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Niu M, Whang H, Wu Z, Jiang S, Chen L. Deletion of Asb15b gene can lead to a significant decrease in zebrafish intermuscular bone. Gene 2024; 923:148561. [PMID: 38754570 DOI: 10.1016/j.gene.2024.148561] [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: 02/06/2024] [Revised: 05/01/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
Intermuscular bones, which are present in numerous economically significant fish species, have a negative impact on the development of aquaculture. The Asb15b gene, primarily expressed in skeletal muscle, plays a crucial role in regulating protein turnover and the development of muscle fibers. It stimulates protein synthesis and controls the differentiation of muscle fibers. In this study, we employed CRISPR/Cas9 technology to generate homozygous zebrafish strains with 7 bp and 49 bp deletions in the Asb15b gene. Subsequent analyses using skeleton staining demonstrated a substantial reduction in the number of intermuscular bones in adult Asb15b-/- -7 bp and Asb15b-/- -49 bp mutants compared to the wild-type zebrafish, with decreases of 30 % (P < 0.001) and 40 % (P < 0.0001), respectively. Histological experiments further revealed that the diameter and number of muscle fibers in adult Asb15b-/- mutants did not exhibit significant changes when compared to wild-type zebrafish. Moreover, qRT-PCR experiments demonstrated significant differences in the expression of bmp6 and runx2b genes, which are key regulators of intermuscular bone development, during different stages of intermuscular bone development in Asb15b-/- mutants. This study strongly suggests that the Asb15b gene plays a crucial role in regulating intermuscular bone development in fish and lays the groundwork for further exploration of the role of the Asb15b gene in zebrafish intermuscular bone development.
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Affiliation(s)
- Minghui Niu
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Fishery Germplasm Resources Exploration and Utilization, Ministry of Education, Shanghai 201306, China
| | - Huamin Whang
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Fishery Germplasm Resources Exploration and Utilization, Ministry of Education, Shanghai 201306, China
| | - Zhichao Wu
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Fishery Germplasm Resources Exploration and Utilization, Ministry of Education, Shanghai 201306, China
| | - Shouwen Jiang
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Fishery Germplasm Resources Exploration and Utilization, Ministry of Education, Shanghai 201306, China
| | - Liangbiao Chen
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Fishery Germplasm Resources Exploration and Utilization, Ministry of Education, Shanghai 201306, China.
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Yang Y, Wang C, Chen S, Liu Y, Jia H, Wang H, He D. Identifying candidate genes and biological pathways in muscle development through multi-tissue transcriptome comparisons between male and female geese. Sci Rep 2024; 14:16474. [PMID: 39014195 PMCID: PMC11252291 DOI: 10.1038/s41598-024-67560-2] [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: 01/18/2024] [Accepted: 07/12/2024] [Indexed: 07/18/2024] Open
Abstract
Males and females have long shown disparities in body weight and height; yet, the underlying mechanisms influencing growth and development remain unclear. Male and female Zhedong White Geese (ZDW) geese have long been selected for large body size and egg production, respectively. This led to a large difference in body weight between males and females, making them a unique model for studying the effects of sex on growth and development. This study aimed to elucidate these mechanisms by comparing the transcriptomes of muscle and pituitary tissues in male and female ZDW geese to identify the critical genes responsible for the effects of sex on growth performance. Our analysis revealed 1101 differentially expressed genes (DEGs) in leg musculature (507 upregulated, 594 downregulated), 773 DEGs in breast musculature (311 upregulated, 462 downregulated), and 517 DEGs in the pituitary gland (281 upregulated, 236 downregulated) between male and female geese. These DEGs were significantly enriched in gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways associated with endocrine metabolism (e.g., hormonal activities), muscle formation (e.g., sarcomere and myofibril), and bone formation (e.g., bone morphogenesis and cartilage formation). The upregulated genes in males were enriched in KEGG pathways involving nutrient digestion and absorption (vitamin and protein), as well as the secretion of digestive juices (gastric acid and bile). Through protein-protein interaction analyses, we also observed high-density gene networks related to muscle fiber development, calcium ion metabolism, mitochondrial respiratory chain, and bone development. Therefore, our multi-tissue transcriptome analysis provides a deeper understanding of the complex and systematic gender-driven effects on growth and development in geese. IGF1, GHRHR, and NCAPG-LCORL and pathways related to myogenesis might play vital roles in gender differences before hormones exert their effect.
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Affiliation(s)
- Yunzhou Yang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Science, Shanghai, 201106, China
| | - Cui Wang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Science, Shanghai, 201106, China
| | - Shufang Chen
- Institute of Animal and Poultry Science, Ningbo Academy of Agricultural Sciences, Ningbo, 315040, China
| | - Yi Liu
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Science, Shanghai, 201106, China
| | - Huiyan Jia
- Institute of Animal and Poultry Science, Ningbo Academy of Agricultural Sciences, Ningbo, 315040, China
| | - Huiying Wang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Science, Shanghai, 201106, China.
| | - Daqian He
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Science, Shanghai, 201106, China.
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Li X, Zhang C, Feng C, Zhang Z, Feng N, Sha H, Luo X, Zou G, Liang H. Transcriptome Analysis Elucidates the Potential Key Genes Involved in Rib Development in bmp6-Deficient Silver Carp ( Hypophthalmichthys molitrix). Animals (Basel) 2024; 14:1451. [PMID: 38791669 PMCID: PMC11117292 DOI: 10.3390/ani14101451] [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: 04/03/2024] [Revised: 05/07/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Bone morphogenetic protein 6 (BMP-6) is a constituent of the TGF-β superfamily, known for its ability to stimulate bone and cartilage formation. The investigation of bmp6's involvement in the formation of intermuscular bones in fish has garnered significant attention in recent years. The rib cage is an important skeletal structure that plays a protective function for internal organs in fish. However, there has been limited research conducted on the effects of the bmp6 gene on rib development. Silver carp is one of four major fish in China, favoured for its affordability and tender muscle. Nevertheless, the presence of numerous intermuscular bones in silver carp significantly hinders the advancement of its palatability and suitability for processing. This study showcases the effective utilisation of CRISPR/Cas9 technology for the purpose of disrupting the bmp6 gene in silver carp, leading to the creation of chimeras in the P0 generation, marking the first instance of such an achievement. The chimeras exhibited complete viability, normal appearance, and partial intermuscular bones loss, with approximately 30% of them displaying rib bifurcation or bending. Subsequently, a transcriptome analysis on ribs of P0 chimeras and wild-type silver carp was conducted, leading to the identification of 934 genes exhibiting differential expression, of which 483 were found to be up-regulated and 451 were found to be down-regulated. The results of the KEGG analysis revealed that the "NF-kappa B signalling pathway", "Hippo signalling pathway", "osteoclast differentiation", and "haematopoietic cell lineage" exhibited enrichment and displayed a significant correlation with bone development. The up-regulated genes such as tnfα, fos, and ctgf in pathways may facilitate the proliferation and differentiation of osteoclasts, whereas the down-regulation of genes such as tgfb2 and tgfbr1 in pathways may hinder the formation and specialisation of osteoblasts, ultimately resulting in rib abnormalities. This study presents novel findings on the impact of bmp6 gene deletion on the rib development of silver carp, while simultaneously investigating the previously unexplored molecular mechanisms underlying rib defects in fish.
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Affiliation(s)
- Xiaohui Li
- Yangtze River Fisheries Research Institude, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (X.L.); (C.Z.); (C.F.); (Z.Z.); (N.F.); (H.S.); (X.L.); (G.Z.)
| | - Chunyan Zhang
- Yangtze River Fisheries Research Institude, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (X.L.); (C.Z.); (C.F.); (Z.Z.); (N.F.); (H.S.); (X.L.); (G.Z.)
- Laboratory of Zooligical Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, China
| | - Cui Feng
- Yangtze River Fisheries Research Institude, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (X.L.); (C.Z.); (C.F.); (Z.Z.); (N.F.); (H.S.); (X.L.); (G.Z.)
| | - Zewen Zhang
- Yangtze River Fisheries Research Institude, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (X.L.); (C.Z.); (C.F.); (Z.Z.); (N.F.); (H.S.); (X.L.); (G.Z.)
- Laboratory of Zooligical Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, China
| | - Nannan Feng
- Yangtze River Fisheries Research Institude, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (X.L.); (C.Z.); (C.F.); (Z.Z.); (N.F.); (H.S.); (X.L.); (G.Z.)
- Laboratory of Zooligical Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, China
| | - Hang Sha
- Yangtze River Fisheries Research Institude, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (X.L.); (C.Z.); (C.F.); (Z.Z.); (N.F.); (H.S.); (X.L.); (G.Z.)
| | - Xiangzhong Luo
- Yangtze River Fisheries Research Institude, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (X.L.); (C.Z.); (C.F.); (Z.Z.); (N.F.); (H.S.); (X.L.); (G.Z.)
| | - Guiwei Zou
- Yangtze River Fisheries Research Institude, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (X.L.); (C.Z.); (C.F.); (Z.Z.); (N.F.); (H.S.); (X.L.); (G.Z.)
| | - Hongwei Liang
- Yangtze River Fisheries Research Institude, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (X.L.); (C.Z.); (C.F.); (Z.Z.); (N.F.); (H.S.); (X.L.); (G.Z.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
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Xiao Z, Chen Y, Wang X, Sun Q, Tu T, Liu J, Nie C, Gao Z. Effect of runx2b deficiency in intermuscular bones on the regulatory network of lncRNA-miRNA-mRNA. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 49:101171. [PMID: 38103500 DOI: 10.1016/j.cbd.2023.101171] [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: 07/27/2023] [Revised: 11/10/2023] [Accepted: 11/30/2023] [Indexed: 12/19/2023]
Abstract
Intermuscular bones (IBs) are mineralized spicules that negatively impact the quality and value of fish products. Runx2b is a crucial modulator in promoting bone formation through regulating osteoblast differentiation. Previous studies suggested that loss of runx2b gene completely inhibited IBs formation in zebrafish. However, how the whole transcriptome, including mRNA and non-coding RNA (ncRNA), affects the IBs development in runx2b-/- zebrafish are not known. The aim of this study was to identify the regulatory networks of differentially expressed (DE) lncRNAs, miRNAs, and mRNAs in zebrafish with and without IBs (runx2b+/+ fish and runx2b-/- fish) utilizing high-throughput sequencing techniques. All together there are 1051 mRNAs, 456 lncRNAs, and 18 miRNAs differentially expressed were found between these two strains. The analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) has highlighted significant pathways linked to the development of IBs, specifically the TGF-beta and Wnt signaling pathways, and a number of genes concentrated on these two signaling pathways related to the formation of IBs. Further, 1989 competing endogenous RNA (ceRNA) networks were created according to the correlation among mRNAs, miRNAs and lncRNAs. The ceRNA networks results revealed 52 ceRNA pairs related to the IBs formation, consisting of 52 mRNAs, 37 lncRNAs, and 6 miRNAs. Of these, we found that dre-miR-2189 was the key element of ceRNA pairs, interacting with 19 mRNAs and 11 lncRNAs, and MSTRG.13175.1 could regulate sp7 expression by interacting with dre-miR-2189 to function in osteogenic differentiation. Subsequent experiments at the cellular level also revealed the interaction mechanism. The outcomes indicated a crucial role of miRNAs and lncRNAs in the development of fish IBs, which offer new views into the functions of ncRNAs involved in IBs formation.
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Affiliation(s)
- Zhengyu Xiao
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Yulong Chen
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Xudong Wang
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiujie Sun
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Tan Tu
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Junqi Liu
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunhong Nie
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
| | - Zexia Gao
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
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5
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Zheng J, He C, Jiang W, Liu S, Li F, Chi M, Cheng S, Liu Y. Screening for IBs-relative genes by transcriptome analysis and generation IBs-less mutants in Culter alburnus. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 47:101106. [PMID: 37413699 DOI: 10.1016/j.cbd.2023.101106] [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: 03/03/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 07/08/2023]
Abstract
Intermuscular bones (IBs), distributed specifically in the myosepta on both sides of lower teleosts, negatively affect palatability and processing. Recent research in zebrafish and several economically important farmed fishes has led to the breakthrough discovery of the mechanism of IBs formation and generation of IBs-loss mutants. This study explored the ossification patterns of IBs in juvenile Culter alburnus. Besides, some key genes and bone-related signaling pathways were identified by transcriptomic data. Furthermore, PCR microarray validation revealed that claudin1 could potentially regulate IBs formation. Additionally, we created several IBs-reduced mutants of C. alburnus by loss of the function of bone morphogenetic proteins 6 (bmp6) gene using CRISPR/Cas9 editing. These results suggested that CRISPR/Cas9-mediated bmp6 knockout was promising approach for breeding IBs-free strain in other cyprinids.
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Affiliation(s)
- Jianbo Zheng
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Changxi He
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Engineering Research Center of Aquaculture, National Demonstration Center for Experimental Fisheries Science Education, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Wenping Jiang
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Shili Liu
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Fei Li
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, China.
| | - Meili Chi
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Shun Cheng
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Yinuo Liu
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
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Qu M, Zhang Y, Gao Z, Zhang Z, Liu Y, Wan S, Wang X, Yu H, Zhang H, Liu Y, Schneider R, Meyer A, Lin Q. The genetic basis of the leafy seadragon's unique camouflage morphology and avenues for its efficient conservation derived from habitat modeling. SCIENCE CHINA. LIFE SCIENCES 2023:10.1007/s11427-022-2317-6. [PMID: 37204606 DOI: 10.1007/s11427-022-2317-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/03/2023] [Indexed: 05/20/2023]
Abstract
The leafy seadragon certainly is among evolution's most "beautiful and wonderful" species aptly named for its extraordinary camouflage mimicking its coastal seaweed habitat. However, limited information is known about the genetic basis of its phenotypes and conspicuous camouflage. Here, we revealed genomic signatures of rapid evolution and positive selection in core genes related to its camouflage, which allowed us to predict population dynamics for this species. Comparative genomic analysis revealed that seadragons have the smallest olfactory repertoires among all ray-finned fishes, suggesting adaptations to the highly specialized habitat. Other positively selected and rapidly evolving genes that serve in bone development and coloration are highly expressed in the leaf-like appendages, supporting a recent adaptive shift in camouflage appendage formation. Knock-out of bmp6 results in dysplastic intermuscular bones with a significantly reduced number in zebrafish, implying its important function in bone formation. Global climate change-induced loss of seagrass beds now severely threatens the continued existence of this enigmatic species. The leafy seadragon has a historically small population size likely due to its specific habitat requirements that further exacerbate its vulnerability to climate change. Therefore, taking climate change-induced range shifts into account while developing future protection strategies.
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Affiliation(s)
- Meng Qu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingyi Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zexia Gao
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhixin Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
- Global Ocean and Climate Research Center, South China Sea Institute of Oceanology, Guangzhou, 510301, China
| | - Yali Liu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shiming Wan
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xin Wang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
| | - Haiyan Yu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
| | - Huixian Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
| | - Yuhong Liu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
| | - Ralf Schneider
- Marine Evolutionary Ecology, Zoological Institute, Kiel University, 24118, Kiel, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, 78464, Konstanz, Germany.
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China.
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Yu J, Guo L, Zhang SH, Zhu QY, Chen RY, Wong BH, Ding GH, Chen J. Transcriptomic analysis of intermuscular bone development in barbel steed (Hemibarbus labeo). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 44:101030. [PMID: 36343604 DOI: 10.1016/j.cbd.2022.101030] [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: 07/26/2022] [Revised: 10/11/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022]
Abstract
Intermuscular bones (IBs), which are little, bony spicules in muscle, are embedded in lower teleosts' myosepta. Despite the importance of studying IB development in freshwater aquaculture species, the genes associated with IB development need to be further explored. In the present study, we identified four stages of IB development in barbel steed (Hemibarbus labeo), namely stage 1: IBs have not emerged, stage 2: a few small IBs have emerged in the tail, stage 3: longer IBs gradually emerged in the tail and stage 4: all of the IBs in the tail are mature and long, via Alizarin red staining. Subsequently, we used the HiseqXTen platform to sequence and de novo assemble the transcriptome of epaxial muscle (between 35th and 40th myomere) of barbel steed at 29 days (stage 1) and 42 days (stage 3) after hatching. A total of 190,814 unigenes were obtained with an average length and N50 of 648 bp and 1027 bp, respectively. We found 2174 differentially expressed genes (DEGs) between stages 1 and 3, of which 378 and 1796 were up- and down-regulated, respectively. Functional enrichment analysis showed that several DEGs functioned in ossification, positive regulation of osteoblast differentiation, osteoblast differentiation, and BMP signaling pathway, and were further enriched in signal pathway, including osteoclast differentiation, TGF-β signaling pathway, cytokine-cytokine receptor interaction, Jak-STAT signaling pathway, and other KEEG pathways. In conclusion, we identified genes that may be related to IB development, such as kazal type serine peptidase inhibitor domain 1 (KAZALD1), extracellular matrix protein 1 (ECM1), tetranectin, bone morphogenetic protein 1 (bmp1), acid phosphatase 5 (ACP5), collagen type XI alpha 1 chain (COL11A1), matrix metallopeptidase 9 (MMP9), pannexin-3 (PANX3), sp7 transcription factor (Sp7), and c-x-c motif chemokine ligand 8 (CXCL8), by comparing the transcriptomes of epaxial muscle before and after IB ossification. This study provided a theoretical basis for identifying the molecular mechanisms underlying IB development in fish.
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Affiliation(s)
- Jing Yu
- College of Ecology, Lishui University, Lishui 323000, China
| | - Ling Guo
- College of Ecology, Lishui University, Lishui 323000, China
| | - Si-Hai Zhang
- College of Ecology, Lishui University, Lishui 323000, China
| | - Qun-Yin Zhu
- College of Ecology, Lishui University, Lishui 323000, China
| | - Ru-Yi Chen
- College of Ecology, Lishui University, Lishui 323000, China
| | - Boon Hui Wong
- Department of Biological Science, National University of Singapore, Singapore 117558, Singapore
| | - Guo-Hua Ding
- College of Ecology, Lishui University, Lishui 323000, China
| | - Jie Chen
- College of Ecology, Lishui University, Lishui 323000, China.
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