1
|
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.
Collapse
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
| |
Collapse
|
2
|
Wan G, Wang Z, Zhang X, Tian Y, Zhou X, Ge L, Xiong G, Wang X, Hu Y. Genomic and transcriptome insight into the structure and immunity role of TRIM proteins in Chinese soft-shelled turtles (Pelodiscus sinensis) after Aeromonas hydrophila infection. Mol Biol Rep 2024; 51:263. [PMID: 38302771 DOI: 10.1007/s11033-023-09139-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/11/2023] [Indexed: 02/03/2024]
Abstract
BACKGROUND TRIM proteins, recognized as a class of E3 ubiquitin ligases, are increasingly acknowledged for their antipathogen immune functions in mammals and fish. In the Chinese soft-shelled turtle (Pelodiscus sinensis), a secondary aquatic reptile that occupies a unique evolutionary position, the TRIM gene has rarely been reported. METHODS AND RESULTS In the present study, 48 PsTRIM proteins were identified from the genome of Pelodiscus sinensis via Hidden Markov Model (HMM) searches and Signal Transduction ATPases with Numerous Domains (SMART) analysis. These PsTRIMs were found across 43 distinct scaffolds, and phylogenetic analyses classified them into three principal clades. The PsTRIMs feature a conserved assembly of either RING-B-box-coiled-coil (RBCC) or B-box-coiled-coil (BBC) domains at the N-terminus, in addition to eight unique domains at the C-terminus, including the B30.2 domain, 19 of which were identified. Expression profiling revealed ubiquitous expression of the 48 PsTRIMs across various P. sinensis tissues. Notably, seven PsTRIMs exhibited significant differential expression in liver transcriptomes following infection with Aeromonas hydrophila. Weighted gene coexpression network analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis implicated PsTRIM14 and PsTRIM28 as key players in host defense against bacterial invasion. Real-time quantitative PCR results indicated that PsTRIM1, PsTRIM2, PsTRIM14, and PsTRIM28 experienced marked upregulation in P. sinensis livers at 12 h post-infection with A. hydrophila. CONCLUSIONS Our study is the first to comprehensively identify and analyze the functions of TRIM genes in P. sinensis, unveiling their considerable diversity and potential roles in modulating immune responses.
Collapse
Affiliation(s)
- Gang Wan
- College of Fisheries, Hunan Agricultural University, Changsha, 410128, China
| | - Ziao Wang
- Hunan Biological and Electromechanical Polytechnic, Changsha, 410127, China
| | - Xingyue Zhang
- College of Fisheries, Hunan Agricultural University, Changsha, 410128, China
| | - Yu Tian
- College of Fisheries, Hunan Agricultural University, Changsha, 410128, China
| | - Xianwen Zhou
- Affair Center of Animal Husbandry and Aquaculture in Xiang Xi Autonomous Prefecture, Jishou, 416000, Hunan, China
| | - Lingrui Ge
- Hunan Biological and Electromechanical Polytechnic, Changsha, 410127, China
| | - Gang Xiong
- Hunan Biological and Electromechanical Polytechnic, Changsha, 410127, China
| | - Xiaoqing Wang
- College of Fisheries, Hunan Agricultural University, Changsha, 410128, China.
| | - Yazhou Hu
- College of Fisheries, Hunan Agricultural University, Changsha, 410128, China.
| |
Collapse
|
3
|
Smith CH, Mejia-Trujillo R, Breton S, Pinto BJ, Kirkpatrick M, Havird JC. Mitonuclear Sex Determination? Empirical Evidence from Bivalves. Mol Biol Evol 2023; 40:msad240. [PMID: 37935058 PMCID: PMC10653589 DOI: 10.1093/molbev/msad240] [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: 06/28/2023] [Revised: 10/04/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023] Open
Abstract
Genetic elements encoded in nuclear DNA determine the sex of an individual in many animals. In certain bivalve lineages that possess doubly uniparental inheritance (DUI), mitochondrial DNA (mtDNA) has been hypothesized to contribute to sex determination. In these cases, females transmit a female mtDNA to all offspring, while male mtDNA (M mtDNA) is transmitted only from fathers to sons. Because M mtDNA is inherited in the same way as Y chromosomes, it has been hypothesized that mtDNA may be responsible for sex determination. However, the role of mitochondrial and nuclear genes in sex determination has yet to be validated in DUI bivalves. In this study, we used DNA, RNA, and mitochondrial short noncoding RNA (sncRNA) sequencing to explore the role of mitochondrial and nuclear elements in the sexual development pathway of the freshwater mussel Potamilus streckersoni (Bivalvia: Unionida). We found that the M mtDNA sheds a sncRNA partially within a male-specific mitochondrial gene that targets a pathway hypothesized to be involved in female development and mitophagy. RNA-seq confirmed the gene target was significantly upregulated in females, supporting a direct role of mitochondrial sncRNAs in gene silencing. These findings support the hypothesis that M mtDNA inhibits female development. Genome-wide patterns of genetic differentiation and heterozygosity did not support a nuclear sex-determining region, although we cannot reject that nuclear factors are involved with sex determination. Our results provide further evidence that mitochondrial loci contribute to diverse, nonrespiratory functions and additional insights into an unorthodox sex-determining system.
Collapse
Affiliation(s)
- Chase H Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | | | - Sophie Breton
- Department of Biological Sciences, University of Montreal, Montreal, Canada
| | - Brendan J Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, USA
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Justin C Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| |
Collapse
|
4
|
Lu M, Hayat R, Zhang X, Jiao Y, Huang J, Huangfu Y, Jiang M, Fu J, Jiang Q, Gu Y, Wang S, Akerberg AA, Su Y, Zhao L. Comparative analysis of the cardiac structure and transcriptome of scallop and snail, perspectives on heart chamber evolution. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:478-491. [PMID: 38045548 PMCID: PMC10689705 DOI: 10.1007/s42995-023-00202-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 10/24/2023] [Indexed: 12/05/2023]
Abstract
The evolution of a two-chambered heart, with an atrium and a ventricle, has improved heart function in both deuterostomes (vertebrates) and some protostomes (invertebrates). Although studies have examined the unique structure and function of these two chambers, molecular comparisons are few and limited to vertebrates. Here, we focus on the two-chambered protostome heart of the mollusks, offering data that may provide a better understanding of heart evolution. Specifically, we asked if the atrium and ventricle differ at the molecular level in the mollusk heart. To do so, we examined two very different species, the giant African land snail (Lissachatina fulica) and the relatively small, aquatic yesso scallop (Mizuhopecten yessoensis), with the assumption that if they exhibited commonality these similarities would likely reflect those across the phylum. We found that, although the hearts of these two species differed histologically, their cardiac gene function enrichments were similar, as revealed by transcriptomic analysis. Furthermore, the atrium and ventricle in each species had distinct gene function clusters, suggesting an evolutionary differentiation of cardiac chambers in mollusks. Finally, to explore the relationship between vertebrate and invertebrate two-chambered hearts, we compared our transcriptomic data with published data from the zebrafish, a well-studied vertebrate model with a two-chambered heart. Our analysis indicated a functional similarity of ventricular genes between the mollusks and the zebrafish, suggesting that the ventricle was differentiated to achieve the same functions in invertebrates and vertebrates. As the first such study on protostomes, our findings offered initial insights into how the two-chambered heart arose, including a possible understanding of its occurrence in both protostomes and deuterostomes. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00202-0.
Collapse
Affiliation(s)
- Meina Lu
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education) and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- College of Fisheries, Ocean University of China, Qingdao, 266003 China
| | - Rabia Hayat
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education) and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Xuejiao Zhang
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education) and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- College of Fisheries, Ocean University of China, Qingdao, 266003 China
| | - Yaqi Jiao
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education) and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Jianyun Huang
- College of Fisheries, Ocean University of China, Qingdao, 266003 China
| | - Yifan Huangfu
- College of Fisheries, Ocean University of China, Qingdao, 266003 China
| | - Mingcan Jiang
- College of Fisheries, Ocean University of China, Qingdao, 266003 China
| | - Jieyi Fu
- College of Fisheries, Ocean University of China, Qingdao, 266003 China
| | - Qingqiu Jiang
- College of Fisheries, Ocean University of China, Qingdao, 266003 China
| | - Yaojia Gu
- College of Fisheries, Ocean University of China, Qingdao, 266003 China
| | - Shi Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- Fang Zongxi Centre for Marine EvoDevo and MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Alexander A. Akerberg
- Division of Basic and Translational Cardiovascular Research, Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115 USA
- Harvard Medical School, Boston, MA 02115 USA
| | - Ying Su
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education) and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Long Zhao
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education) and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- College of Fisheries, Ocean University of China, Qingdao, 266003 China
| |
Collapse
|
5
|
Smith CH, Mejia-Trujillo R, Breton S, Pinto BJ, Kirkpatrick M, Havird JC. Mitonuclear sex determination? Empirical evidence from bivalves. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.05.547839. [PMID: 37461691 PMCID: PMC10349986 DOI: 10.1101/2023.07.05.547839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
Genetic elements encoded in nuclear DNA determine the sex of an individual in many animals. In bivalves, however, mitochondrial DNA (mtDNA) has been hypothesized to contribute to sex determination in lineages that possess doubly uniparental inheritance (DUI). In these cases, females transmit a female mtDNA (F mtDNA) to all offspring, while male mtDNA (M mtDNA) is transmitted only from fathers to sons. Because M mtDNA is inherited in the same way as Y chromosomes, it has been hypothesized that mtDNA may be responsible for sex determination. However, the role of mitochondrial and nuclear genes in sex determination has yet to be validated in DUI bivalves. In this study, we used DNA, RNA, and mitochondrial short non-coding RNA (sncRNA) sequencing to explore the role of mitochondrial and nuclear elements in the sexual development pathway of the freshwater mussel Potamilus streckersoni (Bivalvia: Unionida). We found that the M mtDNA shed a sncRNA partially within a male-specific mitochondrial gene that targeted pathways hypothesized to be involved in female development and mitophagy. RNA-seq confirmed the gene target was significantly upregulated in females, supporting a direct role of mitochondrial sncRNAs in gene silencing. These findings support the hypothesis that M mtDNA inhibits female development. Genome-wide patterns of genetic differentiation and heterozygosity did not support a nuclear sex determining region, although we cannot reject that nuclear factors are involved with sex determination. Our results provide further evidence that mitochondrial loci contribute to diverse, non-respiratory functions and provide a first glimpse into an unorthodox sex determining system.
Collapse
Affiliation(s)
- Chase H. Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | | | - Sophie Breton
- Department of Biological Sciences, University of Montreal, Montreal, Canada
| | - Brendan J. Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI USA
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Justin C. Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| |
Collapse
|
6
|
Zhang Y, He K, Guo X, Jiang J, Qian L, Xu J, Che Z, Huang X, Liu S. Transcriptomic Profiling of Fusarium pseudograminearum in Response to Carbendazim, Pyraclostrobin, Tebuconazole, and Phenamacril. J Fungi (Basel) 2023; 9:jof9030334. [PMID: 36983502 PMCID: PMC10057576 DOI: 10.3390/jof9030334] [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: 01/12/2023] [Revised: 02/09/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023] Open
Abstract
Fusarium pseudograminearum has been identified as a significant pathogen. It causes Fusarium crown rot (FCR), which occurs in several major wheat-producing areas in China. Chemical control is the primary measure with which to control this disease. In this study, transcriptome sequencing (RNA-Seq) was used to determine the different mechanisms of action of four frequently used fungicides including carbendazim, pyraclostrobin, tebuconazole, and phenamacril on F. pseudograminearum. In brief, 381, 1896, 842, and 814 differentially expressed genes (DEGs) were identified under the carbendazim, pyraclostrobin, tebuconazole, and phenamacril treatments, respectively. After the joint analysis, 67 common DEGs were obtained, and further functional analysis showed that the ABC transported pathway was significantly enriched. Moreover, FPSE_04130 (FER6) and FPSE_11895 (MDR1), two important ABC multidrug transporter genes whose expression levels simultaneously increased, were mined under the different treatments, which unambiguously demonstrated the common effects. In addition, Mfuzz clustering analysis and WGCNA analysis revealed that the core DEGs are involved in several critical pathways in each of the four treatment groups. Taken together, these genes may play a crucial function in the mechanisms of F. pseudograminearum's response to the fungicides stress.
Collapse
Affiliation(s)
- Yuan Zhang
- Department of Plant Protection, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China
| | - Kai He
- National Key Laboratory of Veterinary Public Health Security and School of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Xuhao Guo
- Department of Plant Protection, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China
| | - Jia Jiang
- Department of Plant Protection, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China
| | - Le Qian
- Department of Plant Protection, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China
| | - Jianqiang Xu
- Department of Plant Protection, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China
| | - Zhiping Che
- Department of Plant Protection, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China
| | - Xiaobo Huang
- Department of Plant Protection, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China
| | - Shengming Liu
- Department of Plant Protection, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China
| |
Collapse
|
7
|
Liao L, Yao Z, Kong J, Zhang X, Li H, Chen W, Xie Q. Transcriptomic analysis reveals the dynamic changes of transcription factors during early development of chicken embryo. BMC Genomics 2022; 23:825. [PMID: 36513979 PMCID: PMC9746114 DOI: 10.1186/s12864-022-09054-x] [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: 07/12/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The transition from fertilized egg to embryo in chicken requires activation of hundreds of genes that were mostly inactivated before fertilization, which is accompanied with various biological processes. Undoubtedly, transcription factors (TFs) play important roles in regulating the changes in gene expression pattern observed at early development. However, the contribution of TFs during early embryo development of chicken still remains largely unknown that need to be investigated. Therefore, an understanding of the development of vertebrates would be greatly facilitated by study of the dynamic changes in transcription factors during early chicken embryo. RESULTS In the current study, we selected five early developmental stages in White Leghorn chicken, gallus gallus, for transcriptome analysis, cover 17,478 genes with about 807 million clean reads of RNA-sequencing. We have compared global gene expression patterns of consecutive stages and noted the differences. Comparative analysis of differentially expressed TFs (FDR < 0.05) profiles between neighboring developmental timepoints revealed significantly enriched biological categories associated with differentiation, development and morphogenesis. We also found that Zf-C2H2, Homeobox and bHLH were three dominant transcription factor families that appeared in early embryogenesis. More importantly, a TFs co-expression network was constructed and 16 critical TFs were identified. CONCLUSION Our findings provide a comprehensive regulatory framework of TFs in chicken early embryo, revealing new insights into alterations of chicken embryonic TF expression and broadening better understanding of TF function in chicken embryogenesis.
Collapse
Affiliation(s)
- Liqin Liao
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,grid.484195.5Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, Guangzhou, 510642 China ,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642 P. R. China ,Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, Guangdong 510642 P. R. China
| | - Ziqi Yao
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,grid.484195.5Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, Guangzhou, 510642 China
| | - Jie Kong
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,grid.484195.5Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, Guangzhou, 510642 China ,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642 P. R. China
| | - Xinheng Zhang
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,grid.484195.5Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, Guangzhou, 510642 China ,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642 P. R. China
| | - Hongxin Li
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,grid.484195.5Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, Guangzhou, 510642 China ,Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, Guangdong 510642 P. R. China
| | - Weiguo Chen
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642 P. R. China
| | - Qingmei Xie
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,grid.484195.5Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, Guangzhou, 510642 China ,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642 P. R. China ,Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, Guangdong 510642 P. R. China
| |
Collapse
|
8
|
Li Y, Liu L, Zhang L, Wei H, Wu S, Liu T, Shu Y, Yang Y, Yang Z, Wang S, Bao Z, Zhang L. Dynamic transcriptome analysis reveals the gene network of gonadal development from the early history life stages in dwarf surfclam Mulinia lateralis. Biol Sex Differ 2022; 13:69. [PMID: 36461090 PMCID: PMC9716669 DOI: 10.1186/s13293-022-00479-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 11/20/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Gonadal development is driven by a complex genetic cascade in vertebrates. However, related information remains limited in molluscs owing to the long generation time and the difficulty in maintaining whole life cycle in the lab. The dwarf surfclam Mulinia lateralis is considered an ideal bivalve model due to the short generation time and ease to breed in the lab. RESULTS To gain a comprehensive understanding of gonadal development in M. lateralis, we conducted a combined morphological and molecular analysis on the gonads of 30 to 60 dpf. Morphological analysis showed that gonad formation and sex differentiation occur at 35 and 40-45 dpf, respectively; then the gonads go through gametogenic cycle. Gene co-expression network analysis on 40 transcriptomes of 35-60 dpf gonads identifies seven gonadal development-related modules, including two gonad-forming modules (M6, M7), three sex-specific modules (M14, M12, M11), and two sexually shared modules (M15, M13). The modules participate in different biological processes, such as cell communication, glycan biosynthesis, cell cycle, and ribosome biogenesis. Several hub transcription factors including SOX2, FOXZ, HSFY, FOXL2 and HES1 are identified. The expression of top hub genes from sex-specific modules suggests molecular sex differentiation (35 dpf) occurs earlier than morphological sex differentiation (40-45 dpf). CONCLUSION This study provides a deep insight into the molecular basis of gonad formation, sex differentiation and gametogenesis in M. lateralis, which will contribute to a comprehensive understanding of the reproductive regulation network in molluscs.
Collapse
Affiliation(s)
- Yajuan Li
- grid.4422.00000 0001 2152 3263MOE Key Laboratory of Marine Genetics and Breeding & Sars-Fang Centre, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Liangjie Liu
- grid.4422.00000 0001 2152 3263MOE Key Laboratory of Marine Genetics and Breeding & Sars-Fang Centre, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Lijing Zhang
- grid.4422.00000 0001 2152 3263MOE Key Laboratory of Marine Genetics and Breeding & Sars-Fang Centre, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Huilan Wei
- grid.4422.00000 0001 2152 3263MOE Key Laboratory of Marine Genetics and Breeding & Sars-Fang Centre, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Shaoxuan Wu
- grid.4422.00000 0001 2152 3263MOE Key Laboratory of Marine Genetics and Breeding & Sars-Fang Centre, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Tian Liu
- grid.4422.00000 0001 2152 3263MOE Key Laboratory of Marine Genetics and Breeding & Sars-Fang Centre, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Ya Shu
- grid.4422.00000 0001 2152 3263MOE Key Laboratory of Marine Genetics and Breeding & Sars-Fang Centre, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Yaxin Yang
- grid.4422.00000 0001 2152 3263MOE Key Laboratory of Marine Genetics and Breeding & Sars-Fang Centre, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Zujing Yang
- grid.4422.00000 0001 2152 3263MOE Key Laboratory of Marine Genetics and Breeding & Sars-Fang Centre, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Shi Wang
- grid.4422.00000 0001 2152 3263MOE Key Laboratory of Marine Genetics and Breeding & Sars-Fang Centre, Ocean University of China, 5 Yushan Road, Qingdao, China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Biology and Biotechnology & Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China ,grid.4422.00000 0001 2152 3263Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Zhenmin Bao
- grid.4422.00000 0001 2152 3263MOE Key Laboratory of Marine Genetics and Breeding & Sars-Fang Centre, Ocean University of China, 5 Yushan Road, Qingdao, China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Biology and Biotechnology & Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China ,grid.4422.00000 0001 2152 3263Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Lingling Zhang
- grid.4422.00000 0001 2152 3263MOE Key Laboratory of Marine Genetics and Breeding & Sars-Fang Centre, Ocean University of China, 5 Yushan Road, Qingdao, China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Biology and Biotechnology & Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| |
Collapse
|
9
|
Zeng Q, Hu B, Blanco AH, Zhang W, Zhao D, Martínez P, Hong Y. Full-Length Transcriptome Sequences Provide Insight Into Hermaphroditism of Freshwater Pearl Mussel Hyriopsis schlegelii. Front Genet 2022; 13:868742. [PMID: 35401664 PMCID: PMC8987123 DOI: 10.3389/fgene.2022.868742] [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: 02/03/2022] [Accepted: 02/24/2022] [Indexed: 11/13/2022] Open
Abstract
The freshwater mussel Hyriopsis schlegelii is a cultured bivalve in China, and the quality of the pearls produced is affected by the type of gonads. However, because of the lack of a published genome and the complexity of sex determination, research on sex reversal and development of this species is limited. In this study, Illumina RNA-seq and PacBio Isoform Sequencing (Iso-Seq) were combined to analyze the gonads of H. schlegelii. A total of 201,481 high-quality transcripts were generated. The study identified 7,922 differentially expressed genes in three comparison group (females versus males, hermaphrodites versus females, and hermaphrodites versus males). Twenty-four genes were identified as potential sex-related genes, including sox9 and wnt4 involved in sex determination, and vtg, cyp17a1 and 17β-hsd2 involved in gonadal development. We also speculated a possible pathways for the formation of hermaphroditism in H. schlegelii. The data provide a clear view of the transcriptome for H. schlegelii gonads and will be valuable in elucidating the mechanisms of gonad development.
Collapse
Affiliation(s)
- Qi Zeng
- School of Life Sciences, Nanchang University, Nanchang, China
- Key Lab of Aquatic Resources and Utilization of Jiangxi, Nanchang, China
| | - Beijuan Hu
- School of Life Sciences, Nanchang University, Nanchang, China
- Key Lab of Aquatic Resources and Utilization of Jiangxi, Nanchang, China
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang, China
| | - Andres Hortas Blanco
- Department of Zoology Genetics and Physical Anthropology, Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain
| | - Wanchang Zhang
- School of Life Sciences, Nanchang University, Nanchang, China
- Key Lab of Aquatic Resources and Utilization of Jiangxi, Nanchang, China
| | - Daxian Zhao
- School of Life Sciences, Nanchang University, Nanchang, China
- Key Lab of Aquatic Resources and Utilization of Jiangxi, Nanchang, China
| | - Paulino Martínez
- Department of Zoology Genetics and Physical Anthropology, Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain
| | - Yijiang Hong
- School of Life Sciences, Nanchang University, Nanchang, China
- Key Lab of Aquatic Resources and Utilization of Jiangxi, Nanchang, China
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang, China
- *Correspondence: Yijiang Hong,
| |
Collapse
|
10
|
Evensen KG, Robinson WE, Krick K, Murray HM, Poynton HC. Comparative phylotranscriptomics reveals putative sex differentiating genes across eight diverse bivalve species. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 41:100952. [PMID: 34952324 DOI: 10.1016/j.cbd.2021.100952] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Mollusks, especially bivalves, exhibit a great diversity of sex determining mechanisms, including both genetic and environmental sex determination. Some bivalve species can be gonochoristic (separate sexes), while others are hermaphroditic (sequential or simultaneous). Several models have been proposed for specific bivalve species, utilizing information gained from gene expression data, as well as limited RAD-seq data (e.g., from Crassostrea gigas). However, these mechanisms are not as well studied as those in model organisms (e.g., Mus musculus, Drosophila melanogaster, Caenorhabditis elegans) and many genes involved in sex differentiation are not well characterized. We used phylotranscriptomics to better understand which possible sex differentiating genes are in bivalves and how these genes relate to similar genes in diverse phyla. We collected RNAseq data from eight phylogenetically diverse bivalve species: Argopecten irradians, Ensis directus, Geukensia demissa, Macoma tenta, Mercenaria mercenaria, Mya arenaria, Mytilus edulis, and Solemya velum. Using these data, we assembled representative transcriptomes for each species. We then searched for candidate sex differentiating genes using BLAST and confirmed the identity of nine genes using phylogenetics analyses from nine phyla. To increase the confidence of identification, we included ten bivalve genomes in our analyses. From the analysis of doublesex and mab-3 related transcription factor (DMRT) genes, we confirmed the identify of a Mollusk-specific sex determining DMRT gene: DMRT1L. Based on gene expression data from M. edulis and previous research, DMRT1L and FoxL2 are key genes for male and female development, respectively.
Collapse
Affiliation(s)
- K Garrett Evensen
- School for the Environment, University of Massachusetts Boston, 100 William T Morrissey Blvd, Boston, MA 02125, United States of America
| | - William E Robinson
- School for the Environment, University of Massachusetts Boston, 100 William T Morrissey Blvd, Boston, MA 02125, United States of America
| | - Keegan Krick
- School for the Environment, University of Massachusetts Boston, 100 William T Morrissey Blvd, Boston, MA 02125, United States of America
| | - Harry M Murray
- Department of Fisheries and Oceans Canada, 80 East White Hills Road, St John's, NL A1C 5X1, Canada
| | - Helen C Poynton
- School for the Environment, University of Massachusetts Boston, 100 William T Morrissey Blvd, Boston, MA 02125, United States of America.
| |
Collapse
|
11
|
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]
|
12
|
Zheng L, Gu X, Zheng G, Li X, He M, Liu L, Zhou X. Prediction of early recurrence and response to adjuvant Sorafenib for hepatocellular carcinoma after resection. PeerJ 2021; 9:e12554. [PMID: 34900444 PMCID: PMC8628622 DOI: 10.7717/peerj.12554] [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: 05/20/2021] [Accepted: 11/05/2021] [Indexed: 01/27/2023] Open
Abstract
Background Early recurrence of hepatocellular carcinoma (HCC) is a major obstacle to improving the prognosis, and no widely accepted adjuvant therapy guideline for patients post-liver resection is available. Currently, all available methods and biomarkers are insufficient to accurately predict post-operation HCC patients’ risk of early recurrence and their response to adjuvant therapy. Methods In this study, we downloaded four gene expression datasets (GSE14520, GSE54236, GSE87630, and GSE109211) from the Gene Expression Omnibus database and identified 34 common differentially expressed genes associated with HCC dysregulation and response to adjuvant sorafenib. Then, we constructed a novel 11-messenger RNA predictive model by using ROC curves analysis, univariate Cox regression analysis, and LASSO Cox regression analysis. Furthermore, we validated the predictive values of the risk model in GSE14520 and TCGA-LIHC cohorts by using Kaplan–Meier survival analysis, multivariable Cox regression analysis, and decision curve analysis, respectively. Results The risk score model could identify patients with a high risk of HCC recurrence at the early stage and could predict the response of patients to adjuvant sorafenib. Patients with a high risk score had a worse recurrence rate in training cohorts (2-year: p < 0.0001, hazard ratio (HR): 4.658, confidence interval 95% CI [2.895–7.495]; 5-year: p < 0.0001, HR: 3.251, 95% CI [2.155–4.904]) and external validation cohorts (2-year: p < 0.001, HR: 3.65, 95% CI [2.001–6.658]; 5-year: p < 0.001, HR: 3.156, 95% CI [1.78–5.596]). The AUC values of the risk score model for predicting tumor early recurrence were 0.746 and 0.618, and that of the risk score model for predicting the response to adjuvant sorafenib were 0.722 and 0.708 in the different cohort, respectively. Multivariable Cox regression analysis and decision curve analysis also showed that the risk score model was superior to and independent of other clinicopathologic characteristics. Moreover, the risk score model had excellent abilities to predict the overall survival and HCC recurrence of patients with the same tumor stage category. Conclusions Our risk model is a reliable and superior predictive tool. With this model, we could optimize the risk stratification based on early tumor recurrence and could evaluate the response of patients to adjuvant sorafenib after liver resection.
Collapse
Affiliation(s)
- Liming Zheng
- Central Laboratory, The Third People's Hospital of Changzhou, Changzhou, China
| | - Xi Gu
- Department of General Surgery, The Third People's Hospital of Changzhou, Changzhou, China
| | - Guojun Zheng
- Central Laboratory, The Third People's Hospital of Changzhou, Changzhou, China
| | - Xin Li
- Central Laboratory, The Third People's Hospital of Changzhou, Changzhou, China
| | - Meifang He
- Central Laboratory, The Third People's Hospital of Changzhou, Changzhou, China
| | - Longgen Liu
- Central Laboratory, The Third People's Hospital of Changzhou, Changzhou, China
| | - Xike Zhou
- Clinical Lab, Wuxi No. 5 People's Hospital, Wuxi, China
| |
Collapse
|
13
|
Wang YY, Duan SH, Wang GL, Li JL. Integrated mRNA and miRNA expression profile analysis of female and male gonads in Hyriopsis cumingii. Sci Rep 2021; 11:665. [PMID: 33436779 PMCID: PMC7804246 DOI: 10.1038/s41598-020-80264-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/18/2020] [Indexed: 01/29/2023] Open
Abstract
Hyriopsis cumingii is an important species for freshwater pearl cultivation in China. In terms of pearl production, males have larger pearls and better glossiness than females, but there are few reports focusing on the sex of H. cumingii. In this study, six mRNA and six microRNA (miRNA) libraries were prepared from ovaries and testes. Additionally, 28,502 differentially expressed genes (DEGs) and 32 differentially expressed miRNAs (DEMs) were identified. Compared with testis, 14,360 mRNAs and 20 miRNAs were up-regulated in ovary, 14,142 mRNAs and 12 miRNAs were down-regulated. In DEGs, the known genes related to sex determinism and/or differentiation were also identified, such as DMRT1, SOX9, SF1 for males, FOXL2 for females, and other potentially significant candidate genes. Three sex-related pathways have also been identified, which are Wnt, Notch, and TGF-beta. In 32 DEMs, the three miRNAs (miR-9-5p, miR-92, miR-184) were paid more attention, they predicted 28 target genes, which may also be candidates for sex-related miRNAs and genes. Differential miRNAs target genes analysis reveals the pathway associated with oocyte meiosis and spermatogenesis. Overall, the findings of the study provide significant insights to enhance our understanding of sex differentiation and/or sex determination mechanisms for H. cumingii.
Collapse
Affiliation(s)
- Ya-Yu Wang
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306 China ,National Demonstration Center for Experimental Fisheries Science Education, Shanghai, 201306 China ,Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306 China
| | - Sheng-Hua Duan
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306 China ,National Demonstration Center for Experimental Fisheries Science Education, Shanghai, 201306 China ,Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306 China
| | - Gui-Ling Wang
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306 China ,National Demonstration Center for Experimental Fisheries Science Education, Shanghai, 201306 China ,Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306 China
| | - Jia-Le Li
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306 China ,National Demonstration Center for Experimental Fisheries Science Education, Shanghai, 201306 China ,Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306 China
| |
Collapse
|
14
|
Li J, Zhou Y, Zhou Z, Lin C, Wei J, Qin Y, Xiang Z, Ma H, Zhang Y, Zhang Y, Yu Z. Comparative transcriptome analysis of three gonadal development stages reveals potential genes involved in gametogenesis of the fluted giant clam (Tridacna squamosa). BMC Genomics 2020; 21:872. [PMID: 33287701 PMCID: PMC7720611 DOI: 10.1186/s12864-020-07276-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 11/24/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Gonad development and differentiation is an essential function for all sexually reproducing species, and many aspects of these developmental processes are highly conserved among the metazoa. However, the mechanisms underlying gonad development and gametogenesis remain unclear in Tridacna squamosa, a large-size bivalve of great ecological value. They are protandrous simultaneous hermaphrodites, with the male gonad maturing first, eventually followed by the female gonads. In this study, nine gonad libraries representing resting, male and hermaphrodite stages in T. squamosa were performed to identify the molecular mechanisms. RESULTS Sixteen thousand four hundred ninety-one unigenes were annotated in the NCBI non-redundant protein database. Among the annotated unigenes, 5091 and 7328 unigenes were assigned to Gene Ontology categories and the Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway database, respectively. A total of 4763 differentially expressed genes (DEGs) were identified by comparing male to resting gonads, consisting of 3499 which were comparatively upregulated in males and 1264 which were downregulated in males. Six hundred-ninteen DEGs between male and hermaphroditic gonads were identified, with 518 DEGs more strongly expressed in hermaphrodites and 101 more strongly expressed in males. GO (Gene Ontology) and KEGG pathway analyses revealed that various biological functions and processes, including functions related to the endocrine system, oocyte meiosis, carbon metabolism, and the cell cycle, were involved in regulating gonadal development and gametogenesis in T. squamosa. Testis-specific serine/threonine kinases 1 (TSSK1), TSSK4, TSSK5, Doublesex- and mab-3-related transcription factor 1 (DMRT1), SOX, Sperm surface protein 17 (SP17) and other genes were involved in male gonadal development in Tridacna squamosal. Both spermatogenesis- (TSSK4, spermatogenesis-associated protein 17, spermatogenesis-associated protein 8, sperm motility kinase X, SP17) and oogenesis-related genes (zona pellucida protein, Forkhead Box L2, Vitellogenin, Vitellogenin receptor, 5-hydroxytryptamine, 5-hydroxytryptamine receptor) were simultaneously highly expressed in the hermaphroditic gonad to maintain the hermaphroditism of T. squamosa. CONCLUSION All these results from our study will facilitate better understanding of the molecular mechanisms underlying giant clam gonad development and gametogenesis, which can provided a base on obtaining excellent gametes during the seed production process for giant clams.
Collapse
Affiliation(s)
- Jun Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301, China
- Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya Institute of Oceanology Chinese Academy of Sciences, Sanya, 572024, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Yinyin Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301, China
- Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya Institute of Oceanology Chinese Academy of Sciences, Sanya, 572024, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zihua Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301, China
- Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya Institute of Oceanology Chinese Academy of Sciences, Sanya, 572024, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chuanxu Lin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China
| | - Jinkuan Wei
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301, China
- Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya Institute of Oceanology Chinese Academy of Sciences, Sanya, 572024, China
| | - Yanpin Qin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301, China
- Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya Institute of Oceanology Chinese Academy of Sciences, Sanya, 572024, China
| | - Zhiming Xiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301, China
- Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya Institute of Oceanology Chinese Academy of Sciences, Sanya, 572024, China
| | - Haitao Ma
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301, China
- Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya Institute of Oceanology Chinese Academy of Sciences, Sanya, 572024, China
| | - Yang Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301, China
- Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya Institute of Oceanology Chinese Academy of Sciences, Sanya, 572024, China
| | - Yuehuan Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301, China.
- Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya Institute of Oceanology Chinese Academy of Sciences, Sanya, 572024, China.
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China.
| | - Ziniu Yu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301, China.
- Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya Institute of Oceanology Chinese Academy of Sciences, Sanya, 572024, China.
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
15
|
Li YL, Xing TF, Liu JX. Genome-wide association analyses based on whole-genome sequencing of Protosalanx hyalocranius provide insights into sex determination of Salangid fishes. Mol Ecol Resour 2020; 20:1038-1049. [PMID: 32315505 DOI: 10.1111/1755-0998.13172] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 03/28/2020] [Accepted: 04/09/2020] [Indexed: 12/22/2022]
Abstract
Identification of sex determination system and sex-determining genes have important implications in conservation, ecology and evolution. However, much remains to be discovered about the evolution of different sexual determination systems in teleost fishes, of which the mechanisms of sex determination are remarkably variable. In the present study, the whole genomes of 20 males and 20 females of a Salangid fish, Protosalanx hyalocranius, were sequenced and genome wide association analyses were conducted to uncover its sex determination system and putative sex-determining genes. A total of 150 SNPs were significantly associated with sex, which showed high differentiation between sexes (FST ranged from 0.245 to 0.556). Of the 150 sex-associated SNPs, 76 SNPs displayed sex specificity with even coverage of depth and were female heterogametic, which suggested a ZZ/ZW sex determination system. Interestingly, one scaffold containing sex-specific SNPs displayed synteny to the sex chromosome of medaka. Annotations of sex-associated loci suggested that both transcriptional regulators (e.g., FOX genes) and secreted hormones and their receptors might be involved in the sex determination/differentiation of P. hyalocranius. More strikingly, we found a nonsense mutation in one copy of GALNT homology gene of all females, which suggested that "Z dosage" effect might play a vital role in the processes of sex determination/differentiation. These sex-specific loci could be a valuable resource for further research on sex determination of Salangid fishes and the results could contribute to the understanding of sex determination mechanisms and the evolution of sex chromosome in teleost fishes.
Collapse
Affiliation(s)
- Yu-Long Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Teng-Fei Xing
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jin-Xian Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| |
Collapse
|