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Li X, Cao T, Liu H, Fu L, Wang Q. Identification and expression analysis of Sox family genes in echinoderms. BMC Genomics 2024; 25:655. [PMID: 38956468 PMCID: PMC11218330 DOI: 10.1186/s12864-024-10547-0] [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: 04/03/2024] [Accepted: 06/21/2024] [Indexed: 07/04/2024] Open
Abstract
The Sox gene family, a collection of transcription factors widely distributed throughout the animal kingdom, plays a crucial role in numerous developmental processes. Echinoderms occupy a pivotal position in many research fields, such as neuroscience, sex determination and differentiation, and embryonic development. However, to date, no comprehensive study has been conducted to characterize and analyze Sox genes in echinoderms. In the present study, the evolution and expression of Sox family genes across 11 echinoderms were analyzed using bioinformatics methods. The results revealed a total of 70 Sox genes, with counts ranging from 5 to 8 across different echinoderms. Phylogenetic analysis revealed that the identified Sox genes could be categorized into seven distinct classes: the SoxB1 class, SoxB2 class, SoxC class, SoxD class, SoxE class, SoxF class and SoxH class. Notably, the SoxB1, SoxB2, and SoxF genes were ubiquitously present in all the echinoderms studied, which suggests that these genes may be conserved in echinoderms. The spatiotemporal expression patterns observed for Sox genes in the three echinoderms indicated that various Sox members perform distinct functional roles. Notably, SoxB1 is likely involved in echinoderm ovary development, while SoxH may play a crucial role in testis development in starfish and sea cucumber. In general, the present investigation provides a molecular foundation for exploring the Sox gene in echinoderms, providing a valuable resource for future phylogenetic and genomic studies.
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Affiliation(s)
- Xiaojing Li
- Yantai Vocational College, Yantai, 264003, China
| | - Tiangui Cao
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Hui Liu
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Longhai Fu
- Yantai Vocational College, Yantai, 264003, China
| | - Quanchao Wang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China.
- Key Laboratory of Ecological Warning, Protection & Restoration for Bohai Sea, Ministry of Natural Resources, Qingdao, 266061, China.
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Zhang Q, Chen J, Wang W, Lin J, Guo J. Genome-wide investigation of the TGF-β superfamily in scallops. BMC Genomics 2024; 25:24. [PMID: 38166626 PMCID: PMC10763453 DOI: 10.1186/s12864-023-09942-w] [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: 08/01/2023] [Accepted: 12/26/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Transforming growth factor β (TGF-β) superfamily genes can regulate various processes, especially in embryogenesis, adult development, and homeostasis. To understand the evolution and divergence patterns of the TGF-β superfamily in scallops, genome-wide data from the Bay scallop (Argopecten irradians), the Zhikong scallop (Chlamys farreri) and the Yesso scallop (Mizuhopecten yessoensis) were systematically analysed using bioinformatics methods. RESULTS Twelve members of the TGF-β superfamily were identified for each scallop. The phylogenetic tree showed that these genes were grouped into 11 clusters, including BMPs, ADMP, NODAL, GDF, activin/inhibin and AMH. The number of exons and the conserved motif showed some differences between different clusters, while genes in the same cluster exhibited high similarity. Selective pressure analysis revealed that the TGF-β superfamily in scallops was evolutionarily conserved. The spatiotemporal expression profiles suggested that different TGF-β members have distinct functions. Several BMP-like and NODAL-like genes were highly expressed in early developmental stages, patterning the embryonic body plan. GDF8/11-like genes showed high expression in striated muscle and smooth muscle, suggesting that these genes may play a critical role in regulating muscle growth. Further analysis revealed a possible duplication of AMH, which played a key role in gonadal growth/maturation in scallops. In addition, this study found that several genes were involved in heat and hypoxia stress in scallops, providing new insights into the function of the TGF-β superfamily. CONCLUSION Characteristics of the TGF-β superfamily in scallops were identified, including sequence structure, phylogenetic relationships, and selection pressure. The expression profiles of these genes in different tissues, at different developmental stages and under different stresses were investigated. Generally, the current study lays a foundation for further study of their pleiotropic biological functions in scallops.
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Affiliation(s)
- Qian Zhang
- Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, China
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Bioaffiliationersity, Minjiang University, Fuzhou, 350108, China
| | - Jianming Chen
- Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, China.
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Bioaffiliationersity, Minjiang University, Fuzhou, 350108, China.
| | - Wei Wang
- Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, China.
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Bioaffiliationersity, Minjiang University, Fuzhou, 350108, China.
| | - Jingyu Lin
- Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Jiabao Guo
- Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, China
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Riaz Z, Hussain M, Parveen S, Sultana M, Saeed S, Ishaque U, Faiz Z, Tayyab M. In Silico Analysis: Genome-Wide Identification, Characterization and Evolutionary Adaptations of Bone Morphogenetic Protein (BMP) Gene Family in Homo sapiens. Mol Biotechnol 2023:10.1007/s12033-023-00944-3. [PMID: 37914865 DOI: 10.1007/s12033-023-00944-3] [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: 08/21/2023] [Accepted: 10/09/2023] [Indexed: 11/03/2023]
Abstract
We systematically analyzed BMP gene family in H. sapiens to elucidate genetic structure, phylogenetic relationships, adaptive evolution and tissue-specific expression pattern. Total of 13 BMPs genes were identified in the H. sapiens genome. Bone morphogenetic proteins (BMPs) are composed of a variable number of exons ranging from 2 to 21. They exhibit a molecular weight ranging from 31,081.81 to 82,899.61 Da. These proteins possess hydrophilic characteristics, display thermostability, and exhibit a pH range from acidic to basic. We identified four segmental and two tandem duplication events in BMP gene family of H. sapiens. All of the vertebrate species that were studied show the presence of BMPs 1, 2, 3, 4, 5, 6, 7, 8A, and 15, however only Homo sapiens demonstrated the presence of BMP9 and BMP11. The pathway and process enrichment analysis of BMPs genes showed that these were considerably enriched in positive regulation of pathway-restricted SMAD protein phosphorylation (92%) and cartilage development (77%) biological processes. These genes exhibited positive selection signals that were shown to be conserved across vertebrate lineages. The results showed that BMP2/3/5/6/8a/15 proteins underwent adaptive selection at many amino acid locations and increased positive selection was detected in TGF-β propeptide and TGF-β super family domains which were involved in dorso-ventral patterning, limb bud development. More over the expression pattern of BMP genes revealed that BMP1 and BMP5; BMP4 and BMP6 exhibited substantially identical expression patterns in all tissues while BMP10, BMP15, and BMP3 showed tissue-specific expression.
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Affiliation(s)
- Zainab Riaz
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan
| | - Muhammad Hussain
- Department of Veterinary and Animal Sciences, University of Veterinary and Animal Sciences, Lahore, Punjab, Pakistan
| | - Shakeela Parveen
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan.
- Department of Zoology, Wildlife and Fisheries, University of Agriculture, Faisalabad, Punjab, Pakistan.
| | - Mehwish Sultana
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan
| | - Saba Saeed
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan
- Institue of Zoology, University of the Punjab, Lahore, Punjab, Pakistan
| | - Urwah Ishaque
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan
| | - Zunaira Faiz
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan
| | - Muhammad Tayyab
- Department of Zoology, Government College University Faisalabad, Faisalabad, Punjab, Pakistan
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Wang Q, Cao T, Wang C. Genome-wide identification and expression analysis of Dmrt genes in bivalves. BMC Genomics 2023; 24:457. [PMID: 37582778 PMCID: PMC10428544 DOI: 10.1186/s12864-023-09536-6] [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: 03/22/2023] [Accepted: 07/27/2023] [Indexed: 08/17/2023] Open
Abstract
In recent years, some common themes in the development of sex-specific traits in different animal lineages have started to emerge since the discovery of the Dmrt (doublesex-mab3-related transcription factor gene) genes. Bivalves are characterized by a diversity of sexual systems, including simultaneous hermaphroditism, sequential hermaphroditism, and strict gonochorism. However, to date, no research has focused on the genome-wide characterization and analysis of Dmrt genes in bivalves. In this study, the identification and analysis of Dmrt genes in 15 bivalves were performed using bioinformatics methods. A total of 55 Dmrt genes were retrieved in the studied bivalve genomes. The number of Dmrt genes in different species ranged from 3 to 5. The phylogenetic tree showed that Dmrt genes in bivalves can be subdivided into 5 classes: the Dmrt2-like class, Dmrt3-like class, Dmrt4/5-like class, Dsx-like class, and scallop-specific Dmrt class. The Ka/Ks ratios suggested that all Dmrt classes underwent purifying selection pressure. Furthermore, the spatiotemporal expression of Dmrt genes in four bivalve species suggested that different Dmrt genes may have different functions, and scallop-specific Dmrt genes may play a key role in sex determination/differentiation. In general, this study provides a molecular basis for in-depth examination of the functions of Dmrt genes and phylogenomic analyses in bivalves.
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Affiliation(s)
- Quanchao Wang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- Key Laboratory of Ecological Warning, Protection & Restoration for Bohai Sea, Ministry of Natural Resources, Qingdao, 266061, China
| | - Tiangui Cao
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Chunde Wang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China.
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Wang Q, Cao T, Wang Y, Li X, Wang Y. Genome-wide identification and comparative analysis of Dmrt genes in echinoderms. Sci Rep 2023; 13:7664. [PMID: 37169947 PMCID: PMC10175285 DOI: 10.1038/s41598-023-34819-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 05/08/2023] [Indexed: 05/13/2023] Open
Abstract
The Dmrt (Doublesex-mab3-related transcription factor) gene family is a class of crucial transcription factors characterized by one or several conserved DM (Doublesex/Mab-3) domains. Dmrt family genes can participate in various physiological developmental processes, especially in sex determination/differentiation. Echinoderms are extremely important research objects in various fields, such as sex determination/differentiation and neuroscience. However, to date, the genome-wide characterization and analysis of Dmrt genes in echinoderms have not been investigated. In this study, the identification and analysis of Dmrt genes in 11 representative echinoderms were performed using bioinformatics methods. A total of 43 Dmrt genes have been found in the studied echinoderms, and the number of Dmrt genes in different species ranges from 2 to 5. The phylogenetic tree showed that all Dmrt genes from echinoderms can be subdivided into 5 classes, the Dmrt2-like class, Dmrt3-like class, Dmrt4/5-like class, Dsx-like class, and a novel Dmrt (starfish-specific) class. Furthermore, selective pressure assessment suggested that the Dmrt genes underwent purifying selection pressure. In general, this study provides a molecular basis for echinoderm Dmrt genes and may serve as a reference for in-depth phylogenomics.
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Affiliation(s)
- Quanchao Wang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- Key Laboratory of Ecological Warning, Protection and Restoration for Bohai Sea, Ministry of Natural Resources, Qingdao, 266061, China
| | - Tiangui Cao
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Yanxia Wang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Xiaojing Li
- Yantai Vocational College, Yantai, 264670, China
| | - Yue Wang
- Yantai Vocational College, Yantai, 264670, China.
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Lei L, Zhu J, Chen C, Wang Y, Wu C, Qi M, Wang Y, Liu X, Hong X, Yu L, Chen H, Wei C, Liu Y, Li W, Zhu X. Genome-wide identification, evolution and expression analysis of bone morphogenetic protein (BMP) gene family in chinese soft-shell turtle ( Pelodiscus sinensis). Front Genet 2023; 14:1109478. [PMID: 36816024 PMCID: PMC9928969 DOI: 10.3389/fgene.2023.1109478] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 01/19/2023] [Indexed: 02/04/2023] Open
Abstract
Introduction: Bone morphogenetic proteins (BMPs) play a crucial role in bone formation and differentiation. Recent RNA-Seq results suggest that BMPs may be involved in the sex differentiation of P. sinensis, yet more relevant studies about BMPs in P. sinensis are lacking. Methods: Herein, we identified BMP gene family members, analyzed the phylogeny, collinear relationship, scaffold localization, gene structures, protein structures, transcription factors and dimorphic expression by using bioinformatic methods based on genomic and transcriptomic data of P. sinensis. Meanwhile, qRT-PCR was used to verify the RNA-Seq results and initially explore the function of the BMPs in the sex differentiation of P. sinensis. Results: A total of 11 BMP genes were identified, 10 of which were localized to their respective genomic scaffolds. Phylogenetic analysis revealed that BMP genes were divided into eight subfamilies and shared similar motifs ("WII", "FPL", "TNHA", "CCVP", and "CGC") and domain (TGF-β superfamily). The results of the sexually dimorphic expression profile and qRT-PCR showed that Bmp2, Bmp3, Bmp15l, Bmp5, Bmp6 and Bmp8a were significantly upregulated in ovaries, while Bmp2lb, Bmp7, Bmp2bl and Bmp10 were remarkable upregulated in testes, suggesting that these genes may play a role in sex differentiation of P. sinensis. Discussion: Collectively, our comprehensive results enrich the basic date for studying the evolution and functions of BMP genes in P. sinensis.
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Affiliation(s)
- Luo Lei
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, Jiangsu, China
| | - Junxian Zhu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Chen Chen
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China
| | - Yongchang Wang
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China
| | - Congcong Wu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China
| | - Ming Qi
- Zhejiang Fisheries Technical Extension Center, Hangzhou, China
| | - Yakun Wang
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China
| | - Xiaoli Liu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China
| | - Xiaoyou Hong
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China
| | - Lingyun Yu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China
| | - Haigang Chen
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China
| | - Chengqing Wei
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China
| | - Yihui Liu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China
| | - Wei Li
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China,*Correspondence: Xinping Zhu, ; Wei Li,
| | - Xinping Zhu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, Jiangsu, China,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China,*Correspondence: Xinping Zhu, ; Wei Li,
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Wang D, Pan Z, Wang G, Ye B, Wang Q, Zuo Z, Zou J, Xie S. Gonadal Transcriptome Analysis and Sequence Characterization of Sex-Related Genes in Cranoglanis bouderius. Int J Mol Sci 2022; 23:ijms232415840. [PMID: 36555482 PMCID: PMC9779447 DOI: 10.3390/ijms232415840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/21/2022] [Accepted: 10/27/2022] [Indexed: 12/15/2022] Open
Abstract
In China, the Cranoglanis bouderius is classified as a national class II-protected animal. The development of C. bouderius populations has been affected by a variety of factors over the past few decades, with severe declines occurring. Considering the likelihood of continued population declines of the C. bouderius in the future, it is critical to investigate the currently unknown characteristics of gonadal differentiation and sex-related genes for C. bouderius conservation. In this study, the Illumina sequencing platform was used to sequence the gonadal transcriptome of the C. bouderius to identify the pathways and genes related to gonadal development and analyze the expression differences in the gonads. A total of 12,002 DEGs were identified, with 7220 being significantly expressed in the ovary and 4782 being significantly expressed in the testis. According to the functional enrichment results, the cell cycle, RNA transport, apoptosis, Wnt signaling pathway, p53 signaling pathway, and prolactin signaling pathway play important roles in sex development in the C. bouderius. Furthermore, the sequence characterization and evolutionary analysis revealed that AMH, DAX1, NANOS1, and AR of the C. bouderius are highly conserved. Specifically, the qRT-PCR results from various tissues showed significant differences in AMH, DAX1, NANOS1, and AR expression levels in the gonads of both sexes of C. bouderius. These analyses indicated that AMH, DAX1, NANOS1, and AR may play important roles in the differentiation and development of C. bouderius gonads. To our best knowledge, this study is the first to analyze the C. bouderius gonadal transcriptome and identify the structures of sex-related genes, laying the foundation for future research.
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Affiliation(s)
- Dongjie Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zhengkun Pan
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Guoxia Wang
- Key Laboratory of Animal Nutrition and Feed Science (South China) of Ministry of Agriculture, Guangzhou 510640, China
- Key Laboratory of Animal Breeding and Nutrition, Guangdong Public Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Bin Ye
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Qiujie Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zhiheng Zuo
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Jixing Zou
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (J.Z.); (S.X.); Tel.: +86-020-87571321 (J.Z.); +86-020-87571321 (S.X.)
| | - Shaolin Xie
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (J.Z.); (S.X.); Tel.: +86-020-87571321 (J.Z.); +86-020-87571321 (S.X.)
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Duan Y, Zhang W, Chen X, Wang M, Zhong L, Liu J, Bian W, Zhang S. Genome-wide identification and expression analysis of mitogen-activated protein kinase (MAPK) genes in response to salinity stress in channel catfish (Ictalurus punctatus). JOURNAL OF FISH BIOLOGY 2022; 101:972-984. [PMID: 35818162 DOI: 10.1111/jfb.15158] [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: 03/10/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
The mitogen-activated protein kinase (MAPK) gene family has been systematically described in several fish species, but less so in channel catfish (Ictalurus punctatus), which is an important global aquaculture species. In this study, 16 MAPK genes were identified in the channel catfish genome and classified into three subfamilies based on phylogenetic analysis, including six extracellular signal regulated kinase (ERK) genes, six p38-MAPK genes and four C-Jun N-terminal kinase (JNK) genes. All MAPK genes were distributed unevenly across 10 chromosomes, of which three (IpMAPK8, IpMAPK12 and IpMAPK14) underwent teleost-specific whole genome duplication during evolution. Gene expression profiles in channel catfish during salinity stress were analysed using transcriptome sequencing and qRT-PCR (quantitative reverse transcription PCR). Results from reads per kilobase million (RPKM) analysis showed IpMAPK13, IpMAPK14a and IpMAPK14b genes were differentially expressed when compared with other genes between treatment and control groups. Furthermore, three of these genes were validated by qRT-PCR, of which IpMAPK14a expression levels were significantly upregulated in treatment groups (high and low salinity) when compared with the control group, with the highest expression levels in the low salinity group (P < 0.05). Therefore, IpMAPK14a may have important response roles to salinity stress in channel catfish.
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Affiliation(s)
- Yongqiang Duan
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Wenping Zhang
- College of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang, China
| | - Xiaohui Chen
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Minghua Wang
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Liqiang Zhong
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Ju Liu
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Wenji Bian
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
- College of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Shiyong Zhang
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
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