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Chen S, Zhao M, Chen K, Xu J, Li H. A Network of Circular RNA and MicroRNA Sequencing Provides Insights into Pigment Deposition of Changshun Blue Eggshell Chickens. Genes (Basel) 2024; 15:812. [PMID: 38927747 PMCID: PMC11202489 DOI: 10.3390/genes15060812] [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: 05/24/2024] [Revised: 06/17/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Eggshell color plays important biological roles and attracts the attention of both egg retailers and researchers. However, whether non-coding RNAs are involved in pigment deposition among different eggshell colors remains unknown. In this study, RNA sequencing was used to analyse the uterine gland transcriptome (CircRNA and miRNA) of Changshun chicken blue-shell hens producing four different eggshell color eggs including dark blue PK(DB) and light blue (LB), dark brown and greenish (between blue and pink, DP) and pink (p). We found that miR-192-x, targeting SLC16a7, was expressed in DB, DP, and LB groups compared with the PK group, which indicates that miR-192-x may play a role in the blue eggshell color. KEGG and GO analyses showed that the "metabolic pathways" with targeted genes such BLVRA and HMOX1 were detected in dark and light blue color eggshell chickens, which confirms the different ratios of biliverdin and HO-1 involved in the deposition of blue color. As annotated by connectivity analysis, RASGRF1 and RASGRF2, belonging to the RASGRF family, are involved in the Ras signaling pathway, which plays an important role in cell growth, differentiation, metastasis and apoptosis. Our findings enrich the database of circRNA, miRNAs and genes for chicken uterine tissue, which will be useful in accelerating molecular selection for blue eggshell color layers.
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Affiliation(s)
| | | | | | | | - Hua Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528231, China
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Zhao L, Xue H, Elumalai P, Zhu X, Wang L, Zhang K, Li D, Ji J, Luo J, Cui J, Gao X. Sublethal acetamiprid affects reproduction, development and disrupts gene expression in Binodoxys communis. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024:10.1007/s11356-024-33415-6. [PMID: 38656721 DOI: 10.1007/s11356-024-33415-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 04/17/2024] [Indexed: 04/26/2024]
Abstract
At present, understanding of neonicotinoid toxicity in arthropods remains limited. We here evaluated the lethal and sublethal effects of acetamiprid in F0 and F1 generations of Binodoxys communis using a range of sublethal concentrations. The 10% lethal concentration (LC10) and half lethal concentration (LC25) of ACE had negative effects on the B. communis survival rate, adult longevity, parasitism rate, and emergence rate, and significantly prolonged the duration of the developmental cycle. ACE also had intergenerational effects, with some biological indices affected in the F1 generation after pesticide exposure. Transcriptomic analysis demonstrated that differentially expressed genes were enriched in specific pathways including the amino acid metabolism, carbohydrate metabolism, energy metabolism, exogenous metabolism, signal transduction, and glutathione metabolism pathways. These results indicated strong contact toxicity of ACE to B. communis, which may inhibit their biological control capacity. These results improve our understanding of the toxicological mechanisms of parasitic natural enemies in response to insecticide exposure.
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Affiliation(s)
- Likang Zhao
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Hui Xue
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Punniyakotti Elumalai
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Xiangzhen Zhu
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Li Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Kaixin Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Dongyang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Jichao Ji
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Junyu Luo
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Jinjie Cui
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Xueke Gao
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
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Zou Y, Zhang Y, Wu D, Lu Z, Xiao J, Huang H, Fu Q, Guo Z. Multi-omics analysis revealed the differences in lipid metabolism of the gut between adult and juvenile yellowfin tuna ( Thunnus albacares). Front Microbiol 2024; 14:1326247. [PMID: 38274759 PMCID: PMC10808786 DOI: 10.3389/fmicb.2023.1326247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
Introduction Tuna has a cost-effective energy supply to support the regional endothermic and high-speed swimming performance. The gut symbiotic microbiotas and their metabolites play essential roles in tuna's diet digestion, absorption, and energy acquirement, which are often highly related to the ontogenetic development of tuna. Methods We compared gut microbial compositions and metabolites, as well as mRNA expression of the intestine between juvenile and adult yellowfin tuna using 16S rRNA sequencing, metabolomic and transcriptomic, respectively. Results and discussion The results revealed that adults had a significantly higher microbial diversity and abundance of Acinetobacter than juveniles. Regarding the gut microbiota-derived metabolites, fatty acids, especially glycerophospholipid and sphingolipid, were significantly enriched in adults than in juveniles. Moreover, the short-chain fatty acid (butyrate and isobutyrate) contents were significantly higher in adults than in juveniles. To find the relationship between gut microbiotas and host physiology, intestinal transcriptome analysis demonstrated that the enriched pathways of differential expression genes (DEGs) in adult tuna were the lipid metabolism pathway, including "fat digestion and absorption," "cholesterol metabolism," "steroid hormone biosynthesis," "glycerolipid metabolism," and "glycerophospholipid metabolism." However, protein digestion and absorption and pancreatic secretion pathways were significantly enriched in the juveniles. The conjoint analysis indicated that the enriched pathways of both differential metabolites (DMs) and DEGs were remarkably related to the regulation of glycerophospholipids metabolism in adult tunas. This study highlights the role of gut microbiotas in fish nutrition metabolism. These findings provide new insights into the view of ontogenetic shifts of gut microbiotas and their metabolites on host health and gut function in endothermic and high-speed swimming marine fish species.
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Affiliation(s)
- Ying Zou
- School of Life and Health Sciences, School of Marine Science and Engineering, School of Food Science and Engineering, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Yanjie Zhang
- School of Life and Health Sciences, School of Marine Science and Engineering, School of Food Science and Engineering, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Di Wu
- School of Life and Health Sciences, School of Marine Science and Engineering, School of Food Science and Engineering, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Zhiyuan Lu
- School of Life and Health Sciences, School of Marine Science and Engineering, School of Food Science and Engineering, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Juan Xiao
- School of Life and Health Sciences, School of Marine Science and Engineering, School of Food Science and Engineering, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Hai Huang
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, China
| | - Qiongyao Fu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Control of Tropical Diseases, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
| | - Zhiqiang Guo
- School of Life and Health Sciences, School of Marine Science and Engineering, School of Food Science and Engineering, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
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Deng ZC, Yang JC, Huang YX, Zhao L, Zheng J, Xu QB, Guan L, Sun LH. Translocation of gut microbes to epididymal white adipose tissue drives lipid metabolism disorder under heat stress. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2877-2895. [PMID: 37480471 DOI: 10.1007/s11427-022-2320-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 03/08/2023] [Indexed: 07/24/2023]
Abstract
Heat stress induces multi-organ damage and serious physiological dysfunction in mammals, and gut bacteria may translocate to extra-intestinal tissues under heat stress pathology. However, whether gut bacteria translocate to the key metabolic organs and impair function as a result of heat stress remains unknown. Using a heat stress-induced mouse model, heat stress inhibited epididymal white adipose tissue (eWAT) expansion and induced lipid metabolic disorder but did not damage other organs, such as the heart, liver, spleen, or muscle. Microbial profiling analysis revealed that heat stress shifted the bacterial community in the cecum and eWAT but not in the inguinal white adipose tissue, blood, heart, liver, spleen, or muscle. Notably, gut-vascular barrier function was impaired, and the levels of some bacteria, particularly Lactobacillus, were higher in the eWAT, as confirmed by catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) staining when mice were under heat stress. Moreover, integrated multi-omics analysis showed that the eWAT microbiota was associated with host lipid metabolism, and the expression of genes involved in the lipid metabolism in eWAT was upregulated under heat stress. A follow-up microbial supplementation study after introducing Lactobacillus plantarum to heat-stressed mice revealed that the probiotic ameliorated heat stress-induced loss of eWAT and dyslipidemia and reduced gut bacterial translocation to the eWAT by improving gut barrier function. Overall, our findings suggest that gut bacteria, particularly Lactobacillus spp., play a crucial role in heat stress-induced lipid metabolism disorder and that there is therapeutic potential for using probiotics, such as Lactobacillus plantarum.
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Affiliation(s)
- Zhang-Chao Deng
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jia-Cheng Yang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yu-Xuan Huang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ling Zhao
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qing-Biao Xu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Leluo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Lv-Hui Sun
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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Cao Y, Li J, Qiu S, Ni S, Duan Y. ACSM5 inhibits ligamentum flavum hypertrophy by regulating lipid accumulation mediated by FABP4/PPAR signaling pathway. Biol Direct 2023; 18:75. [PMID: 37957699 PMCID: PMC10644428 DOI: 10.1186/s13062-023-00436-z] [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: 08/18/2023] [Accepted: 11/05/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Ligamentum flavum (LF) hypertrophy is the main cause of lumbar spinal canal stenosis (LSCS). Previous studies have shown that LF hypertrophy tissue exhibits abnormal lipid accumulation, but the regulatory mechanism remains unclear. The objective of this study was to explore the function and potential mechanism of ACSM5 in LF lipid accumulation. METHODS To assess the ACSM5 expression levels, lipid accumulation and triglyceride (TG) level in LF hypertrophy and normal tissue, we utilized RT-qPCR, western blot, oil red O staining, and TG assay kit. The pearson correlation coefficient assay was used to analyze the correlation between ACSM5 levels and lipid accumulation or TG levels in LF hypertrophy tissue. The role of ACSM5 in free fatty acids (FFA)-induced lipid accumulation in LF cells was assessed in vitro, and the role of ACSM5 in LF hypertrophy in mice was verified in vivo. To investigate the underlying mechanisms of ACSM5 regulating lipid accumulation in LF, we conducted the mRNA sequencing, bioinformatics analysis, and rescue experiments. RESULTS In this study, we found that ACSM5, which was significantly down-regulated in LF tissues, correlated with lipid accumulation. In vitro cell experiments demonstrated that overexpression of ACSM5 significantly inhibited FFA-induced lipid accumulation and fibrosis in LF cells. In vivo animal experiments further confirmed that overexpression of ACSM5 inhibited LF thickening, lipid accumulation, and fibrosis. Mechanistically, ACSM5 inhibited lipid accumulation of LF cells by inhibiting FABP4-mediated PPARγ signaling pathway, thereby improving hypertrophy and fibrosis of LF. CONCLUSIONS our findings elucidated the important role of ACSM5 in the regulation of LF lipid accumulation and provide insight into potential therapeutic interventions for the treatment of LF hypertrophy. This study further suggested that therapeutic strategies targeting lipid deposition may be an effective potential approach to treat LF hypertrophy-induced LSCS.
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Affiliation(s)
- Yanlin Cao
- Department of Spine Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jianjun Li
- Department of Spine Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Sujun Qiu
- Department of Spine Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Songjia Ni
- Department of Orthopaedic Trauma, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yang Duan
- Department of Spine Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
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Song X, Lin Y, Zhang Y, Wang Z, Li X, Liu J, Jiang W, Chen J, Wu L, Rong J, Xu K, Wang G. Long-Term Tetrabromobisphenol A Exposure Induces Gut Microbiota Imbalance and Metabolic Disorders via the Peroxisome Proliferator-Activated Receptor Signaling Pathway in the Regenerated Gut of Apostichopus japonicus. BIOLOGY 2023; 12:1365. [PMID: 37997964 PMCID: PMC10669644 DOI: 10.3390/biology12111365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/08/2023] [Accepted: 10/12/2023] [Indexed: 11/25/2023]
Abstract
Tetrabromobisphenol A (TBBPA), a commonly utilized brominated flame retardant, is found in many types of abiotic and biotic matrices. TBBPA can increase oxidative stress, disrupt the endocrine system, cause neurodevelopmental disorders and activate peroxisome proliferator-activated receptors to modulate lipid deposits in aquatic animals. However, the toxic mechanism of TBBPA on the gut microbiota and intestinal health remains unclear. Apostichopus japonicus is an ideal model for studying the relationship between environmental contaminants and intestinal health due to its unique capacity for evisceration and quickly regenerated intestine. In the present study, we investigated the toxic mechanism of TBBPA on the gut microbiota and intestinal health in the regenerated intestine of A. japonicus. The results show that TBBPA exposure decreased the health of the regenerated intestine and the enzymatic activities, alpha diversity indices, and the relative abundance of the gut microbiota. Transcriptome analysis shows that TBBPA exposure affected lipid metabolism via the PPAR signaling pathway during the process of intestinal regeneration in A. japonicus, suggesting that TBBPA exposure can affect the composition and function of the gut microbiota and intestinal health in the regenerated intestine of A. japonicus. These results provide a basis for further research on the potential toxicity of TBBPA to the intestinal health in animals.
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Affiliation(s)
- Xiaojun Song
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Ying Lin
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Yinfeng Zhang
- College of Medicine, Qingdao University, Qingdao 266021, China
| | - Zi Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Xiaohan Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Jixiang Liu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Wenwen Jiang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Jianing Chen
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Linxuan Wu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Junjie Rong
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Kefeng Xu
- Marine Science Research Institute of Shandong Province, National Oceanographic Center, Qingdao 266104, China
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Guodong Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
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Song F, Wang CG, Mao JZ, Wang TL, Liang XL, Hu CW, Zhang Y, Han L, Chen Z. PANoptosis-based molecular subtyping and HPAN-index predicts therapeutic response and survival in hepatocellular carcinoma. Front Immunol 2023; 14:1197152. [PMID: 37398672 PMCID: PMC10311484 DOI: 10.3389/fimmu.2023.1197152] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/25/2023] [Indexed: 07/04/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) is a highly prevalent and fatal cancer. The role of PANoptosis, a novel form of programmed cell death, in HCC is yet to be fully understood. This study focuses on identifying and analyzing PANoptosis-associated differentially expressed genes in HCC (HPAN_DEGs), aiming to enhance our understanding of HCC pathogenesis and potential treatment strategies. Methods We analyzed HCC differentially expressed genes from TCGA and IGCG databases and mapped them to the PANoptosis gene set, identifying 69 HPAN_DEGs. These genes underwent enrichment analyses, and consensus clustering analysis was used to determine three distinct HCC subgroups based on their expression profiles. The immune characteristics and mutation landscape of these subgroups were evaluated, and drug sensitivity was predicted using the HPAN-index and relevant databases. Results The HPAN_DEGs were mainly enriched in pathways associated with the cell cycle, DNA damage, Drug metabolism, Cytokines, and Immune receptors. We identified three HCC subtypes (Cluster_1, SFN+PDK4-; Cluster_2, SFN-PDK4+; Cluster_3, SFN/PDK4 intermediate expression) based on the expression profiles of the 69 HPAN_DEGs. These subtypes exhibited distinct clinical outcomes, immune characteristics, and mutation landscapes. The HPAN-index, generated by machine learning using the expression levels of 69 HPAN_DEGs, was identified as an independent prognostic factor for HCC. Moreover, the high HPAN-index group exhibited a high response to immunotherapy, while the low HPAN-index group showed sensitivity to small molecule targeted drugs. Notably, we observed that the YWHAB gene plays a significant role in Sorafenib resistance. Conclusion This study identified 69 HPAN_DEGs crucial to tumor growth, immune infiltration, and drug resistance in HCC. Additionally, we discovered three distinct HCC subtypes and constructed an HPAN-index to predict immunotherapeutic response and drug sensitivity. Our findings underscore the role of YWHAB in Sorafenib resistance, presenting valuable insights for personalized therapeutic strategy development in HCC.
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Affiliation(s)
- Fei Song
- Department of Hepatobiliary Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Cheng-Gui Wang
- Department of Hepatobiliary Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Jia-Zhen Mao
- Department of Hepatobiliary Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Tian-Lun Wang
- Department of Hepatobiliary Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Xiao-Liang Liang
- Department of Hepatobiliary Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Chen-Wei Hu
- Department of Hepatobiliary Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Yu Zhang
- Department of Hepatobiliary Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Lu Han
- Jiangsu Vocational College of Medicine, Yancheng, China
| | - Zhong Chen
- Department of Hepatobiliary Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
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Peng F, Zhou L, Lu W, Gan R, Lu M, Li Z, Zhang X, Wang Y, Gui J. Genomic and Transcriptional Profiles of Kelch-like ( klhl) Gene Family in Polyploid Carassius Complex. Int J Mol Sci 2023; 24:8367. [PMID: 37176071 PMCID: PMC10179623 DOI: 10.3390/ijms24098367] [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: 12/14/2022] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Genome duplication supplies raw genetic materials and has been thought to be essential for evolutionary innovation and ecological adaptation. Here, we select Kelch-like (klhl) genes to study the evolution of the duplicated genes in the polyploid Carassius complex, including amphidiploid C. auratus and amphitriploid C. gibelio. Phylogenetic, chromosomal location and read coverage analyses indicate that most of Carassius klhl genes exhibit a 2:1 relationship with zebrafish orthologs and confirm two rounds of polyploidy, an allotetraploidy followed by an autotriploidy, occurred during Carassius evolution. The lineage-specific expansion and biased retention/loss of klhl genes are also found in Carassius. Transcriptome analyses across eight adult tissues and seven embryogenesis stages reveal varied expression dominance and divergence between the two species. The expression of klhls in response to Carassius herpesvirus 2 infection shows different expression changes corresponding to distinct herpesvirus resistances in three C. gibelio gynogenetic clones. Finally, we find that most C. gibelio klhl genes possess three alleles except eight genes that have lost one or two alleles due to genome rearrangement. The allele expression bias is prosperous for Cgklhl genes and varies during embryogenesis owning to the sequential expression manner of the alleles. The current study provides global insights into the genomic and transcriptional evolution of duplicated genes in a given superfamily resulting from multiple rounds of polyploidization.
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Affiliation(s)
- 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
| | - 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
| | - Weijia 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
| | - Ruihai Gan
- 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
| | - 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
| | - 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
| | - Xiaojuan 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
| | - 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
| | - Jianfang 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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9
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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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10
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Zhou YL, Wu JJ, Gong GR, Liu M, Li Z, Guo XF, Wei WY, Zhang XJ, Mei J, Zhou L, Wang ZW, Gui JF. Barbel regeneration and function divergence in red-tail catfish (Hemibagrus wyckioides) based on the chromosome-level genomes and comparative transcriptomes. Int J Biol Macromol 2023; 232:123374. [PMID: 36702216 DOI: 10.1016/j.ijbiomac.2023.123374] [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: 09/27/2022] [Revised: 01/04/2023] [Accepted: 01/13/2023] [Indexed: 01/24/2023]
Abstract
Catfish (Siluriformes) are one of the most diverse vertebrate orders and are characterized by whisker-like barbels, which are important sensory organs in most of teleosts. However, their specific biological functions are still unclear. Red-tail catfish (Hemibagrus wyckioides) is well-known catfish species with four pairs of barbels, of which the maxillary barbels reach two-thirds of the body length. In this study, a 776.58 Mb high-quality chromosome-level genome was assembled into 29 chromosomes. Comparative genome data indicated that the barbeled regeneration gene ccl33 has expanded into 11 tandemly duplicated copies. Transcriptome data revealed the functional differentiation of different barbels and suggested that the maxillary barbel might be necessary for water temperature perception. Taste receptor genes were also characterized in teleosts with different food habits. Selection pressures were revealed to affect the sugar-based solute transport domain of the sweet taste receptor gene t1r2 in carnivorous fishes. In addition, the bitter taste receptor gene t2r200 was found to be lost from the genomes of four catfish species. Therefore, our study provides a genomic foundation for understanding the regeneration and functional differentiation of barbels in red-tail catfish and also reveals novel insights into the feeding evolution of fish species with different feeding habits.
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Affiliation(s)
- Yu-Lin Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, University of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Jun-Jie Wu
- Yunnan Institute of Fishery Sciences Research, Kunming 650111, China
| | - Gao-Rui Gong
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Min Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, University of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, University of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xin-Feng Guo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, University of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Wen-Yu Wei
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, University of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, University of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Jie Mei
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, University of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhong-Wei Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, University of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, University of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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11
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Fan X, Guo J, Jia X, Mao X, Zhou Y, Wang Y, Guo X, Shen J, Huai N, Zhang K, Abdusalam A, Hu H, Zhu H, Jia C, Cheng L, Li X, Zhang Z. Reproductive Toxicity and Teratogenicity of Fluorene-9-bisphenol on Chinese Medaka ( Oryzias sinensis): A Study from Laboratory to Field. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:561-569. [PMID: 36443945 DOI: 10.1021/acs.est.2c05753] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Fluorene-9-bisphenol (BHPF), a bisphenol A (BPA) substitute, has been increasingly used as a material in syntheses of polymers that are widely used in road markings, artificial tracks, coating floors, building paints, etc., increasing the likelihood of BHPF contamination in the aquatic environment due to its release from the products. However, to date, it is unknown whether it may have actual impacts on fish in real environments. In this study, a 105-day exposure experiment of BHPF at various concentrations (0.01, 0.1, 1, and 10 μg/L) on Chinese medaka (Oryzias sinensis) was performed under laboratory conditions and found decreased fecundity, such as lower egg qualities and quantities, retarded oogenesis, and atretic follicles in the fish and deformed eyes and bodies in its F1 generation. Toxico-transcriptome analyses showed that estrogen-responsive genes were significantly suppressed by BHPF, indicating that antagonist properties of BHPF on estrogen receptors might be causes for the decreased fecundity. Field investigations (Beijing) demonstrated that BHPF was detectable in 60% surface waters, with a mean concentration of 10.49 ± 6.33 ng/L, by gas chromatography-mass spectrometry, and similar effects in wild Chinese medaka were also observed, some of which the parameters were found to be obviously correlated with the BHPF levels in corresponding waters.
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Affiliation(s)
- Xiaolin Fan
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing 100871, China
| | - Jilong Guo
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing 100871, China
| | - Xiaojing Jia
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing 100871, China
| | - Xingtai Mao
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing 100871, China
| | - Ying Zhou
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing 100871, China
| | - Yue Wang
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing 100871, China
| | - Xuan Guo
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing 100871, China
| | - Jiashu Shen
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing 100871, China
| | - Narma Huai
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing 100871, China
| | - Kailun Zhang
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing 100871, China
| | - Abida Abdusalam
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing 100871, China
| | - Hongxia Hu
- Fisheries Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100068, China
| | - Hua Zhu
- Fisheries Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100068, China
| | - Chengxia Jia
- Fisheries Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100068, China
| | - Lan Cheng
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing 100871, China
| | - Xiqing Li
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing 100871, China
| | - Zhaobin Zhang
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing 100871, China
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12
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Zhao Y, Chen S, Yuan J, Shi Y, Wang Y, Xi Y, Qi X, Guo Y, Sheng X, Liu J, Zhou L, Wang C, Xing K. Comprehensive Analysis of the lncRNA-miRNA-mRNA Regulatory Network for Intramuscular Fat in Pigs. Genes (Basel) 2023; 14:168. [PMID: 36672909 PMCID: PMC9859044 DOI: 10.3390/genes14010168] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/26/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Intramuscular fat (IMF) is an essential trait closely related to meat quality. The IMF trait is a complex quantitative trait that is regulated by multiple genes. In order to better understand the process of IMF and explore the key factors affecting IMF deposition, we identified differentially expressed mRNA, miRNA, and lncRNA in the longissimus dorsi muscle (LD) between Songliao Black (SL) pigs and Landrace pigs. We obtained 606 differentially expressed genes (DEGs), 55 differentially expressed miRNAs (DEMs), and 30 differentially expressed lncRNAs (DELs) between the SL pig and Landrace pig. Enrichment results from GO and KEGG indicate that DEGs are involved in fatty acid metabolism and some pathways related to glycogen synthesis. We constructed an lncRNA-miRNA-mRNA interaction network with 18 DELs, 11 DEMs, and 42 DEGs. Finally, the research suggests that ARID5B, CPT1B, ACSL1, LPIN1, HSP90AA1, IRS1, IRS2, PIK3CA, PIK3CB, and PLIN2 may be the key genes affecting IMF deposition. The LncRNAs MSTRG.19948.1, MSTRG.13120.1, MSTRG.20210.1, and MSTRG.10023.1, and the miRNAs ssc-miRNA-429 and ssc-miRNA-7-1, may play a regulatory role in IMF deposition through their respective target genes. Our research provides a reference for further understanding the regulatory mechanism of IMF.
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Affiliation(s)
- Yanhui Zhao
- Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Shaokang Chen
- Beijing Animal Husbandry Station, Beijing 100101, China
| | - Jiani Yuan
- Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Yumei Shi
- Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Yan Wang
- Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Yufei Xi
- Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Xiaolong Qi
- Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Yong Guo
- Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Xihui Sheng
- Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Jianfeng Liu
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Lei Zhou
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Chuduan Wang
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Kai Xing
- Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
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13
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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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14
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Comparative genome anatomy reveals evolutionary insights into a unique amphitriploid fish. Nat Ecol Evol 2022; 6:1354-1366. [PMID: 35817827 PMCID: PMC9439954 DOI: 10.1038/s41559-022-01813-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 05/25/2022] [Indexed: 12/21/2022]
Abstract
Triploids are rare in nature because of difficulties in meiotic and gametogenic processes, especially in vertebrates. The Carassius complex of cyprinid teleosts contains sexual tetraploid crucian carp/goldfish (C. auratus) and unisexual hexaploid gibel carp/Prussian carp (C. gibelio) lineages, providing a valuable model for studying the evolution and maintenance mechanism of unisexual polyploids in vertebrates. Here we sequence the genomes of the two species and assemble their haplotypes, which contain two subgenomes (A and B), to the chromosome level. Sequencing coverage analysis reveals that C. gibelio is an amphitriploid (AAABBB) with two triploid sets of chromosomes; each set is derived from a different ancestor. Resequencing data from different strains of C. gibelio show that unisexual reproduction has been maintained for over 0.82 million years. Comparative genomics show intensive expansion and alterations of meiotic cell cycle-related genes and an oocyte-specific histone variant. Cytological assays indicate that C. gibelio produces unreduced oocytes by an alternative ameiotic pathway; however, sporadic homologous recombination and a high rate of gene conversion also exist in C. gibelio. These genomic changes might have facilitated purging deleterious mutations and maintaining genome stability in this unisexual amphitriploid fish. Overall, the current results provide novel insights into the evolutionary mechanisms of the reproductive success in unisexual polyploid vertebrates. Genome sequencing and haplotype assembly of two cyprinid teleosts, a sexual tetraploid and an unisexual hexaploid, reveal insights into the evolutionary mechanisms underpinning the reproductive success of unisexual polyploid vertebrates.
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15
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Wang MT, Li Z, Ding M, Yao TZ, Yang S, Zhang XJ, Miao C, Du WX, Shi Q, Li S, Mei J, Wang Y, Wang ZW, Zhou L, Li XY, Gui JF. 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] [MESH Headings] [Grants] [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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Affiliation(s)
- Ming-Tao Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhi 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, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Miao Ding
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design, Institute of Hydrobiology, 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, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Sheng Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design, Institute of Hydrobiology, 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, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chun Miao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design, Institute of Hydrobiology, 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, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qian Shi
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shun 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, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Mei
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design, Institute of Hydrobiology, 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, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design, Institute of Hydrobiology, 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, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design, Institute of Hydrobiology, 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, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
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16
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Tong JF, Zhou L, Li S, Lu LF, Li ZC, Li Z, Gan RH, Mou CY, Zhang QY, Wang ZW, Zhang XJ, Wang Y, Gui JF. Two Duplicated Ptpn6 Homeologs Cooperatively and Negatively Regulate RLR-Mediated IFN Response in Hexaploid Gibel Carp. Front Immunol 2021; 12:780667. [PMID: 34899743 PMCID: PMC8662705 DOI: 10.3389/fimmu.2021.780667] [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: 09/21/2021] [Accepted: 11/11/2021] [Indexed: 01/28/2023] Open
Abstract
Src homology region 2 domain-containing phosphatase 1 (SHP1), encoded by the protein tyrosine phosphatase nonreceptor type 6 (ptpn6) gene, belongs to the family of protein tyrosine phosphatases (PTPs) and participates in multiple signaling pathways of immune cells. However, the mechanism of SHP1 in regulating fish immunity is largely unknown. In this study, we first identified two gibel carp (Carassius gibelio) ptpn6 homeologs (Cgptpn6-A and Cgptpn6-B), each of which had three alleles with high identities. Then, relative to Cgptpn6-B, dominant expression in adult tissues and higher upregulated expression of Cgptpn6-A induced by polyinosinic-polycytidylic acid (poly I:C), poly deoxyadenylic-deoxythymidylic (dA:dT) acid and spring viremia of carp virus (SVCV) were uncovered. Finally, we demonstrated that CgSHP1-A (encoded by the Cgptpn6-A gene) and CgSHP1-B (encoded by the Cgptpn6-B gene) act as negative regulators of the RIG-I-like receptor (RLR)-mediated interferon (IFN) response via two mechanisms: the inhibition of CaTBK1-induced phosphorylation of CaMITA shared by CgSHP1-A and CgSHP1-B, and the autophagic degradation of CaMITA exclusively by CgSHP1-A. Meanwhile, the data support that CgSHP1-A and CgSHP1-B have sub-functionalized and that CgSHP1-A overwhelmingly dominates CgSHP1-B in the process of RLR-mediated IFN response. The current study not only sheds light on the regulative mechanism of SHP1 in fish immunity, but also provides a typical case of duplicated gene evolutionary fates.
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Affiliation(s)
- 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.,Hubei Hongshan Laboratory, 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
| | - 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
| | - Zhuo-Cong 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
| | - 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.,Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
| | - Rui-Hai Gan
- 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
| | - 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.,Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 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.,Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, 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
| | - 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.,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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17
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Global Analysis of Transcriptome and Translatome Revealed That Coordinated WNT and FGF Regulate the Carapacial Ridge Development of Chinese Soft-Shell Turtle. Int J Mol Sci 2021; 22:ijms222212441. [PMID: 34830331 PMCID: PMC8621500 DOI: 10.3390/ijms222212441] [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: 08/29/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 12/16/2022] Open
Abstract
The turtle carapace is composed of severely deformed fused dorsal vertebrae, ribs, and bone plates. In particular, the lateral growth in the superficial layer of turtle ribs in the dorsal trunk causes an encapsulation of the scapula and pelvis. The recent study suggested that the carapacial ridge (CR) is a new model of epithelial–mesenchymal transition which is essential for the arrangement of the ribs. Therefore, it is necessary to explore the regulatory mechanism of carapacial ridge development to analyze the formation of the turtle shell. However, the current understanding of the regulatory network underlying turtle carapacial ridge development is poor due to the lack of both systematic gene screening at different carapacial ridge development stages and gene function verification studies. In this study, we obtained genome-wide gene transcription and gene translation profiles using RNA sequencing and ribosome nascent-chain complex mRNA sequencing from carapacial ridge tissues of Chinese soft-shell turtle at different development stages. A correlation analysis of the transcriptome and translatome revealed that there were 129, 670, and 135 codifferentially expressed genes, including homodirection and opposite-direction differentially expressed genes, among three comparison groups, respectively. The pathway enrichment analysis of codifferentially expressed genes from the Kyoto Encyclopedia of Genes and Genomes showed dynamic changes in signaling pathways involved in carapacial ridge development. Especially, the results revealed that the Wnt signaling pathway and MAPK signaling pathway may play important roles in turtle carapacial ridge development. In addition, Wnt and Fgf were expressed during the carapacial ridge development. Furthermore, we discovered that Wnt5a regulated carapacial ridge development through the Wnt5a/JNK pathway. Therefore, our studies uncover that the morphogenesis of the turtle carapace might function through the co-operation between conserved WNT and FGF signaling pathways. Consequently, our findings revealed the dynamic signaling pathways acting on the carapacial ridge development of Chinese soft-shell turtle and provided new insights into uncover the molecular mechanism underlying turtle shell morphogenesis.
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18
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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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19
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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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20
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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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21
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Zhang XJ, Zhou L, Lu WJ, Du WX, Mi XY, Li Z, Li XY, Wang ZW, Wang Y, Duan M, Gui JF. Comparative transcriptomic analysis reveals an association of gibel carp fatty liver with ferroptosis pathway. BMC Genomics 2021; 22:328. [PMID: 33952209 PMCID: PMC8101161 DOI: 10.1186/s12864-021-07621-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 04/14/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Fatty liver has become a main problem that causes huge economic losses in many aquaculture modes. It is a common physiological or pathological phenomenon in aquaculture, but the causes and occurring mechanism are remaining enigmatic. METHODS Each three liver samples from the control group of allogynogenetic gibel carp with normal liver and the overfeeding group with fatty liver were collected randomly for the detailed comparison of histological structure, lipid accumulation, transcriptomic profile, latent pathway identification analysis (LPIA), marker gene expression, and hepatocyte mitochondria analyses. RESULTS Compared to normal liver, larger hepatocytes and more lipid accumulation were observed in fatty liver. Transcriptomic analysis between fatty liver and normal liver showed a totally different transcriptional trajectory. GO terms and KEGG pathways analyses revealed several enriched pathways in fatty liver, such as lipid biosynthesis, degradation accumulation, peroxidation, or metabolism and redox balance activities. LPIA identified an activated ferroptosis pathway in the fatty liver. qPCR analysis confirmed that gpx4, a negative regulator of ferroptosis, was significantly downregulated while the other three positively regulated marker genes, such as acsl4, tfr1 and gcl, were upregulated in fatty liver. Moreover, the hepatocytes of fatty liver had more condensed mitochondria and some of their outer membranes were almost ruptured. CONCLUSIONS We reveal an association between ferroptosis and fish fatty liver for the first time, suggesting that ferroptosis might be activated in liver fatty. Therefore, the current study provides a clue for future studies on fish fatty liver problems.
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Affiliation(s)
- Xiao-Juan Zhang
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei-Jia Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen-Xuan Du
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiang-Yuan Mi
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhong-Wei Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ming Duan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian-Fang Gui
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China.
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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22
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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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