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Chen L, Huang Y, Pan QH, Wang MY, Liang JJ, Chen TS. The Chinese medaka (Oryzias sinensis) dmrt1 gene converts females to males in medaka (Oryzias latipes). Biochim Biophys Acta Gen Subj 2024; 1868:130664. [PMID: 38942152 DOI: 10.1016/j.bbagen.2024.130664] [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: 01/13/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 06/30/2024]
Abstract
BACKGROUND Chinese medaka (Oryzias sinensis) is widely distributed in freshwater rivers in China. Similar to the medaka (Oryzias latipes), Chinese medaka has the characteristics of small size, rapid reproductive cycle, and strong adaptability, which makes it suitable as a model organism for studies in basic biology and environmental toxicology. Chinese medaka exhibits distinct sexual dimorphism. However, due to the lack of complete genomic information, the regulation of sex determination and differentiation-related genes in Chinese medaka remains unclear. METHODS Chinese medaka dmrt1 (Osdmrt1) was cloned by PCR, and transgenic individuals of medaka [Tg(CMV:Osdmrt1)] overexpressing Osdmrt1 were generated to investigate the role of Osdmrt1 in sex determination. Western blot was used to validate the integration of the Osdmrt1 into the medaka genome. Tissue sectioning and HE staining were used to identify Tg(CMV:Osdmrt1) physiological gender and phenotype. qRT-PCR was used to analyze the expression of gonad-specific genes. RESULTS Osdmrt1 was cloned and identified, and it shared similar evolutionary relationships with medaka dmrt1. Tg(CMV:Osdmrt1) exhibited partial sex reversal from female to male in the F2 generation, with genetically female individuals developing testes and producing functional sperm. Additionally, the secondary sexual characteristics of the transgenic females also changed to males. CONCLUSION The Chinese medaka dmrt1 gene could convert females to males in medaka. GENERAL SIGNIFICANCE These results not only elucidate the function of Chinese medaka dmrt1, but also accumulate knowledge for studying the function of economically important fish genes in model fish by transgenic technology.
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Affiliation(s)
- Lei Chen
- State Key Laboratory of Mariculture Breeding; Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Fisheries College of Jimei University, 43 Yindou Road, Jimei District, Xiamen 361021, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College of Jimei University, Xiamen 361021, China
| | - Yan Huang
- State Key Laboratory of Mariculture Breeding; Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Fisheries College of Jimei University, 43 Yindou Road, Jimei District, Xiamen 361021, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College of Jimei University, Xiamen 361021, China
| | - Qi-Hua Pan
- State Key Laboratory of Mariculture Breeding; Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Fisheries College of Jimei University, 43 Yindou Road, Jimei District, Xiamen 361021, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College of Jimei University, Xiamen 361021, China
| | - Meng-Yang Wang
- State Key Laboratory of Mariculture Breeding; Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Fisheries College of Jimei University, 43 Yindou Road, Jimei District, Xiamen 361021, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College of Jimei University, Xiamen 361021, China
| | - Jing-Jie Liang
- State Key Laboratory of Mariculture Breeding; Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Fisheries College of Jimei University, 43 Yindou Road, Jimei District, Xiamen 361021, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College of Jimei University, Xiamen 361021, China
| | - Tian-Sheng Chen
- State Key Laboratory of Mariculture Breeding; Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Fisheries College of Jimei University, 43 Yindou Road, Jimei District, Xiamen 361021, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College of Jimei University, Xiamen 361021, China.
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Kong D, Zhao X, Pan Y, Song N. Gonadal transcriptome analysis of sex-biased gene and genome-wide investigation of dmrt gene family in Acanthogobius ommaturus. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 50:101204. [PMID: 38342067 DOI: 10.1016/j.cbd.2024.101204] [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: 11/09/2023] [Revised: 01/18/2024] [Accepted: 02/05/2024] [Indexed: 02/13/2024]
Abstract
Acanthogobius ommaturus is one of the largest goby fish, and widely distributed in the Northwestern Pacific as an annual benthic fish. This study aims to report the gonadal transcriptome of A. ommaturus and identify differentially expressed genes (DEGs) between sexes. A total of 5460 (27.94 %) DEGs were detected from genome, with 3301 (16.89 %) biased towards males and 2159 (11.05 %) towards females. Analysis of 76 known vertebrate sex-related genes revealed multiple key genes, including the male-biased genes dmrt1 (Doublesex and Mab-3 related transcription factor 1) and amh (Anti-Mullerian Hormone), and the female-biased genes foxl2 (Forkhead Box L2) and cyp19a1a (Cytochrome P450 Aromatase 19 Subfamily A1). Furthermore, a genome-wide gene family analysis focused on the most significantly differentially expressed male-biased gene, dmrt1, was conducted using the chromosomal-level genome. Six Aodmrt genes were identified and subjected to phylogenetic and protein interaction network analyses. To validate the expression pattern, quantitative real-time PCR (qRT-PCR) was performed and compared with gonadal transcriptome data. The results showed that only dmrt1 exhibited significant male-bias, while the expression levels and sex differences of other dmrt genes in the gonads were inconclusive. Interestingly, the other dmrt genes displayed higher expression levels in other tissues, suggesting currently unknown functions. In conclusion, this study provides valuable genetic information contributing to the understanding of the sex determination mechanism of A. ommaturus and bony fish.
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Affiliation(s)
- Delong Kong
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Xiang Zhao
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Yu Pan
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Na Song
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, China.
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Li F, Chen S, Zhang T, Pan L, Liu C, Bian L. Gonadal Transcriptome Sequencing Analysis Reveals the Candidate Sex-Related Genes and Signaling Pathways in the East Asian Common Octopus, Octopus sinensis. Genes (Basel) 2024; 15:682. [PMID: 38927618 PMCID: PMC11202624 DOI: 10.3390/genes15060682] [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: 04/11/2024] [Revised: 05/10/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
The East Asian common octopus (Octopus sinensis) is an economically important species among cephalopods. This species exhibits a strict dioecious and allogamous reproductive strategy, along with a phenotypic sexual dimorphism, where the third right arm differentiates into hectocotylus in males. However, our understanding of the molecular mechanisms that underlie sex determination and differentiation in this species remains limited. In the present study, we surveyed gene-expression profiles in the immature male and female gonads of O. sinensis based on the RNA-seq, and a total of 47.83 Gb of high-quality data were generated. Compared with the testis, we identified 8302 differentially expressed genes (DEGs) in the ovary, of which 4459 genes were up-regulated and 3843 genes were down-regulated. Based on the GO enrichment, many GO terms related to sex differentiation were identified, such as sex differentiation (GO: 0007548), sexual reproduction (GO: 0019953) and male sex differentiation (GO: 0046661). A KEGG classification analysis identified three conserved signaling pathways that related to sex differentiation, including the Wnt signaling pathway, TGF-β signaling pathway and Notch signaling pathway. Additionally, 21 sex-related DEGs were selected, of which 13 DEGs were male-biased, including Dmrt1, Foxn5, Foxj1, Sox30, etc., and 8 DEGs were female-biased, including Sox14, Nanos3, β-tubulin, Suh, etc. Ten DEGs were used to verify the expression patterns in the testis and ovary using the RT-qPCR method, and the results showed that the expression level shown by RT-qPCR was consistent with that from the RNA-seq, which confirmed the reliability of the transcriptome data. The results presented in this study will not only contribute to our understanding of sex-formation mechanisms in O. sinensis but also provide the foundational information for further investigating the molecular mechanisms that underline its gonadal development and facilitate the sustainable development of octopus artificial breeding.
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Affiliation(s)
- Fenghui Li
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (F.L.); (S.C.); (L.P.); (C.L.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| | - Siqing Chen
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (F.L.); (S.C.); (L.P.); (C.L.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| | - Tao Zhang
- Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China;
| | - Luying Pan
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (F.L.); (S.C.); (L.P.); (C.L.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| | - Changlin Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (F.L.); (S.C.); (L.P.); (C.L.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| | - Li Bian
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (F.L.); (S.C.); (L.P.); (C.L.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
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He Z, Xiao F, Yang D, Deng F, Ding W, He Z, Wang S, Chen Q, Wang H, Chen M, Gao K, Xiong J, Tang Z, Zhang M, Yan T. Protein expression patterns and metal metabolites in a protogynous hermaphrodite fish, the ricefield eel (Monopterus albus). BMC Genomics 2024; 25:500. [PMID: 38773374 PMCID: PMC11106920 DOI: 10.1186/s12864-024-10397-w] [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: 10/20/2023] [Accepted: 05/08/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND The ricefield eel Monopterus albus undergoes a natural sex change from female to male during its life cycle, and previous studies have shown the potential mechanisms of this transition at the transcriptional and protein levels. However, the changes in protein levels have not been fully explored, especially in the intersexual stage. RESULTS In the present study, the protein expression patterns in the gonadal tissues from five different periods, the ovary (OV), early intersexual stage gonad (IE), middle intersexual stage gonad (IM), late intersexual stage gonad (IL), and testis (TE), were determined by untargeted proteomics sequencing. A total of 5125 proteins and 394 differentially expressed proteins (DEPs) were detected in the gonadal tissues. Of the 394 DEPs, there were 136 between the OV and IE groups, 20 between the IM and IE groups, 179 between the IL and IM groups, and 59 between the TE and IL groups. Three candidate proteins, insulin-like growth factor 2 mRNA-binding protein 3 isoform X1 (Igf2bp3), triosephosphate isomerase (Tpi), and Cu-Zn superoxide dismutase isoform X1 [(Cu-Zn) Sod1], were validated by western blotting to verify the reliability of the data. Furthermore, metal metabolite-related proteins were enriched in the IL vs. IM groups and TE vs. IL groups, which had close relationships with sex change, including Cu2+-, Ca2+-, Zn2+- and Fe2+/Fe3+-related proteins. Analysis of the combined transcriptome data revealed consistent protein/mRNA expression trends for two metal metabolite-related proteins/genes [LOC109953912 and calcium Binding Protein 39 Like (cab39l)]. Notably, we detected significantly higher levels of Cu2+ during the sex change process, suggesting that Cu2+ is a male-related metal metabolite that may have an important function in male reproductive development. CONCLUSIONS In summary, we analyzed the protein profiles of ricefield eel gonadal tissues in five sexual stages (OV, IE, IM, IL, and TE) and verified the plausibility of the data. After preforming the functional enrichment of metal metabolite-related DEPs, we detected the contents of the metal metabolites Zn2+, Cu2+, Ca2+, and Fe2+/Fe3+ at these five stages and screened for (Cu-Zn) Sod1 and Mmp-9 as possible key proteins in the sex reversal process.
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Affiliation(s)
- Zhi He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
- Fish Resources and Environment in Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Feng Xiao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Deying Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
- Fish Resources and Environment in Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Faqiang Deng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wenxiang Ding
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhide He
- Fish Resources and Environment in Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Siqi Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiqi Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Haochen Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mingqiang Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Kuo Gao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jinxing Xiong
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ziting Tang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
- Fish Resources and Environment in Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mingwang Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
- Fish Resources and Environment in Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Taiming Yan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
- Fish Resources and Environment in Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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Liu X, Xu H, Peng M, Zhou C, Wei C, Hong X, Li W, Chen C, Ji L, Zhu X. Screening of temperature-responsive signalling molecules during sex differentiation in Asian yellow pond turtle (Mauremys mutica). BMC Genomics 2024; 25:383. [PMID: 38637759 PMCID: PMC11025153 DOI: 10.1186/s12864-024-10275-5] [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: 01/02/2024] [Accepted: 04/01/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND The Asian yellow pond turtle (Mauremys mutica) is an important commercial freshwater aquaculture species in China. This species is a highly sexually dimorphic species, with males growing at a faster rate than females and exhibits temperature-dependent sex determination (TSD), in which the incubation temperature during embryonic development determines the sexual fate. However, the mechanisms of the sex determination or sex differentiation in the Asian yellow pond turtle are remain a mystery. RESULTS Temperature-specific gonadal transcriptomics of the Asian yellow pond turtle were performed during the thermosensitive period (stage 15) using RNA-seq technology to identify candidate genes that initiate gonadal differentiation. We uncovered candidates that were the first to respond to temperature. These candidates were sexually dimorphic in expression, reflecting differences in gonadal (Cirbp, Runx1) and germline differentiation (Vasa, Nanos1, Piwil2), gametogenesis (Hmgb3, Zar1, Ovoinhibitor-like, Kif4), steroid hormone biosynthesis (Hsd17b5, Hsd17b6), heat shock (Dnajb6, Hsp90b1, Hsp90aa1) and transient receptor potential channel genes (Trpm1, Trpm4, Trpm6, Trpv1). CONCLUSIONS Our work will provide important genetic information to elucidate the mechanisms of sex control in the Asian yellow pond turtles, and will contribute important genetic resources for further studies of temperature-dependent sex determination in turtles.
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Affiliation(s)
- 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, 510380, Guangzhou, China
- College of Life Science and Fisheries, Shanghai Ocean University, 201306, Shanghai, China
| | - Haoyang Xu
- 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, 510380, Guangzhou, China
- College of Life Science and Fisheries, Shanghai Ocean University, 201306, Shanghai, China
| | - Mingwei Peng
- 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, 510380, Guangzhou, China
- School of Fishery, Zhejiang Ocean University, 316000, Zhoushan, China
| | - Chenyao Zhou
- 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, 510380, Guangzhou, China
- School of Fishery, Zhejiang Ocean University, 316000, Zhoushan, 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, 510380, Guangzhou, 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, 510380, Guangzhou, 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, 510380, Guangzhou, China
- College of Life Science and Fisheries, Shanghai Ocean University, 201306, 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, 510380, Guangzhou, China
| | - Liqin Ji
- 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, 510380, Guangzhou, China
| | - 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, 510380, Guangzhou, China.
- College of Life Science and Fisheries, Shanghai Ocean University, 201306, Shanghai, China.
- School of Fishery, Zhejiang Ocean University, 316000, Zhoushan, China.
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Zhao C, Bian C, Mu X, Zhang X, Shi Q. Gonadal transcriptome sequencing reveals sexual dimorphism in expression profiling of sex-related genes in Asian arowana ( Scleropages formosus). Front Genet 2024; 15:1381832. [PMID: 38666292 PMCID: PMC11043485 DOI: 10.3389/fgene.2024.1381832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
Asia arowana (Scleropages formosus) is an ornamental fish with high economic value, while its sex determination mechanism is still poorly understood. By far, no morphological evidence or molecular marker has been developed for effective distinguishment of genders, which poses a critical challenge to our captive breeding efforts. In this study, we sequenced gonadal transcriptomes of adult Asian arowanas and revealed differential expression profiling of sex-related genes. Based on the comparative transcriptomics analysis of testes (n = 3) and ovaries (n = 3), we identified a total of 8,872 differentially expressed genes (DEGs) and 18,490 differentially expressed transposable elements (TEs) between male and female individuals. Interestingly, the expression of TEs usually has been more significantly testis-biased than related coding genes. As expected, several genes related to females (such as foxl2 and cyp19a1a) are significantly transcribed in the ovary, and some genes related to male gonad development (such as dmrt1, gsdf and amh) are highly expressed in the testis. This sexual dimorphism is valuable for ascertaining the differential expression patterns of sex-related genes and enriching the genetic resources of this economically important species. These valuable genetic materials thereby provide instructive references for gender identification and one-to-one breeding practices so as to expand fish numbers for a rapid elevation of economic value.
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Affiliation(s)
- Chenxi Zhao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, China
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, China
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Xidong Mu
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Xinhui Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, China
| | - Qiong Shi
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, China
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
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Zhu J, Wang Y, Chen C, Ji L, Hong X, Liu X, Chen H, Wei C, Zhu X, Li W. Identification of Sex-Specific Markers and Candidate Genes Using WGS Sequencing Reveals a ZW-Type Sex-Determination System in the Chinese Soft-Shell Turtle ( Pelodiscus sinensis). Int J Mol Sci 2024; 25:819. [PMID: 38255893 PMCID: PMC10815769 DOI: 10.3390/ijms25020819] [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: 11/24/2023] [Revised: 01/02/2024] [Accepted: 01/07/2024] [Indexed: 01/24/2024] Open
Abstract
Male and female Chinese soft-shelled turtles (Pelodiscus sinensis) have sex-dimorphic growth patterns, and males have higher commercial value because of their larger size and thicker calipash. Thus, developing sex-specific markers is beneficial to studies on all-male breeding in P. sinensis. Here, we developed an accurate and efficient workflow for the screening of sex-specific sequences with ZW or XY sex determination systems. Based on this workflow, female and male P. sinensis reference genomes of 2.23 Gb and 2.26 Gb were obtained using de novo assembly. After aligning and filtering, 4.01 Mb female-specific sequences were finally identified. Subsequently, the seven developed sex-specific primer pairs were 100% accurate in preliminary, population, and embryonic validation. The presence and absence of bands for the primers of P44, P45, P66, P67, P68, and P69, as well as two and one bands for the PB1 primer, indicate that the embryos are genetically female and male, respectively. NR and functional annotations identified several sex-determining candidate genes and related pathways, including Ran, Eif4et, and Crkl genes, and the insulin signaling pathway and the cAMP signaling pathway, respectively. Collectively, our results reveal that a ZW-type sex-determination system is present in P. sinensis and provide novel insights for the screening of sex-specific markers, sex-control breeding, and the studies of the sex determination mechanism of P. sinensis.
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Affiliation(s)
- Junxian Zhu
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China;
- 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 510380, China; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - 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 510380, China; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - 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 510380, China; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - Liqin Ji
- 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 510380, China; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - 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 510380, China; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - 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 510380, China; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - 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 510380, China; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - 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 510380, China; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - Xinping Zhu
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China;
- 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 510380, China; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - Wei Li
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China;
- 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 510380, China; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
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8
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Liu S, Han C, Huang J, Li M, Yang J, Li G, Lin H, Li S, Zhang Y. Genome-wide identification, evolution and expression of TGF-β signaling pathway members in mandarin fish (Siniperca chuatsi). Int J Biol Macromol 2023; 253:126949. [PMID: 37722635 DOI: 10.1016/j.ijbiomac.2023.126949] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 09/01/2023] [Accepted: 09/13/2023] [Indexed: 09/20/2023]
Abstract
Members of the transforming growth factor β (TGF-β) signaling pathway regulate diverse cellular biological processes in embryonic and tissue development. We took mandarin fish (Siniperca chuatsi) as the research object to identify all members of the TGF-β signaling pathway, measure their expression pattern in the key period post hatching, and further explore their possible role in the process of sex regulation. Herein, we identified eighty-three TGF-β signaling pathway members and located them on chromosomes based on the genome of mandarin fish. TGF-β signaling pathway members were highly conserved since each TGF-β subfamily clustered with orthologs from other species. Transcriptome analysis, qRT-PCR and in situ hybridization demonstrated that most mandarin fish TGF-β signaling pathway members presented stage-specific and/or sex-dimorphic expression during gonadal development, and different members of the TGF-β signaling pathway participated in different stages of gonadal development. Taken together, our results provide new insight into the role of TGF-β signaling pathway members in the sex regulation of mandarin fish.
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Affiliation(s)
- Shiyan Liu
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Guangzhou 510275, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266373, China
| | - Chong Han
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Guangzhou 510275, China; School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Jingjun Huang
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Guangzhou 510275, China
| | - Meihui Li
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Guangzhou 510275, China
| | - Jiayu Yang
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Guangzhou 510275, China
| | - Guifeng Li
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Guangzhou 510275, China
| | - Haoran Lin
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Guangzhou 510275, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266373, China
| | - Shuisheng Li
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Guangzhou 510275, China.
| | - Yong Zhang
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Guangzhou 510275, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266373, China.
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9
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Liu S, Lian Y, Song Y, Chen Q, Huang J. De Novo Assembly, Characterization and Comparative Transcriptome Analysis of the Gonads of Jade Perch ( Scortum barcoo). Animals (Basel) 2023; 13:2254. [PMID: 37508032 PMCID: PMC10376888 DOI: 10.3390/ani13142254] [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: 04/11/2023] [Revised: 06/24/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
Due to the high meat yield and rich nutritional content, jade perch (Scortum barcoo) has become an important commercial aquaculture species in China. Jade perch has a slow growth rate, taking 3-4 years to reach sexual maturity, and has almost no difference in body size between males and females. However, the study of its gonad development and reproduction regulation is still blank, which limited the yield increase. Herein, the gonad transcriptomes of juvenile males and females of S. barcoo were identified for the first time. A total of 107,060 unigenes were successfully annotated. By comparing male and female gonad transcriptomes, a total of 23,849 differentially expressed genes (DEGs) were identified, of which 9517 were downregulated, and 14,332 were upregulated in the testis. In addition, a large number of DEGs involved in sex differentiation, gonadal development and differentiation and gametogenesis were identified, and the differential expression patterns of some genes were further verified using real-time fluorescence quantitative PCR. The results of this study will provide a valuable resource for further studies on sex determination and gonadal development of S. barcoo.
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Affiliation(s)
- Shiyan Liu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yingying Lian
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yikun Song
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Qinghua Chen
- South China Institute of Environmental Science, MEE, Guangzhou 510610, China
| | - Jianrong Huang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
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10
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Lu M, Zhang QC, Zhu ZY, Peng F, Li Z, Wang Y, Li XY, Wang ZW, Zhang XJ, Zhou L, Gui JF. An efficient approach to synthesize sterile allopolyploids through the combined reproduction mode of ameiotic oogenesis and sperm-egg fusion in the polyploid Carassius complex. Sci Bull (Beijing) 2023; 68:1038-1050. [PMID: 37173259 DOI: 10.1016/j.scib.2023.04.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 04/05/2023] [Accepted: 04/10/2023] [Indexed: 05/15/2023]
Abstract
The association between polyploidy and reproduction transition, which is an intriguing issue in evolutionary genetics, can also be exploited as an approach for genetic improvement in agriculture. Recently, we generated novel amphitriploids (NA3n) by integrating the genomes of the gynogenetic Carassius gibelio and sexual C. auratus, and found gynogenesis was recovered in most NA3n females (NA3n♀I). Here, we discovered a unique reproduction mode, termed ameio-fusiongenesis, which combines the abilities of both ameiotic oogenesis and sperm-egg fusion, in a few NA3n females (NA3n♀II). These females inherited ameiotic oogenesis to produce unreduced eggs from gynogenetic C. gibelio and sperm-egg fusion from sexual C. auratus. Subsequently, we utilized this unique reproduction mode to generate a group of synthetic alloheptaploids by crossing NA3n♀II with Megalobrama amblycephala. They contained all chromosomes of maternal NA3n♀II and a chromosomal set of paternal M. amblycephala. Intergenomic chromosome translocations between NA3n♀II and M. amblycephala were also observed in a few somatic cells. Primary oocytes of the alloheptaploid underwent severe apoptosis owing to incomplete double-strand break repair at prophase I. Although spermatocytes displayed similar chromosome behavior at prophase I, they underwent apoptosis due to chromosome separation failure at metaphase I. Therefore, the alloheptaploid females and males were all sterile. Finally, we established a sustainable clone for the large-scale production of NA3n♀II and developed an efficient approach to synthesize diverse allopolyploids containing genomes of different cyprinid species. These findings not only broaden our understanding of reproduction transition but also offer a practical strategy for polyploidy breeding and heterosis fixing.
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Affiliation(s)
- Meng Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qin-Can Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zi-Yu Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Peng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhong-Wei Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Molecular cloning and characterization of Sirt1 and its role in the follicle of juvenile Chinese soft-shelled turtle (Pelodiscus sinensis). Gene 2023; 860:147211. [PMID: 36708847 DOI: 10.1016/j.gene.2023.147211] [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: 09/29/2022] [Revised: 12/26/2022] [Accepted: 01/13/2023] [Indexed: 01/27/2023]
Abstract
Sirt1 is a member of the Sirtuins family that regulates ovarian senescence, follicular development, and oocyte maturation in vertebrates. To understand its role in the ovary of Pelodiscus sinensis, we cloned the full-length cDNA of Ps-Sirt1 and characterized its potential function by intraperitoneally injecting agonist (resveratrol) and antagonist (EX527) in the female juvenile turtle. The full-length cDNA of Ps-Sirt1 was 2106 bp, comprising 203 bp 5'UTR, a 226 bp 3'UTR, and a 1677 bp ORF encoding 558 amino acids. The calculated molecular weight of predicted protein was 63 kDa, and the isoelectric point was 4.65. The predicted protein comprised a conserved Sir2 domain. Amino acid sequence alignment and phylogenetic analyses showed that Ps-Sirt1 was most closely related to turtles, and distantly related to fish. Expression pattern analysis showed Ps-Sirt1 was highest expressed in ovary, followed by testis, liver, heart, and brain. In the ovarian differentiation processes, Sirt1 showed significantly higher expression at embryonic stage 15 and 21. In the testis differentiation process, Sirt1 expression was downregulated at embryonic stages 15-19. Activated and inactivated Sirt1 decreased the number of primordial follicles in juvenile turtles. Bcl2, Bax, mTOR, and rpS6 expressions were up-regulated, whereas GnRH, Fshb, p50, and p65 were down-regulated after agonist treatment. The inaction of Sirt1 with antagonist up-regulated GnRH, Fshb, p65, p53, Foxo3a, Bcl2, Bax, mTOR, and rpS6, but down-regulated p50. In summary, Sirt1 might be involved in the ovarian follicle development of P. sinensis.
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12
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Wei WY, Gong Y, Guo XF, Liu M, Zhou YL, Li Z, Zhou L, Wang ZW, Gui JF. Gonadal transcriptomes reveal sex-biased expression genes associated with sex determination and differentiation in red-tail catfish (Hemibagrus wyckioides). BMC Genomics 2023; 24:183. [PMID: 37024792 PMCID: PMC10077648 DOI: 10.1186/s12864-023-09264-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/21/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND Red-tail catfish (Hemibagrus wyckioides) is an important commercially farmed catfish in southern China. Males of red-tail catfish grow faster than females, suggesting that all-male catfish will produce more significant economic benefits in aquaculture practice. However, little research has been reported on sex determination and gonadal development in red-tail catfish. RESULTS In this study, we performed the first transcriptomic analysis of male and female gonads at four developmental stages at 10, 18, 30, and 48 days post hatching (dph) using RNA-seq technology. A total of 23,588 genes were screened in 24 sequenced samples, of which 28, 213, 636, and 1381 differentially expressed genes (DEGs) were detected at four developmental stages, respectively. Seven candidate genes of sex determination and differentiation were further identified. Real-time quantitative PCR (RT-qPCR) further confirmed that anti-Mullerian hormone (amh), growth differentiation factor 6a (gdf6a), testis-specific gene antigen 10 (tsga10), and cytochrome P450 family 17 subfamily A (cyp17a) were highly expressed mainly in the male, while cytochrome P450 family 19 subfamily A polypeptide 1b (cyp19a1b), forkhead box L2 (foxl2), and hydroxysteroid 17-beta dehydrogenase 1 (hsd17b1) were highly expressed in the female. The KEGG pathway enrichment data showed that these identified DEGs were mainly involved in steroid hormone biosynthesis and TGF-β signaling pathways. CONCLUSIONS Based on RNA-seq data of gonads at the early developmental stages, seven DEGs shared by the four developmental stages were identified, among which amh and gdf6a may be the male-biased expression genes, while foxl2, cyp19a1b and hsd17b1 may be the female-biased expression genes in red-tail catfish. Our study will provide crucial genetic information for the research on sex control in red-tail catfish, as well as for exploring the evolutionary processes of sex determination mechanisms in fish.
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Affiliation(s)
- Wen-Yu Wei
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yi Gong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin-Fen Guo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Min Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu-Lin Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhong-Wei Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Identification of sex-specific splicing via comparative transcriptome analysis of gonads from sea cucumber Apostichopus japonicus. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 45:101031. [PMID: 36371882 DOI: 10.1016/j.cbd.2022.101031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/31/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
Alternative splicing (AS) is an essential post-transcriptional regulation mechanism for sex differentiation and gonadal development, which has rarely been reported in marine invertebrates. Sea cucumber (Apostichopus japonicus) is an economically important marine benthic echinoderm with a potential XX/XY sex determination mechanism, whose molecular mechanism in the gonadal differentiation has not been clearly understood. In this study, we analyzed available RNA-seq datasets of male and female gonads to explore if AS mechanism exerts an essential function in sex differentiation and gonadal development of A. japonicus. In our results, a total of 20,338 AS events from 7219 alternatively spliced genes, and 189 sexually differential alternative splicing (DAS) events from 156 genes were identified in gonadal transcriptome of sea cucumber. Gene Ontology analysis indicated that these DAS genes were significantly enriched in spermatogenesis-related GO terms. Maximal Clique Centrality (MCC) was then applied for protein-protein interaction (PPI) analysis to search for protein interactions and hub DAS gene. Among all DAS genes, we identified 10 DAS genes closely related to spermatogenesis and (or) sperm motility and a hub gene dnah1. Thus, this study revealed that alternative isoforms were generated from certain genes in female and male gonads through alternative splicing, which may provide direct evidence that alternative splicing mechanisms participate in female and male gonads. These results suggested a novel perspective for explaining the molecular mechanisms underlying gonadal differentiation between male and female sea cucumbers.
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14
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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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Identification and Characterization of Sex-Biased miRNAs in the Golden Pompano ( Trachinotus blochii). Animals (Basel) 2022; 12:ani12233342. [PMID: 36496865 PMCID: PMC9739008 DOI: 10.3390/ani12233342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/25/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
The golden pompano (Trachinotus blochii) is a marine fish of considerable commercial importance in China. It shows notable sexual size dimorphism; the growth rate of females is faster than that of males. Therefore, sex-biased research is of great importance in T. blochii breeding. However, there have been few studies on sex differentiation and mechanisms underlying sex determination in T. blochii. MicroRNAs (miRNAs) play crucial roles in sex differentiation and determination in animals. However, limited miRNA data are available on fish. In this study, two small RNA libraries prepared from the gonads of T. blochii were constructed and sequenced. The RNA-seq analysis yielded 1366 known and 69 novel miRNAs with 289 significantly differentially expressed miRNAs (p < 0.05). Gene ontology (GO) analysis confirmed that the TFIIA transcription factor complex (GO: 0005672) was the most significantly enriched GO term. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the differentially expressed miRNAs and target genes were mainly related to sex determination and gonadal developmental signaling pathways, specifically the Wnt signaling pathway, MAPK signaling pathway, and steroid biosynthetic pathway. MiRNA-mRNA co-expression network analysis strongly suggested a role for sex-biased miRNAs in sex determination/differentiation and gonadal development. For example, gata4, foxo3, wt1, and sf1 genes were found to be regulated by bta-miR-2898; esr2 and foxo3 by novel_176, and ar by oar-let-7b. Quantitative real-time polymerase chain reaction analysis of selected mRNAs and miRNAs validated the integrated analysis. This study established a set of sex-biased miRNAs that are potential regulatory factors in gonadal development in T. blochii. These results provide new insight into the function of miRNAs in sex differentiation and determination in T. blochii and highlight some key miRNAs for future studies.
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Yu P, Wang Y, Li Z, Jin H, Li LL, Han X, Wang ZW, Yang XL, Li XY, Zhang XJ, Zhou L, Gui JF. Causal gene identification and desirable trait recreation in goldfish. SCIENCE CHINA LIFE SCIENCES 2022; 65:2341-2353. [DOI: 10.1007/s11427-022-2194-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/11/2022] [Indexed: 11/16/2022]
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17
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Gong G, Xiong Y, Xiao S, Li XY, Huang P, Liao Q, Han Q, Lin Q, Dan C, Zhou L, Ren F, Zhou Q, Gui JF, Mei J. Origin and chromatin remodeling of young X/Y sex chromosomes in catfish with sexual plasticity. Natl Sci Rev 2022; 10:nwac239. [PMID: 36846302 PMCID: PMC9945428 DOI: 10.1093/nsr/nwac239] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 08/22/2022] [Accepted: 10/21/2022] [Indexed: 11/15/2022] Open
Abstract
Assembly of a complete Y chromosome is a significant challenge in animals with an XX/XY sex-determination system. Recently, we created YY-supermale yellow catfish by crossing XY males with sex-reversed XY females, providing a valuable model for Y-chromosome assembly and evolution. Here, we assembled highly homomorphic Y and X chromosomes by sequencing genomes of the YY supermale and XX female in yellow catfish, revealing their nucleotide divergences with only less than 1% and with the same gene compositions. The sex-determining region (SDR) was identified to locate within a physical distance of 0.3 Mb by FST scanning. Strikingly, the incipient sex chromosomes were revealed to originate via autosome-autosome fusion and were characterized by a highly rearranged region with an SDR downstream of the fusion site. We found that the Y chromosome was at a very early stage of differentiation, as no clear evidence of evolutionary strata and classical structure features of recombination suppression for a rather late stage of Y-chromosome evolution were observed. Significantly, a number of sex-antagonistic mutations and the accumulation of repetitive elements were discovered in the SDR, which might be the main driver of the initial establishment of recombination suppression between young X and Y chromosomes. Moreover, distinct three-dimensional chromatin organizations of the Y and X chromosomes were identified in the YY supermales and XX females, as the X chromosome exhibited denser chromatin structure than the Y chromosome, while they respectively have significantly spatial interactions with female- and male-related genes compared with other autosomes. The chromatin configuration of the sex chromosomes as well as the nucleus spatial organization of the XX neomale were remodeled after sex reversal and similar to those in YY supermales, and a male-specific loop containing the SDR was found in the open chromatin region. Our results elucidate the origin of young sex chromosomes and the chromatin remodeling configuration in the catfish sexual plasticity.
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Affiliation(s)
- Gaorui Gong
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Xiong
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Shijun Xiao
- Jiaxing Key Laboratory for New Germplasm Breeding of Economic Mycology, Jiaxing 314000, China
| | - Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Peipei Huang
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China,School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Qian Liao
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingqing Han
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaohong Lin
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China,State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Cheng Dan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Fan Ren
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | | | - Jie Mei
- Corresponding author. E-mail:
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18
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Wei W, He J, Yaqoob MA, Gui L, Ren J, Li J, Li M. Integrated mRNA and miRNA Expression Profile Analysis of Female and Male Gonads in Acrossocheilus fasciatus. BIOLOGY 2022; 11:1296. [PMID: 36138775 PMCID: PMC9495813 DOI: 10.3390/biology11091296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/18/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
MicroRNAs (miRNAs) are regarded as key regulators in gonadal development and sex determination in diverse organisms. However, the functions of miRNAs in gonads of Acrossocheilus fasciatus, an economically important freshwater species in the south of China, are still unclear. Here, high-throughput sequencing was performed to investigate the mRNA and miRNAs on gonads of A. fasciatus. In total, 49,447 unigenes were obtained, including 11,635 differentially expressed genes (DEGs), among which 4147 upregulated genes and 7488 downregulated genes in the testis compared to the ovary, while 300 (237 known, and 63 novel) miRNAs with 36 differentially expressed miRNAs (DEMs) were identified, from which 17 upregulated and 19 downregulated DEMs. GO and KEGG enrichment analysis were performed to analyze the potential biological functions of DEGs and DEMs. Using qRT-PCR, 9 sex-related genes and 9 miRNAs were selected to verify the sequencing data. By dual-luciferase reporter assay, miR-22a-5p and miR-22b-5p interaction with piwil1, and miR-10d-5p interaction with piwil2 were identified. These findings could provide a reference for miRNA-regulated sex control of A. fasciatus and may reveal new insights into aquaculture and breeding concepts.
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Affiliation(s)
- Wenbo Wei
- Key Laboratory of Integrated Rice-Fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
| | - Jiamei He
- Key Laboratory of Integrated Rice-Fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
| | - Muhammad Amjad Yaqoob
- Key Laboratory of Integrated Rice-Fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
| | - Lang Gui
- Key Laboratory of Integrated Rice-Fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
| | - Jianfeng Ren
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
| | - Mingyou Li
- Key Laboratory of Integrated Rice-Fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
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Knytl M, Forsythe A, Kalous L. A Fish of Multiple Faces, Which Show Us Enigmatic and Incredible Phenomena in Nature: Biology and Cytogenetics of the Genus Carassius. Int J Mol Sci 2022; 23:ijms23158095. [PMID: 35897665 PMCID: PMC9330404 DOI: 10.3390/ijms23158095] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 11/16/2022] Open
Abstract
Sexual vs. asexual reproduction—unisexual vs. bisexual populations—diploid vs. polyploid biotypes—genetic vs. environmental sex determination: all these natural phenomena are associated with the genus of teleost fish, Carassius. This review places emphasis on two Carassius entities with completely different biological characteristics: one globally widespread and invasive Carassius gibelio, and the other C. carassius with a decreasing trend of natural occurrence. Comprehensive biological and cytogenetic knowledge of both entities, including the physical interactions between them, can help to balance the advantages of highly invasive and disadvantages of threatened species. For example, the benefits of a wide-ranged colonization can lead to the extinction of native species or be compensated by parasitic enemies and lead to equilibrium. This review emphasizes the comprehensive biology and cytogenetic knowledge and the importance of the Carassius genus as one of the most useful experimental vertebrate models for evolutionary biology and genetics. Secondly, the review points out that effective molecular cytogenetics should be used for the identification of various species, ploidy levels, and hybrids. The proposed investigation of these hallmark characteristics in Carassius may be applied in conservation efforts to sustain threatened populations in their native ranges. Furthermore, the review focuses on the consequences of the co-occurrence of native and non-native species and outlines future perspectives of Carassius research.
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Affiliation(s)
- Martin Knytl
- Department of Cell Biology, Faculty of Science, Charles University, 12843 Prague, Czech Republic
- Correspondence:
| | - Adrian Forsythe
- Department of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, 75236 Uppsala, Sweden;
| | - Lukáš Kalous
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 16521 Prague, Czech Republic;
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20
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Liu F, Xu H, Ni W, Wang Y, Hong X, Li W, Yu L, Chen C, Wei C, Liu X, Zhu X. Temporal variation in DNA methylation during gonadal development in a reptile with temperature-dependent sex determination. Biol Reprod 2022; 107:1217-1227. [PMID: 35835578 DOI: 10.1093/biolre/ioac142] [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: 01/12/2022] [Revised: 05/04/2022] [Accepted: 07/05/2022] [Indexed: 11/14/2022] Open
Abstract
DNA methylation plays a significant role in transducing external environmental signals to a cellular response in reptiles; however, whether the methylation patterns are conserved across species remains unclear. Here, we examined the genome-wide DNA methylation differentiation between male and female hatchling gonads of the temperature-dependent sex determination (TSD) Mauremys mutica (M. mutica) using methylation-dependent restriction-site associated DNA sequencing (MethylRAD-seq) to test differentially methylated genes underlying sexual development. Several categories, including heat shock genes (HSP90A, HSP30C), histone- (KDM8) and ubiquitin-related genes (TRIM39), kinases (WNK3) and gonad differentiation or gonadal development related genes (HSD17B8, HSD17B12), were identified as candidates for future study. Additionally, we identified several regulatory pathways potentially mediating TSD thermosensitivity such as the GnRH signaling pathway and calcium signaling pathway. These findings provide evidence that sexually dimorphic DNA methylation may be associated with sex determination or sex differentiation in TSD M. mutica.
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Affiliation(s)
- Fang Liu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 51038
| | - Haoyang Xu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 51038.,College of Life Science and Fisheries, Shanghai Ocean University, Shanghai, China, 201306
| | - Wei Ni
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 51038.,College of Life Science and Fisheries, Shanghai Ocean University, Shanghai, China, 201306
| | - Yakun Wang
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 51038
| | - Xiaoyou Hong
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 51038
| | - Wei Li
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 51038
| | - Lingyun Yu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 51038
| | - Chen Chen
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 51038
| | - Chengqing Wei
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 51038
| | - Xiaoli Liu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 51038
| | - Xinping Zhu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 51038.,College of Life Science and Fisheries, Shanghai Ocean University, Shanghai, China, 201306
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21
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Two duplicated gsdf homeologs cooperatively regulate male differentiation by inhibiting cyp19a1a transcription in a hexaploid fish. PLoS Genet 2022; 18:e1010288. [PMID: 35767574 PMCID: PMC9275722 DOI: 10.1371/journal.pgen.1010288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/12/2022] [Accepted: 06/08/2022] [Indexed: 01/10/2023] Open
Abstract
Although evolutionary fates and expression patterns of duplicated genes have been extensively investigated, how duplicated genes co-regulate a biological process in polyploids remains largely unknown. Here, we identified two gsdf (gonadal somatic cell-derived factor) homeologous genes (gsdf-A and gsdf-B) in hexaploid gibel carp (Carassius gibelio), wherein each homeolog contained three highly conserved alleles. Interestingly, gsdf-A and gsdf-B transcription were mainly activated by dmrt1-A (dsx- and mab-3-related transcription factor 1) and dmrt1-B, respectively. Loss of either gsdf-A or gsdf-B alone resulted in partial male-to-female sex reversal and loss of both caused complete sex reversal, which could be rescued by a nonsteroidal aromatase inhibitor. Compensatory expression of gsdf-A and gsdf-B was observed in gsdf-B and gsdf-A mutants, respectively. Subsequently, we determined that in tissue culture cells, Gsdf-A and Gsdf-B both interacted with Ncoa5 (nuclear receptor coactivator 5) and blocked Ncoa5 interaction with Rora (retinoic acid-related orphan receptor-alpha) to repress Rora/Ncoa5-induced activation of cyp19a1a (cytochrome P450, family 19, subfamily A, polypeptide 1a). These findings illustrate that Gsdf-A and Gsdf-B can regulate male differentiation by inhibiting cyp19a1a transcription in hexaploid gibel carp and also reveal that Gsdf-A and Gsdf-B can interact with Ncoa5 to suppress cyp19a1a transcription in vitro. This study provides a typical case of cooperative mechanism of duplicated genes in polyploids and also sheds light on the conserved evolution of sex differentiation.
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22
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Zhu C, Liu H, Pan Z, Cheng L, Sun Y, Wang H, Chang G, Wu N, Ding H, Zhao H, Zhang L, Yu X. Insights into chromosomal evolution and sex determination of Pseudobagrus ussuriensis (Bagridae, Siluriformes) based on a chromosome-level genome. DNA Res 2022; 29:6647841. [PMID: 35861402 PMCID: PMC9358014 DOI: 10.1093/dnares/dsac028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/20/2022] [Indexed: 12/01/2022] Open
Abstract
Pseudobagrus ussuriensis is an aquaculture catfish with significant sexual dimorphism. In this study, a chromosome-level genome with a size of 741.97 Mb was assembled for female P. ussuriensis. A total of 26 chromosome-level contigs covering 97.34% of the whole-genome assembly were obtained with an N50 of 28.53 Mb and an L50 of 11. A total of 24,075 protein-coding genes were identified, with 91.54% (22,039) genes being functionally annotated. Based on the genome assembly, four chromosome evolution clusters of catfishes were identified and the formation process of P. ussuriensis chromosomes was predicted. A total of 55 sex-related quantitative trait loci (QTLs) with a phenotypic variance explained value of 100% were located on chromosome 8 (chr08). The QTLs and other previously identified sex-specific markers were located in a sex-determining region of 16.83 Mb (from 6.90 to 23.73 Mb) on chr08, which was predicted as the X chromosome. The sex-determining region comprised 554 genes, with 135 of which being differently expressed between males and females/pseudofemales, and 16 candidate sex-determining genes were screened out. The results of this study provided a useful chromosome-level genome for genetic, genomic and evolutionary studies of P. ussuriensis, and also be useful for further studies on sex-determination mechanism analysis and sex-control breeding of this fish.
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Affiliation(s)
- Chuankun Zhu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai’an 223300, China
| | - Haiyang 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 510380, China
| | - Zhengjun Pan
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai’an 223300, China
| | - Lei Cheng
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences , Harbin 150070, China
| | - Yanhong Sun
- Wuhan Aquaculture Science Research Institute , Wuhan 430207, China
| | - Hui Wang
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai’an 223300, China
| | - Guoliang Chang
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai’an 223300, China
| | - Nan Wu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai’an 223300, China
| | - Huaiyu Ding
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai’an 223300, China
| | - Haitao Zhao
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai’an 223300, China
| | - Lei Zhang
- Key Laboratory of Fishery Sustainable Development and Water Environment Protection of Huai’an City, Huai’an Sub Center of the Institute of Hydrobiology, Chinese Academy of Sciences , Huai’an 223002, China
| | - Xiangsheng Yu
- Huai’an Fisheries Technical Guidance Station , Huai’an 223001, China
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23
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Lu LF, Jiang JY, Du WX, Wang XL, Li ZC, Zhou XY, Zhang C, Mou CY, Chen DD, Li Z, Zhou L, Gui JF, Li XY, Li S. Fish female-biased gene cyp19a1a leads to female antiviral response attenuation between sexes by autophagic degradation of MITA. PLoS Pathog 2022; 18:e1010626. [PMID: 35727817 PMCID: PMC9249237 DOI: 10.1371/journal.ppat.1010626] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 07/01/2022] [Accepted: 05/30/2022] [Indexed: 11/19/2022] Open
Abstract
From insects to mammals, both innate and adaptive immune response are usually higher in females than in males, with the sex chromosome and hormonal differences considered the main reasons. Here, we report that zebrafish cyp19a1a (cytochrome P450, family 19, subfamily A, polypeptide 1a), an autosomal gene with female-biased expression, causes female fish to exhibit a lower antiviral response. First, we successfully constructed an infection model by intraperitoneal injection of spring viremia of carp virus (SVCV) into zebrafish (Danio rerio) and Carassius auratus herpesvirus (CaHV) in gibel carp (Carassius gibelio). Specifically, female fish were more vulnerable to viral infection than males, accompanied by a significantly weaker interferon (IFN) expression. After screening several candidates, cyp19a1a, which was highly expressed in female fish tissues, was selected for further analysis. The IFN expression and antiviral response were significantly higher in cyp19a1a-/- than in cyp19a1a+/+. Further investigation of the molecular mechanism revealed that Cyp19a1a targets mediator of IRF3 activation (MITA) for autophagic degradation. Interestingly, in the absence of MITA, Cyp19a1a alone could not elicit an autophagic response. Furthermore, the autophagy factor ATG14 (autophagy-related 14) was found interacted with Cyp19a1a to either promote or attenuate Cyp19a1a-mediated MITA degradation by either being overexpressed or knocked down, respectively. At the cellular level, both the normal and MITA-enhanced cellular antiviral responses were diminished by Cyp19a1a. These findings demonstrated a sex difference in the antiviral response based on a regulation mechanism controlled by a female-biased gene besides sex chromosome and hormonal differences, supplying the current understanding of sex differences in fish.
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Affiliation(s)
- Long-Feng Lu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing-Yu Jiang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Xuan Du
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xue-Li Wang
- University of Chinese Academy of Sciences, Beijing, China
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Zhuo-Cong Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Yu Zhou
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Can Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cheng-Yan Mou
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dan-Dan Chen
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhi Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
| | - Li Zhou
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
| | - Jian-Fang Gui
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
| | - Xi-Yin Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- * E-mail: (X-YL); (SL)
| | - Shun Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- * E-mail: (X-YL); (SL)
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24
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Lei L, Chen C, Zhu J, Wang Y, Liu X, Liu H, Geng L, Su J, Li W, Zhu X. Transcriptome analysis reveals key genes and pathways related to sex differentiation in the Chinese soft-shelled turtle (Pelodiscus sinensis). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 42:100986. [PMID: 35447559 DOI: 10.1016/j.cbd.2022.100986] [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: 01/20/2022] [Revised: 03/14/2022] [Accepted: 04/03/2022] [Indexed: 06/14/2023]
Abstract
Most vertebrates exhibit sexual dimorphisms in size, colour, behaviour, physiology and many others. The Chinese soft-shelled turtle (Pelodiscus sinensis) male individuals reach a larger size than females which produce significant economic implications in aquaculture. However, the mechanisms of sex determination and plastic patterns of sex differentiation in P. sinensis remain unclear. Here, comparative transcriptome analysis on male and female embryonic gonads prior to gonad formation and stages mediated gonadal differentiation of P. sinensis were performed to characterize the potential sex-related genes and their molecular pathways in P. sinensis. A total of 6369 differentially expressed genes (DEGs) were identified from day 9 and day 16 and assigned to 626 GO pathways and 161 KEGG signalling pathways, including ovarian steroidogenesis pathway, steroid hormone biosynthesis pathways, and the GnRH signalling pathway (P < 0.05). Moreover, protein interaction network analyses revealed that Akr1c3, Sult2b1, Sts, Cyp3a, Cyp1b1, Sox30 and Lhx9 might be key candidate genes for sex differentiation in P. sinensis. These data provide a genomic rationale for the sex differentiation of P. sinensis and enrich the candidate gene pool for sex differentiation.
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Affiliation(s)
- Luo Lei
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, Jiangsu 214081, PR China; Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangdong, Guangzhou 510380, PR China
| | - Chen Chen
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangdong, Guangzhou 510380, PR China
| | - Junxian Zhu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangdong, Guangzhou 510380, PR China
| | - Yakun Wang
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangdong, Guangzhou 510380, PR China
| | - Xiaoli Liu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangdong, Guangzhou 510380, PR China
| | - Haiyang Liu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangdong, Guangzhou 510380, PR China
| | - Lulu Geng
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, Jiangsu 214081, PR China
| | - Junyu Su
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangdong, Guangzhou 510380, PR China
| | - Wei Li
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangdong, Guangzhou 510380, PR China.
| | - Xinping Zhu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, Jiangsu 214081, PR China; Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangdong, Guangzhou 510380, PR China.
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Guan WZ, Jiang K, Lai XL, Dong YT, Qiu GF. Comprehensive Transcriptome Analysis of Gonadal and Somatic Tissues for Identification of Sex-Related Genes in the Largemouth Bass Micropterus salmoides. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:588-598. [PMID: 35384611 DOI: 10.1007/s10126-022-10127-x] [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: 12/12/2021] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
Largemouth bass (Micropterus salmoides) is an economically important fish. It can spawn many times during a breeding season, and there are no obvious morphological characteristics to distinguish male and female juvenile fish. So far, little is known about the genes regulating their sexual development in this species. Here, we performed RNA sequencing (RNA-Seq) analysis of the testis, ovary, and somatic tissue to identify sex-related genes in the largemouth bass. A total of 51,672 unigenes were obtained via the transcriptome analysis, and 5900 differential expression genes (DEGs), including 3028 up-regulated and 2872 down-regulated DEGs, were obtained in the somatic tissue, testis, and ovary. DEGs were retrieved by making comparisons: somatic tissue vs testis (1733-up and 1382-down), testis vs ovary (841-up and 807-down), and ovary vs somatic tissue (454-up and 683-down). Finally, functional annotation identified 22 key sex-related DEGs, including 13 testis-biased DEGs (dmrt1, cyp11b1, sox9, spata4, spata22, spata17, fshr, fem-1a, wt1, daz1, amh, vasa, and piwi1) and 9 ovary-biased DEGs (foxl2, gdf9, zp3, sox3, cyp19a, bmp15, fem-1b, fig. la, and piwi2). This result was further confirmed by the tissue expression detection via RT-PCR and RT-qPCR. Protein-protein interacting (PPI) network analysis revealed that the testis-specific dmrt1 interacts directly with the testis-biased DEGs (cyp11b1 and spata4) and the ovary-biased DEGs (foxl2, gdf9, zp3, sox3, cyp19a, and bmp15), suggesting that the dmrt1 as a sex-determining gene can play a dual role through inducing the testis-biased DEGs and inhibiting the ovary-biased DEGs during the testicular development. Our present results provide useful molecular data for a better understanding of sexual development in the largemouth bass.
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Affiliation(s)
- Wen-Zhi Guan
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of AgricultureShanghai Engineering Research Center of AquaculturePudong New Area, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306, China
- Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Zhejiang, China
| | - Kai Jiang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of AgricultureShanghai Engineering Research Center of AquaculturePudong New Area, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306, China
| | - Xing-Lin Lai
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of AgricultureShanghai Engineering Research Center of AquaculturePudong New Area, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306, China
| | - Yao-Ting Dong
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of AgricultureShanghai Engineering Research Center of AquaculturePudong New Area, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306, China
| | - Gao-Feng Qiu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of AgricultureShanghai Engineering Research Center of AquaculturePudong New Area, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306, China.
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Li XY, Mei J, Ge CT, Liu XL, Gui JF. Sex determination mechanisms and sex control approaches in aquaculture animals. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1091-1122. [PMID: 35583710 DOI: 10.1007/s11427-021-2075-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/14/2022] [Indexed: 01/21/2023]
Abstract
Aquaculture is one of the most efficient modes of animal protein production and plays an important role in global food security. Aquaculture animals exhibit extraordinarily diverse sexual phenotypes and underlying mechanisms, providing an ideal system to perform sex determination research, one of the important areas in life science. Moreover, sex is also one of the most valuable traits because sexual dimorphism in growth, size, and other economic characteristics commonly exist in aquaculture animals. Here, we synthesize current knowledge of sex determination mechanisms, sex chromosome evolution, reproduction strategies, and sexual dimorphism, and also review several approaches for sex control in aquaculture animals, including artificial gynogenesis, application of sex-specific or sex chromosome-linked markers, artificial sex reversal, as well as gene editing. We anticipate that better understanding of sex determination mechanisms and innovation of sex control approaches will facilitate sustainable development of aquaculture.
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Affiliation(s)
- Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jie Mei
- College of Fisheries, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chu-Tian Ge
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, China
| | - Xiao-Li Liu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan, 430072, China.
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Chromosome-level genome assembly of Asian yellow pond turtle (Mauremys mutica) with temperature-dependent sex determination system. Sci Rep 2022; 12:7905. [PMID: 35550586 PMCID: PMC9098631 DOI: 10.1038/s41598-022-12054-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/21/2022] [Indexed: 12/14/2022] Open
Abstract
Knowledge of sex determination has important implications in physiology, ecology and genetics, but the evolutionary mechanisms of sex determination systems in turtles have not been fully elucidated, due to a lack of reference genomes. Here, we generate a high-quality genome assembly of Asian yellow pond turtle (Mauremys mutica) using continuous long-read (PacBio platform), Illumina, and high-throughput chromatin conformation capture (Hi-C) technologies. The M. mutica haplotype has a genome size of 2.23 Gb with a contig N50 of 8.53 Mb and scaffold N50 of 141.98 Mb. 99.98% sequences of the total assembly are anchored to 26 pseudochromosomes. Comparative genomics analysis indicated that the lizard-snake-tuatara clade diverged from the bird-crocodilian-turtle clade at approximately 267.0-312.3 Mya. Intriguingly, positive selected genes are mostly enriched in the calcium signaling pathway and neuroactive ligand-receptor interaction, which are involved in the process of temperature-dependent sex determination. These findings provide important evolutionary insights into temperature-dependent sex determination system.
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28
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Sex-specific regulation of development, growth and metabolism. Semin Cell Dev Biol 2022; 138:117-127. [PMID: 35469676 DOI: 10.1016/j.semcdb.2022.04.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 03/07/2022] [Accepted: 04/14/2022] [Indexed: 12/13/2022]
Abstract
Adult females and males of most species differ in many aspects of their morphology, physiology and behavior, in response to sex-specific selective pressures that maximize fitness. While we have an increasingly good understanding of the genetic mechanisms that initiate these differences, the sex-specific developmental trajectories that generate them are much less well understood. Here we review recent advances in the sex-specific regulation of development focusing on two models where this development is increasingly well understood: Sexual dimorphism of body size in the fruit fly Drosophila melanogaster and sexual dimorphism of horns in the horned beetle Onthophagus taurus. Because growth and development are also supported by metabolism, the regulation of sex-specific metabolism during and after development is an important aspect of the generation of female and male phenotypes. Hitherto, the study of sex-specific development has largely been independent of the study of sex-specific metabolism. Nevertheless, as we discuss in this review, recent research has begun to reveal considerable overlap in the cellular and physiological mechanisms that regulate sex-specific development and metabolism.
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Guo XF, Zhou YL, Liu M, Li Z, Zhou L, Wang ZW, Gui JF. A High-Density Genetic Map and QTL Fine Mapping for Growth- and Sex-Related Traits in Red Swamp Crayfish ( Procambarus clarkii). Front Genet 2022; 13:852280. [PMID: 35242171 PMCID: PMC8886229 DOI: 10.3389/fgene.2022.852280] [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: 01/11/2022] [Accepted: 01/26/2022] [Indexed: 01/24/2023] Open
Abstract
Red swamp crayfish (Procambarus clarkii) is a commercially important species in global aquaculture and most successfully invasive freshwater shrimp in China. In order to determine the genetic basis of growth- and sex-related traits, a high-density genetic linkage map was constructed using 2b-RAD sequencing technology in a full-sib family. The consensus map contains 4,878 SNP markers assigned to 94 linkage groups (LGs) and spanned 6,157.737 cM with an average marker interval of 1.26 cM and 96.93% genome coverage. The quantitative trait locus (QTL) mapping for growth and sex traits was performed for the first time. QTL mapping uncovers 28 QTLs for growth-related traits in nine LGs, explaining 7.9-14.4% of the phenotypic variation, and identifies some potential candidate growth-related genes such as mih, lamr, golgb1, nurf301, and tbcd1 within the QTL intervals. A single major locus for sex determination was revealed in LG20 that explains 59.3-63.7% of the phenotypic variations. Some candidate sex-related genes, such as vps4bl, ssrf, and acot1, were identified in the QTL intervals and found to be differentially expressed in the muscle tissues between the females and the males. Furthermore, the identified SNPs were revealed to be female heterozygotes, suggesting that red swamp crayfish might have the female heterogametic ZZ/ZW sex determination system. The present study provides a valuable resource for marker-assisted selection and genetic improvement and for further genetic and genomic research in red swamp crayfish.
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Affiliation(s)
- Xin-Fen Guo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Lin Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China,Key Laboratory of Ministry of Water Resources for Ecological Impacts of Hydraulic-Projects and Restoration of Aquatic Ecosystem, Institute of Hydroecology, Ministry of Water Resources, Chinese Academy of Sciences, Wuhan, China
| | - Min Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhong-Wei Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China,*Correspondence: Zhong-Wei Wang,
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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30
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He P, Zhu P, Wei P, Zhuo X, Ma Y, Chen X, Lin Y, Xu Y, Luo H, Peng J. Gonadal transcriptomic analysis and differentially expressed genes between the testes and ovaries in Trachinotus ovatus. AQUACULTURE AND FISHERIES 2022. [DOI: 10.1016/j.aaf.2020.09.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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31
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Grinshpan N, Abayed FA, Wahl M, Ner-Gaon H, Manor R, Sagi A, Shay T. The transcriptional landscape of the giant freshwater prawn: Embryonic development and early sexual differentiation mechanisms. Front Endocrinol (Lausanne) 2022; 13:1059936. [PMID: 36568080 PMCID: PMC9767951 DOI: 10.3389/fendo.2022.1059936] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
The giant freshwater prawn pjMacrobrachium rosenbergii is one of the best studied species in aquaculture. However, the transcriptional changes associated with embryonic development and the sexual differentiation mechanism of M. rosenbergii remain to be elucidated. To characterize the embryonic development of this prawn and to determine whether differential expression and differential splicing play roles in the early sexual differentiation of M. rosenbergii, we profiled five developmental days of male and female embryos by RNA sequencing. We identified modules of co-expressed genes representing waves of transcription that correspond to physiological processes in early embryonic development (such as the maternal-to-zygotic transition) up to preparation for life outside the egg (development of muscles, cuticle etc.). Additionally, we found that hundreds of genes are differentially expressed between sexes, most of them uncharacterized, suggesting that the sex differentiation mechanism of M. rosenbergii might contain clade-specific elements. The resulting first-of-a-kind transcriptional map of embryonic development of male and female M. rosenbergii will guide future studies to reveal the roles of specific genes and splicing isoforms in the embryonic development and sexual differentiation process of M. rosenbergii.
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Affiliation(s)
- Nufar Grinshpan
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Faiza A.A. Abayed
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Melody Wahl
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Hadas Ner-Gaon
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Rivka Manor
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Amir Sagi
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- *Correspondence: Amir Sagi, ; Tal Shay,
| | - Tal Shay
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- *Correspondence: Amir Sagi, ; Tal Shay,
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32
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Liu X, Dai S, Wu J, Wei X, Zhou X, Chen M, Tan D, Pu D, Li M, Wang D. Roles of anti-Müllerian hormone and its duplicates in sex determination and germ cell proliferation of Nile tilapia. Genetics 2021; 220:6486528. [PMID: 35100374 PMCID: PMC9208641 DOI: 10.1093/genetics/iyab237] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 12/17/2021] [Indexed: 12/30/2022] Open
Abstract
Duplicates of amh are crucial for fish sex determination and differentiation. In Nile tilapia, unlike in other teleosts, amh is located on X chromosome. The Y chromosome amh (amhΔ-y) is mutated with 5 bp insertion and 233 bp deletion in the coding sequence, and tandem duplicate of amh on Y chromosome (amhy) has been identified as the sex determiner. However, the expression of amh, amhΔ-y, and amhy, their roles in germ cell proliferation and the molecular mechanism of how amhy determines sex is still unclear. In this study, expression and functions of each duplicate were analyzed. Sex reversal occurred only when amhy was mutated as revealed by single, double, and triple mutation of the 3 duplicates in XY fish. Homozygous mutation of amhy in YY fish also resulted in sex reversal. Earlier and higher expression of amhy/Amhy was observed in XY gonads compared with amh/Amh during sex determination. Amhy could inhibit the transcription of cyp19a1a through Amhr2/Smads signaling. Loss of cyp19a1a rescued the sex reversal phenotype in XY fish with amhy mutation. Interestingly, mutation of both amh and amhy in XY fish or homozygous mutation of amhy in YY fish resulted in infertile females with significantly increased germ cell proliferation. Taken together, these results indicated that up-regulation of amhy during the critical period of sex determination makes it the sex-determining gene, and it functions through repressing cyp19a1a expression via Amhr2/Smads signaling pathway. Amh retained its function in controlling germ cell proliferation as reported in other teleosts, while amhΔ-y was nonfunctionalized.
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Affiliation(s)
- Xingyong Liu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Shengfei Dai
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Jiahong Wu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xueyan Wei
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xin Zhou
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Mimi Chen
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Dejie Tan
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Deyong Pu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Minghui Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China,Corresponding author: Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China. ; Corresponding author: Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China,Corresponding author: Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China. ; Corresponding author: Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
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Fuad MMH, Vetešník L, Šimková A. Is gynogenetic reproduction in gibel carp (Carassius gibelio) a major trait responsible for invasiveness? JOURNAL OF VERTEBRATE BIOLOGY 2021. [DOI: 10.25225/jvb.21049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Md Mehedi Hasan Fuad
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic; e-mail: ,
| | - Lukáš Vetešník
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic; e-mail: ,
| | - Andrea Šimková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic; e-mail: ,
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Ruan R, Feng T, Li Y, Yue H, Ye H, Du H, Liu Q, Ruan J, Li C, Wei Q. Screening and identification of female-specific DNA sequences in octaploid sturgeon using comparative genomics with high-throughput sequencing. Genomics 2021; 113:4237-4244. [PMID: 34785350 DOI: 10.1016/j.ygeno.2021.11.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/15/2021] [Accepted: 11/10/2021] [Indexed: 10/19/2022]
Abstract
In this study, six candidate female-specific DNA sequences of octaploid Amur sturgeon (Acipenser schrenckii) were identified using comparative genomic approaches with high-throughput sequencing data. Their specificity was confirmed by traditional PCR. Two of these sex-specific sequences were also validated as female-specific in other eight sturgeon species and two hybrid sturgeons. The identified female-specific DNA fragments suggest that the family Acipenseridae has a ZZ/ZW sex-determining system. However, one of the two DNA sequences has been deleted in some sturgeons such as Sterlet sturgeon (Acipenser ruthenus), Beluga (Huso huso) and Kaluga (H. dauricus). The difference of sex-specific sequences among sturgeons indicates that there are different sex-specific regions among species of sturgeon. This study not only provided the sex-specific DNA sequences for management, conservation and studies of sex-determination mechanisms in sturgeons, but also confirmed the capability of the workflow to identify sex-specific DNA sequences in the polyploid species with complex genomes.
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Affiliation(s)
- Rui Ruan
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Tong Feng
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Ying Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Huamei Yue
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Huan Ye
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Hao Du
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Jue Ruan
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
| | - Chuangju Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China.
| | - Qiwei Wei
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China.
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Comparative transcriptomic analysis reveals the gonadal development-related gene response to environmental temperature in Mauremys mutica. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 40:100925. [PMID: 34689019 DOI: 10.1016/j.cbd.2021.100925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/11/2021] [Accepted: 10/14/2021] [Indexed: 01/15/2023]
Abstract
The Asian yellow pond turtle (Mauremys mutica) displays temperature-dependent sex determination (TSD), in which incubation temperature during embryonic development determines the sexual fate of the individual. However, the mechanism of the sex determination/differentiation of Mauremys mutica remains a mystery. Here, we first analyzed the temperature-specific gonadal transcriptomes of Mauremys mutica prior to gonad formation and gonads during the thermosensitive period. We uncovered a list of candidates that respond to temperature stimuli enriched in several categories, such as heat shock protein family members dnajb6a, dnaja4, hspa8 and hsp90aa1, temperature sensor genes mmp17 and mmp28, and putative novel temperature-responsive genes tmco6, gria3 and eif3f. Notably, striking differences were identified in the expression profiles of genes underlying sexual development, such as tex15, insr, igf1r, cirbp, esr1, dmrt2 and Serpinh1. Moreover, we analyzed the similarity and divergence of the timecourse of gene expression among Mauremys mutica and two other reported TSD turtles (Trachemys scripta and Chrysemys picta). The shared genes revealed the common gonad-specific regulatory mechanisms existing in these three TSD turtles that initiate their sexual development. Therefore, our findings could provide basic data to elucidate the mechanisms of sex determination/differentiation of M. mutica, even contributing to further understanding of these mechanisms in other TSD turtles.
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Mou CY, Li S, Lu LF, Wang Y, Yu P, Li Z, Tong JF, Zhang QY, Wang ZW, Zhang XJ, Wang GX, Zhou L, Gui JF. Divergent Antiviral Mechanisms of Two Viperin Homeologs in a Recurrent Polyploid Fish. Front Immunol 2021; 12:702971. [PMID: 34531856 PMCID: PMC8438203 DOI: 10.3389/fimmu.2021.702971] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/09/2021] [Indexed: 12/03/2022] Open
Abstract
Polyploidy and subsequent diploidization provide genomic opportunities for evolutionary innovations and adaptation. The researches on duplicated gene evolutionary fates in recurrent polyploids have seriously lagged behind that in paleopolyploids with diploidized genomes. Moreover, the antiviral mechanisms of Viperin remain largely unclear in fish. Here, we elaborate the distinct antiviral mechanisms of two viperin homeologs (Cgviperin-A and Cgviperin-B) in auto-allo-hexaploid gibel carp (Carassius gibelio). First, Cgviperin-A and Cgviperin-B showed differential and biased expression patterns in gibel carp adult tissues. Subsequently, using co-immunoprecipitation (Co-IP) screening analysis, both CgViperin-A and CgViperin-B were found to interact with crucian carp (C. auratus) herpesvirus (CaHV) open reading frame 46 right (ORF46R) protein, a negative herpesvirus regulator of host interferon (IFN) production, and to promote the proteasomal degradation of ORF46R via decreasing K63-linked ubiquitination. Additionally, CgViperin-B also mediated ORF46R degradation through autophagosome pathway, which was absent in CgViperin-A. Moreover, we found that the N-terminal α-helix domain was necessary for the localization of CgViperin-A and CgViperin-B at the endoplasmic reticulum (ER), and the C-terminal domain of CgViperin-A and CgViperin-B was indispensable for the interaction with degradation of ORF46R. Therefore, the current findings clarify the divergent antiviral mechanisms of the duplicated viperin homeologs in a recurrent polyploid fish, which will shed light on the evolution of teleost duplicated genes.
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Affiliation(s)
- Cheng-Yan Mou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shun Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Long-Feng Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Peng Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
| | - Jin-Feng Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qi-Ya Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhong-Wei Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
| | - Guang-Xin Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
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37
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Ding M, Li XY, Zhu ZX, Chen JH, Lu M, Shi Q, Wang Y, Li Z, Zhao X, Wang T, Du WX, Miao C, Yao TZ, Wang MT, Zhang XJ, Wang ZW, Zhou L, Gui JF. Genomic anatomy of male-specific microchromosomes in a gynogenetic fish. PLoS Genet 2021; 17:e1009760. [PMID: 34491994 PMCID: PMC8448357 DOI: 10.1371/journal.pgen.1009760] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 09/17/2021] [Accepted: 08/09/2021] [Indexed: 11/19/2022] Open
Abstract
Unisexual taxa are commonly considered short-lived as the absence of meiotic recombination is supposed to accumulate deleterious mutations and hinder the creation of genetic diversity. However, the gynogenetic gibel carp (Carassius gibelio) with high genetic diversity and wide ecological distribution has outlived its predicted extinction time of a strict unisexual reproduction population. Unlike other unisexual vertebrates, males associated with supernumerary microchromosomes have been observed in gibel carp, which provides a unique system to explore the rationales underlying male occurrence in unisexual lineage and evolution of unisexual reproduction. Here, we identified a massively expanded satellite DNA cluster on microchromosomes of hexaploid gibel carp via comparing with the ancestral tetraploid crucian carp (Carassius auratus). Based on the satellite cluster, we developed a method for single chromosomal fluorescence microdissection and isolated three male-specific microchromosomes in a male metaphase cell. Genomic anatomy revealed that these male-specific microchromosomes contained homologous sequences of autosomes and abundant repetitive elements. Significantly, several potential male-specific genes with transcriptional activity were identified, among which four and five genes displayed male-specific and male-biased expression in gonads, respectively, during the developmental period of sex determination. Therefore, the male-specific microchromosomes resembling common features of sex chromosomes may be the main driving force for male occurrence in gynogenetic gibel carp, which sheds new light on the evolution of unisexual reproduction.
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Affiliation(s)
- Miao Ding
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhi-Xuan Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jun-Hui Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- ShenZhen People’s Hospital, Shenzhen, China
| | - Meng Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qian Shi
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tao Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Xuan Du
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chun Miao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tian-Zi Yao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ming-Tao Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhong-Wei Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
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Rappaport Y, Achache H, Falk R, Murik O, Ram O, Tzur YB. Bisection of the X chromosome disrupts the initiation of chromosome silencing during meiosis in Caenorhabditis elegans. Nat Commun 2021; 12:4802. [PMID: 34376665 PMCID: PMC8355143 DOI: 10.1038/s41467-021-24815-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 07/01/2021] [Indexed: 01/04/2023] Open
Abstract
During meiosis, gene expression is silenced in aberrantly unsynapsed chromatin and in heterogametic sex chromosomes. Initiation of sex chromosome silencing is disrupted in meiocytes with sex chromosome-autosome translocations. To determine whether this is due to aberrant synapsis or loss of continuity of sex chromosomes, we engineered Caenorhabditis elegans nematodes with non-translocated, bisected X chromosomes. In early meiocytes of mutant males and hermaphrodites, X segments are enriched with euchromatin assembly markers and active RNA polymerase II staining, indicating active transcription. Analysis of RNA-seq data showed that genes from the X chromosome are upregulated in gonads of mutant worms. Contrary to previous models, which predicted that any unsynapsed chromatin is silenced during meiosis, our data indicate that unsynapsed X segments are transcribed. Therefore, our results suggest that sex chromosome chromatin has a unique character that facilitates its meiotic expression when its continuity is lost, regardless of whether or not it is synapsed.
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Affiliation(s)
- Yisrael Rappaport
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hanna Achache
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Roni Falk
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Omer Murik
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Oren Ram
- Department of Biological Chemistry, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yonatan B Tzur
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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Duan W, Gao FX, Chen ZW, Gao Y, Gui JF, Zhao Z, Shi Y. A sex-linked SNP mutation in amhr2 is responsible for male differentiation in obscure puffer (Takifugu obscurus). Mol Biol Rep 2021; 48:6035-6046. [PMID: 34341900 DOI: 10.1007/s11033-021-06606-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/27/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Anti-Mullerian hormone receptor type II (Amhr2) is a key receptor of Amh signaling in regulating gonad development. The amhr2 gene has been identified in numerous species, including a few teleost fishes. However, the roles of Amhr2 in Amh signaling in fish are poorly studied. METHODS AND RESULTS In this study, an amhr2 homolog from obscure puffer (Takifugu obscurus) was identified, and its molecular characteristics were systematically analyzed. Expression analysis revealed that amhr2 was highly expressed in the gonads of adult pufferfish and significantly upregulated during sex differentiation. Significantly, a sex-linked SNP site was verified in obscure puffer amhr2. Females exhibited a homozygous genotype (C/C), while males possessed a heterozygous genotype (C/G), resulting in an amino acid variation (His/Asp384) in the kinase domain of Amhr2. Then, the functions of the different Amhr2 genotypes were further investigated. The male genotype protein (Amhr2D384) showed an enhanced ability to interact with the type I receptor (Bmpr1a) compared to the female genotype (Amhr2H384). The phosphorylation levels of Smads and activity of the target gene (id3) induced by the male genotype were also much higher than those induced by the female genotype. These results confirmed that the male genotype had an enhanced effect on the Amh signaling pathway compared with the female genotype. CONCLUSIONS This study provides direct experimental evidence for the roles of different Amhr2 genotypes in pufferfish and suggests that amhr2 is responsible for male sex differentiation in obscure puffer.
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Affiliation(s)
- Wen Duan
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
| | - Fan-Xiang Gao
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China.,State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zi-Wei Chen
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
| | - Yang Gao
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
| | - Jian-Fang Gui
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China.,State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zhe Zhao
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
| | - Yan Shi
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China.
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40
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Xing TF, Li YL, Liu JX. Female-specific genomic regions and molecular sex identification of the clearhead icefish (Protosalanx hyalocranius). BMC Genomics 2021; 22:495. [PMID: 34215185 PMCID: PMC8254354 DOI: 10.1186/s12864-021-07830-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/16/2021] [Indexed: 01/29/2023] Open
Abstract
Background The clearhead icefish, Protosalanx hyalocranius, is an economically important fishery species in China. Since 1980s, P. hyalocranius was widely introduced into lakes and reservoirs of northern China for aquaculture. However, the lack of a rapid and cost-effective sex identification method based on sex specific genetic markers has hindered study on sex determination mechanisms and breeding applications. Results Female-specific genomic regions were discovered by comparing whole genome re-sequencing data of both males and females. Two female-specific genomic regions larger than 50 bp were identified, and one (598 bp) contained a putative FOXI gene, which was paralogous to another FOXI gene with sex-associated SNPs. The two FOXI sequences displayed significant length difference with nine deletions of total length of 230 bp. This deletion-type structural variation could be easily and efficiently detected by traditional PCR and agarose gel electrophoresis with one 569 bp band for males and two bands (569 and 339 bp) for females, which were validated in 50 females and 40 males with known phenotypic sexes. Conclusions The results provided structural genomic evidence for the ZZ/ZW sex determination system in P. hyalocranius discovered in our previous study with association analysis of SNPs. Moreover, the female-specific markers and rapid and cost-effective PCR-based genetic sex identification method should have applications in further studies of sex determination mechanism for this species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07830-9.
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Affiliation(s)
- Teng-Fei Xing
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, 266237, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, 266071, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Long Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China. .,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, 266237, Qingdao, China. .,Center for Ocean Mega-Science, Chinese Academy of Sciences, 266071, Qingdao, China.
| | - Jin-Xian Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, 266237, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, 266071, Qingdao, China
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41
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Zhao X, Li Z, Ding M, Wang T, Wang MT, Miao C, Du WX, Zhang XJ, Wang Y, Wang ZW, Zhou L, Li XY, Gui JF. Genotypic Males Play an Important Role in the Creation of Genetic Diversity in Gynogenetic Gibel Carp. Front Genet 2021; 12:691923. [PMID: 34122529 PMCID: PMC8194356 DOI: 10.3389/fgene.2021.691923] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/05/2021] [Indexed: 12/12/2022] Open
Abstract
Unisexual lineages are commonly considered to be short-lived in the evolutionary process as accumulation of deleterious mutations stated by Muller’s ratchet. However, the gynogenetic hexaploid gibel carp (Carassius gibelio) with existence over 0.5 million years has wider ecological distribution and higher genetic diversity than its sexual progenitors, which provides an ideal model to investigate the underlying mechanisms on countering Muller’s ratchet in unisexual taxa. Unlike other unisexual lineages, the wild populations of gibel carp contain rare and variable proportions of males (1–26%), which are determined via two strategies including genotypic sex determination and temperature-dependent sex determination. Here, we used a maternal gibel carp from strain F to be mated with a genotypic male from strain A+, a temperature-dependent male from strain A+, and a male from another species common carp (Cyprinus carpio), respectively. When the maternal individual was mated with the genotypic male, a variant of gynogenesis was initiated, along with male occurrence, accumulation of microchromosomes, and creation of genetic diversity in the offspring. When the maternal individual was mated with the temperature-dependent male and common carp, typical gynogenesis was initiated that all the offspring showed the same genetic information as the maternal individual. Subsequently, we found out that the genotypic male nucleus swelled and contacted with the female nucleus after fertilization although it was extruded from the female nucleus eventually, which might be associated with the genetic variation in the offspring. These results reveal that genotypic males play an important role in the creation of genetic diversity in gynogenetic gibel carp, which provides insights into the evolution of unisexual reproduction.
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Affiliation(s)
- Xin Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Miao Ding
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Tao Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ming-Tao Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chun Miao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Xuan Du
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhong-Wei Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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Gan RH, Wang Y, Li Z, Yu ZX, Li XY, Tong JF, Wang ZW, Zhang XJ, Zhou L, Gui JF. Functional Divergence of Multiple Duplicated Foxl2 Homeologs and Alleles in a Recurrent Polyploid Fish. Mol Biol Evol 2021; 38:1995-2013. [PMID: 33432361 PMCID: PMC8097289 DOI: 10.1093/molbev/msab002] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Evolutionary fates of duplicated genes have been widely investigated in many polyploid plants and animals, but research is scarce in recurrent polyploids. In this study, we focused on foxl2, a central player in ovary, and elaborated the functional divergence in gibel carp (Carassius gibelio), a recurrent auto-allo-hexaploid fish. First, we identified three divergent foxl2 homeologs (Cgfoxl2a-B, Cgfoxl2b-A, and Cgfoxl2b-B), each of them possessing three highly conserved alleles and revealed their biased retention/loss. Then, their abundant sexual dimorphism and biased expression were uncovered in hypothalamic-pituitary-gonadal axis. Significantly, granulosa cells and three subpopulations of thecal cells were distinguished by cellular localization of CgFoxl2a and CgFoxl2b, and the functional roles and the involved process were traced in folliculogenesis. Finally, we successfully edited multiple foxl2 homeologs and/or alleles by using CRISPR/Cas9. Cgfoxl2a-B deficiency led to ovary development arrest or complete sex reversal, whereas complete disruption of Cgfoxl2b-A and Cgfoxl2b-B resulted in the depletion of germ cells. Taken together, the detailed cellular localization and functional differences indicate that Cgfoxl2a and Cgfoxl2b have subfunctionalized and cooperated to regulate folliculogenesis and gonad differentiation, and Cgfoxl2b has evolved a new function in oogenesis. Therefore, the current study provides a typical case of homeolog/allele diversification, retention/loss, biased expression, and sub-/neofunctionalization in the evolution of duplicated genes driven by polyploidy and subsequent diploidization from the recurrent polyploid fish.
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Affiliation(s)
- Rui-Hai Gan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhao-Xi Yu
- Ningxia Fisheries Research Institute, Yinchuan, China
| | - Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jin-Feng Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhong-Wei Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
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Sox9a, not sox9b is required for normal cartilage development in zebrafish. AQUACULTURE AND FISHERIES 2021. [DOI: 10.1016/j.aaf.2019.12.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Guo S, Zhong Y, Zhang Y, Zhu Y, Guo J, Fu Y, Li M. Transcriptome analysis provides insights into long noncoding RNAs in medaka gonads. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 39:100842. [PMID: 33962104 DOI: 10.1016/j.cbd.2021.100842] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/19/2021] [Accepted: 04/22/2021] [Indexed: 10/21/2022]
Abstract
Long non-coding RNAs (lncRNAs) are gradually regarded as regulators in sex determination and gonad development of various animals. Medaka (Oryzias latipes) is an excellent reproductive research model with sex-determining genes. However, the regulation of gonadal lncRNAs on medaka reproductive development remains unknown. Here, 5317 lncRNAs were obtained from medaka ovary and testis by Illumina HiSeq4000, among which 177 lncRNAs were up-regulated and 120 lncRNAs were down-regulated in the testis compared to the ovary. In addition, 6904 cis-regulated target genes were predicted from 3099 lncRNAs. GO and KEGG enrichment analysis showed that these target genes were mainly involved in phosphorylation, metabolic, metabolism of xenobiotics by cytochrome P450, insulin secretion, and GnRH signaling pathways. Furthermore, six highly expressed lncRNAs were randomly selected to verify the sequencing data by quantitative real time PCR (qRT-PCR). Next, in situ hybridization revealed that one of the sex-biased lncRNA MSTRG.14827.1 was highly expressed in immature germ cells, indicating MSTRG.14827.1 may play a key role in gametogenesis. Taken together, this study provides emerging lncRNA libraries and opens new avenues for future investigation of lncRNAs in medaka.
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Affiliation(s)
- Shaoyu Guo
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
| | - Ying Zhong
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
| | - Yu Zhang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
| | - Yefei Zhu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
| | - Jing Guo
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
| | - Yuanshuai Fu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China.
| | - Mingyou Li
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China.
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Zhang C, Li Q, Zhu L, He W, Yang C, Zhang H, Sun Y, Zhou L, Sun Y, Zhu S, Wu C, Tao M, Zhou Y, Zhao R, Tang C, Liu S. Abnormal meiosis in fertile and sterile triploid cyprinid fish. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1917-1928. [PMID: 33893980 DOI: 10.1007/s11427-020-1900-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 03/09/2021] [Indexed: 11/25/2022]
Abstract
Meiosis is the key process for producing mature gametes. A natural fertile triploid Carassius auratus population (3nDTCC) and an artificially derived sterile triploid crucian carp (3nCC) have been previously observed, providing suitable model organisms for investigating meiosis characteristics in triploid fish. In the present study, the microstructures and ultrastructures of spermatogenesis were studied in these fishes. TdT-mediated dUTP nick end labeling detection was performed to investigate the apoptosis of spermatocytes. Fluorescence in situ hybridization was employed to trace chromatin pairing. In addition, the mRNA expressions of cell cycle-related genes (i.e., cell division control 2 and cell cycle protein B) were determined by quantitative realtime polymerase chain reaction to illustrate the molecular mechanism of abnormal meiosis in the 3nCC. The results showed that the 3nCC undergoes an irregular prophase I, with the chromosomes distributed in a unipolar radial manner and exhibiting partial pairing, hindered metaphase I, and degenerated cells in the subsequent stages. Meanwhile, the 3nDTCC presented a relatively regular meiotic prophase I with complete conjugate chromosome pairs and chromosomes distributed along the karyotheca, which were presented as a ring structure by slicing. Only the spreads with 130-150 irregular chromosomes can be easily detected in the 3nDTCC, suggesting that it may undergo an abnormal metaphase I. This study provides new insights into the meiosis of fertile and sterile triploid cyprinid fish.
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Affiliation(s)
- Chun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Qi Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - La Zhu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Wangchao He
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Conghui Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Hui Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Yu Sun
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Luojing Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Yuandong Sun
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Shurun Zhu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Chang Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Yi Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Rurong Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Chenchen Tang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
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Hu Q, Liu Y, Liao X, Tian H, Ji X, Zhu J, Xiao H. A high-density genetic map construction and sex-related loci identification in Chinese Giant salamander. BMC Genomics 2021; 22:230. [PMID: 33794798 PMCID: PMC8017863 DOI: 10.1186/s12864-021-07550-0] [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: 05/01/2020] [Accepted: 03/24/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Chinese giant salamander Andrias davidianus is an important amphibian species in China because of its increasing economic value, protection status and special evolutionary position from aquatic to terrestrial animal. Its large genome presents challenges to genetic research. Genetic linkage mapping is an important tool for genome assembly and determination of phenotype-related loci. RESULTS In this study, we constructed a high-density genetic linkage map using ddRAD sequencing technology to obtain SNP genotyping data of members from an full-sib family which sex had been determined. A total of 10,896 markers were grouped and oriented into 30 linkage groups, representing 30 chromosomes of A. davidianus. The genetic length of LGs ranged from 17.61 cM (LG30) to 280.81 cM (LG1), with a mean inter-locus distance ranging from 0.11(LG3) to 0.48 cM (LG26). The total genetic map length was 2643.10 cM with an average inter-locus distance of 0.24 cM. Three sex-related loci and four sex-related markers were found on LG6 and LG23, respectively. CONCLUSION We constructed the first High-density genetic linkage map and identified three sex-related loci in the Chinese giant salamander. Current results are expected to be a useful tool for future genomic studies aiming at the marker-assisted breeding of the species.
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Affiliation(s)
- Qiaomu Hu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, Hubei, China.
| | - Yang Liu
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xiaolin Liao
- Key Laboratory of Ecological Impacts of Hydraulic-Projects and Restoration of Aquatic Ecosystem of Ministry of Water Resources, Institute of Hydroecology, Ministry of Water Resources and Chinese Academy of Sciences, Wuhan, 430079, China
| | - Haifeng Tian
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, Hubei, China
| | - Xiangshan Ji
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Jiajie Zhu
- Guangxi Academy of Fishery Sciences, Nanning, 530021, Guangxi Province, China
| | - Hanbing Xiao
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, Hubei, China
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Yu P, Wang Y, Yang WT, Li Z, Zhang XJ, Zhou L, Gui JF. Upregulation of the PPAR signaling pathway and accumulation of lipids are related to the morphological and structural transformation of the dragon-eye goldfish eye. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1031-1049. [PMID: 33428077 DOI: 10.1007/s11427-020-1814-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 08/19/2020] [Indexed: 02/07/2023]
Abstract
Goldfish comprise around 300 different strains with drastically altered and aesthetical morphologies making them suitable models for evolutionary developmental biology. The dragon-eye strain is characterized by protruding eyes (analogous to those of Chinese dragons). Although the strain has been selected for about 400 years, the mechanism of its eye development remains unclear. In this study, a stable dragon-eye goldfish strain with a clear genetic background was rapidly established and studied. We found that upregulation of the PPAR signaling pathway accompanied by an increase in lipid accumulation might trigger the morphological and structural transformation of the eye in dragon-eye goldfish. At the developmental stage of proptosis (eye protrusion), downregulation of the phototransduction pathway was consistent with the structural defects and myopia of the dragon-eye strain. With the impairment of retinal development, cytokine-induced inflammation was activated, especially after proptosis, similar to the pathologic symptoms of many human ocular diseases. In addition, differentially expressed transcription factors were significantly enriched in the PAX and homeobox families, two well-known transcription factor families involved in eye development. Therefore, our findings reveal the dynamic changes in key pathways during eye development in dragon-eye goldfish, and provide insights into the molecular mechanisms underlying drastically altered eyes in goldfish and human ocular disease.
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Affiliation(s)
- Peng Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen-Tao Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Han YL, Sun ZH, Chang S, Wen B, Song J, Zuo RT, Chang YQ. Application of SNP in Genetic Sex Identification and Effect of Estradiol on Gene Expression of Sex-Related Genes in Strongylocentrotus intermedius. Front Endocrinol (Lausanne) 2021; 12:756530. [PMID: 34858332 PMCID: PMC8632358 DOI: 10.3389/fendo.2021.756530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/22/2021] [Indexed: 11/26/2022] Open
Abstract
Sea urchin (Strongylocentrotus intermedius) is an economically important mariculture species in Asia, and its gonads are the only edible part. The efficiency of genetic breeding in sea urchins is hampered due to the inability to distinguish gender by appearance. In this study, we first identified a sex-associated single nucleotide polymorphism (SNP) by combining type IIB endonuclease restriction site-associated DNA sequencing (2b-RAD-seq) and genome survey. Importantly, this SNP is located within spata4, a gene specifically expressed in male. Knocking down of spata4 by RNA interference (RNAi) in male individuals led to the downregulation of other conserved testis differentiation-related genes and germ cell marker genes. We also revealed that sex ratio in this validated culture population of S. intermedius is not 1:1. Moreover, after a 58-day feeding experiment with estradiol, the expression levels of several conserved genes that are related to testis differentiation, ovary differentiation, and estrogen metabolism were dynamically changed. Taken together, our results will contribute toward improving breeding efficiency, developing sex-controlled breeding, and providing a solid base for understanding sex determination mechanisms in sea urchins.
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Affiliation(s)
| | - Zhi-Hui Sun
- *Correspondence: Zhi-Hui Sun, ; Ya-Qing Chang,
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Effects of gonadotropin-releasing hormone analog (GnRHa) immunization on the gonadal transcriptome and proteome of tilapia (Oreochromis niloticus). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 37:100780. [PMID: 33296765 DOI: 10.1016/j.cbd.2020.100780] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 11/15/2020] [Accepted: 11/18/2020] [Indexed: 11/21/2022]
Abstract
Gonadotropin releasing hormone (GnRH) plays an important role in the regulation of vertebrate reproduction. Studies have shown that immunization against GnRHa can induce sexually sterile tilapia. To explore the mechanism behind this, in this study, RNA-seq and data-independent acquisition (DIA) techniques were used to study the transcriptome and proteome of the gonad of tilapia immunized with GnRHa. 644 differentially expressed genes (80 upregulated and 564 downregulated) and 1150 differentially expressed proteins (351 upregulated and 799 downregulated) were identified. There were 209 genes with consistent differential expression patterns in the transcriptomic and proteomic analyses, of which 9 were upregulated and 200 downregulated, indicating that the gonad gene expression was inhibited by GnRHa immunization. The downregulated genes were particularly involved in the functions of single-organism process, binding, cellular process, metabolic process and catalytic activity, and associated with the pathways including ECM-receptor interaction, focal adhesion, cardiac muscle contraction and oxidative phosphorylation. The expression of six differentially expressed genes involved in the GnRH signaling pathway was all downregulated. In addition, several important functional genes related to gonadal development after GnRHa immunization were screened. This study confirmed the expression of corresponding genes was affected by GnRHa on the gonad development in tilapia at the molecular level, and laid a foundation for elucidating the mechanism of GnRHa immunization.
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Cross I, García E, Rodríguez ME, Arias-Pérez A, Portela-Bens S, Merlo MA, Rebordinos L. The genomic structure of the highly-conserved dmrt1 gene in Solea senegalensis (Kaup, 1868) shows an unexpected intragenic duplication. PLoS One 2020; 15:e0241518. [PMID: 33137109 PMCID: PMC7605655 DOI: 10.1371/journal.pone.0241518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 10/15/2020] [Indexed: 01/17/2023] Open
Abstract
Knowing the factors responsible for sex determination in a species has significant theoretical and practical implications; the dmrt1 gene (Doublesex and Mab-3 (DM)-related Transcription factor 1) plays this role in diverse animal species. Solea senegalensis is a commercially important flat fish in which females grow 30% faster than males. It has 2n = 42 chromosomes and an XX / XY chromosome system for sex determination, without heteromorph chromosomes but with sex proto-chromosome. In the present study, we are providing the genomic structure and nucleotide sequence of dmrt1 gene obtained from cDNA from male and female adult gonads. A cDNA of 2027 containing an open-reading frame (ORF) of 1206 bp and encoding a 402 aa protein it is described for dmrt1 gene of S. senegalensis. Multiple mRNA isoforms indicating a high variable system of alternative splicing in the expression of dmrt1 of the sole in gonads were studied. None isoforms could be related to sex of individuals. The genomic structure of the dmrt1 of S. senegalensis showed a gene of 31400 bp composed of 7 exons and 6 introns. It contains an unexpected duplication of more than 10399 bp, involving part of the exon I, exons II and III and a SINE element found in the sequence that it is proposed as responsible for the duplication. A mature miRNA of 21 bp in length was localized at 336 bp from exon V. Protein-protein interacting networks of the dmrt1 gene showed matches with dmrt1 protein from Cynoglossus semilaevis and a protein interaction network with 11 nodes (dmrt1 plus 10 other proteins). The phylogenetic relationship of the dmrt1 gene in S. senegalensis is consistent with the evolutionary position of its species. The molecular characterization of this gene will enhance its functional analysis and the understanding of sex differentiation in Solea senegalensis and other flatfish.
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Affiliation(s)
- Ismael Cross
- Area de Genética, CASEM, Universidad de Cádiz, Puerto Real, Cádiz, Spain
| | - Emilio García
- Area de Genética, CASEM, Universidad de Cádiz, Puerto Real, Cádiz, Spain
| | - María E. Rodríguez
- Area de Genética, CASEM, Universidad de Cádiz, Puerto Real, Cádiz, Spain
| | | | | | - Manuel A. Merlo
- Area de Genética, CASEM, Universidad de Cádiz, Puerto Real, Cádiz, Spain
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