae family through maximum likelihood (ML) reconstruction. The results showed that the genome sequence has a full length of 16,591 bp, which includes 13 PCGs, 22 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA), and 2 non-coding regions (CR D-loop and light chain sub-chain replication origin OL). Overall, the elongate loach shared the same gene arrangement and composition of the mitochondrial genes with other teleost fishes. The Ka/Ks ratios of all mitochondrial PCGs were less than 1, indicating that all of the PCGs were evolving under purifying selection. Genome comparison analyses showed a significant sequence homology of species of Leptobotia. A significant identity between L. elongata and the other five Leptobotia species was observed in the visualization result, except for L. mantschurica, which lacked the tRNA-Arg gene and had a shorter tRNA-Asp gene. The phylogenetic tree revealed that the Cobitidae species examined here can be grouped into two clades, with the elongate loach forming a sister relationship with L. microphthalma. This study could provide additional inferences for a better understanding of the phylogenetic relationships among Cobitidae species.
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Affiliation(s)
- Zhenlin Ke
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, 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; (Z.K.); (M.H.); (H.L.); (T.J.)
- Key Laboratory of Aquatic Science of Chongqing, Chongqing 400175, China
| | - Kangqi Zhou
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China; (K.Z.); (Z.L.); (X.P.)
| | - Mengdan Hou
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, 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; (Z.K.); (M.H.); (H.L.); (T.J.)
- Key Laboratory of Aquatic Science of Chongqing, Chongqing 400175, China
| | - Hui Luo
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, 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; (Z.K.); (M.H.); (H.L.); (T.J.)
- Key Laboratory of Aquatic Science of Chongqing, Chongqing 400175, China
| | - Zhe Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China; (K.Z.); (Z.L.); (X.P.)
| | - Xianhui Pan
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China; (K.Z.); (Z.L.); (X.P.)
| | - Jian Zhou
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu 611731, China
| | - Tingsen Jing
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, 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; (Z.K.); (M.H.); (H.L.); (T.J.)
- Key Laboratory of Aquatic Science of Chongqing, Chongqing 400175, China
| | - Hua Ye
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, 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; (Z.K.); (M.H.); (H.L.); (T.J.)
- Key Laboratory of Aquatic Science of Chongqing, Chongqing 400175, China
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Martyniuk CJ, Simmons D. Sex-specific omic responses in animal physiology and toxicology. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 42:100990. [PMID: 35500499 DOI: 10.1016/j.cbd.2022.100990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Christopher J Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida Genetics Institute, Interdisciplinary Program in Biomedical Sciences in Neuroscience, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA.
| | - Denina Simmons
- Faculty of Science, Ontario Tech University, Oshawa, ON, Canada
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