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Wang J, Nie H. Genome-wide identification and expression analysis of Sox gene family in the Manila clam (Ruditapes philippinarum). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 50:101244. [PMID: 38749209 DOI: 10.1016/j.cbd.2024.101244] [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: 04/03/2024] [Revised: 04/30/2024] [Accepted: 05/07/2024] [Indexed: 05/27/2024]
Abstract
Sox transcription factors are vital in numerous fundamental biological processes. In this study, nine Sox gene family members were discovered in the Ruditapes philippinarum genome, classified into the SoxB1, SoxB2, SoxC, SoxD, SoxE, and SoxF groups, marking the first genome-wide identification of this gene family in R. philippinarum. Analyses of phylogeny, exon-intron structures, and domains bolster the support for their categorization and annotation. Furthermore, transcriptomic analyses across various developmental stages revealed that RpSox4, RpSox5, RpSox9, and RpSox11 were significantly expressed in the D-larval stage. Additionally, investigations into transcriptomes of clams with different shell colors indicated that most sox genes exhibited their highest expression levels in orange clams, followed by zebra, white zebra, and white clams, and the results of transcriptomes analysis in different tissues indicated that 8 Sox genes (except RpSox17) were highly expressed in the mantle tissue. Moreover, qPCR was used to detect the expression of Sox gene in R. philippinarum at different developmental periods, different shell colors and different tissues, and the results showed consistency with those of the transcriptomes. This study's findings lay the groundwork for additional exploration into the role of the Sox gene in melanin production in R. philippinarum shells.
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Affiliation(s)
- Jiadi Wang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China; Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian 116023, China
| | - Hongtao Nie
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China; Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian 116023, China.
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Sun Y, Wen H, Tian Y, Mao X, Li X, Li J, Hu Y, Liu Y, Li J, Li Y. HSP90 and HSP70 Families in Lateolabrax maculatus: Genome-Wide Identification, Molecular Characterization, and Expression Profiles in Response to Various Environmental Stressors. Front Physiol 2021; 12:784803. [PMID: 34880782 PMCID: PMC8646100 DOI: 10.3389/fphys.2021.784803] [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: 09/28/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
Heat shock proteins (HSPs) are a large class of highly conserved chaperons, which play important roles in response to elevated temperature and other environmental stressors. In the present study, 5 HSP90 genes and 17 HSP70 genes were systematically characterized in spotted seabass (Lateolabrax maculatus). The evolutionary footprint of HSP genes was revealed via the analysis of phylogeny, chromosome location, and gene copy numbers. In addition, the gene structure features and the putative distribution of heat shock elements (HSEs) and hypoxia response elements (HREs) in the promoter regions were analyzed. The protein-protein interaction (PPI) network analyses results indicated the potential transcriptional regulation between the heat shock factor 1 (HSF1) and HSPs and a wide range of interactions among HSPs. Furthermore, quantitative (q)PCR was performed to detect the expression profiles of HSP90 and HSP70 genes in gill, liver, and muscle tissues after heat stress, meanwhile, the expression patterns in gills under alkalinity and hypoxia stresses were determined by analyzing RNA-Seq datasets. Results showed that after heat stress, most of the examined HSP genes were significantly upregulated in a tissue-specific and time-dependent manners, and hsp90aa1.1, hsp90aa1.2, hsp70.1, and hsp70.2 were the most intense responsive genes in all three tissues. In response to alkalinity stress, 11 out of 13 significantly regulated HSP genes exhibited suppressed expression patterns. Alternatively, among the 12 hypoxia-responsive-expressed HSP genes, 7 genes showed induced expressions, while hsp90aa1.2, hsp70.1, and hsp70.2 had more significant upregulated changes after hypoxic challenge. Our findings provide the essential basis for further functional studies of HSP genes in response to abiotic stresses in spotted seabass.
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Affiliation(s)
- Yalong Sun
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
| | - Haishen Wen
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
| | - Yuan Tian
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
| | - Xuebin Mao
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
| | - Xiurong Li
- Quality and Safety Center of Agricultural and Livestock Products, Bayannaoer, China
| | - Junjie Li
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
| | - Yanbo Hu
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
| | - Yang Liu
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
| | - Jifang Li
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
| | - Yun Li
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
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