1
|
Wang Q, Lei Y, Lin H, Chen X, Mo W, Guan B, Deng H. Gonadal Transcriptomic Analysis Reveals Novel Sex-Related Genes in Bactrocera dorsalis. INSECTS 2024; 15:424. [PMID: 38921139 PMCID: PMC11203884 DOI: 10.3390/insects15060424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 05/15/2024] [Accepted: 05/18/2024] [Indexed: 06/27/2024]
Abstract
Bactrocera dorsalis (Hendel) (Diptera: Tephritidae) is one of the most devastating agricultural pests worldwide due to its high reproductive and invasive abilities. The elucidation of its gonadal developmental characteristics and the identification of sex-related genes will provide a useful genetic basis for reproductive-based pest control. Here, the gonadal transcriptome of B. dorsalis was sequenced, and novel gonad-specific expressed genes were analyzed. A total of 1338, 336, 35, and 479 differentially expressed genes (DEGs) were found in the testis (TE), ovary (OV), female accessory gland (FAG), and male accessory gland (MAG), respectively. Furthermore, 463 highly expressed gonad-specific genes were identified, with the TE having the highest number of specific highly expressed genes, at 402, followed by 51 in the OV, 9 in the MAG, and only 1 in the FAG. Strikingly, approximately half of highly expressed gonad-specific genes were uncharacterized. Then, it was found that 35, 17, 3, 2, and 1 of 202 uncharacterized highly expressed TE-specific genes encoded proteins that contained transmembrane domains, signal peptides, high-mobility group boxes, the zinc finger domain, and the BTB/POZ domain, respectively. Interestingly, approximately 40% of uncharacterized highly expressed gonad-specific genes encoding proteins were not predicted to possess functional motifs or domains. Finally, the spatiotemporal expression and sequence characterization of six novel highly expressed gonad-specific genes were analyzed. Altogether, our findings provide a valuable dataset for future functional analyses of sex-related genes and potential target sites for pest control.
Collapse
Affiliation(s)
- Qin Wang
- Guangdong Key Laboratory of Insect Developmental Biology and Applied Technology, South China Normal University, Guangzhou 510631, China; (Q.W.); (Y.L.); (H.L.); (X.C.); (W.M.); (B.G.)
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Yuxuan Lei
- Guangdong Key Laboratory of Insect Developmental Biology and Applied Technology, South China Normal University, Guangzhou 510631, China; (Q.W.); (Y.L.); (H.L.); (X.C.); (W.M.); (B.G.)
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Hongjie Lin
- Guangdong Key Laboratory of Insect Developmental Biology and Applied Technology, South China Normal University, Guangzhou 510631, China; (Q.W.); (Y.L.); (H.L.); (X.C.); (W.M.); (B.G.)
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Xiaoxin Chen
- Guangdong Key Laboratory of Insect Developmental Biology and Applied Technology, South China Normal University, Guangzhou 510631, China; (Q.W.); (Y.L.); (H.L.); (X.C.); (W.M.); (B.G.)
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Wanyu Mo
- Guangdong Key Laboratory of Insect Developmental Biology and Applied Technology, South China Normal University, Guangzhou 510631, China; (Q.W.); (Y.L.); (H.L.); (X.C.); (W.M.); (B.G.)
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Boyang Guan
- Guangdong Key Laboratory of Insect Developmental Biology and Applied Technology, South China Normal University, Guangzhou 510631, China; (Q.W.); (Y.L.); (H.L.); (X.C.); (W.M.); (B.G.)
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Huimin Deng
- Guangdong Key Laboratory of Insect Developmental Biology and Applied Technology, South China Normal University, Guangzhou 510631, China; (Q.W.); (Y.L.); (H.L.); (X.C.); (W.M.); (B.G.)
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| |
Collapse
|
2
|
Li C, Cai R, Shi W, Zhang H, Liu Z, Xie F, Chen Y, Hong Q. Comparative transcriptome analysis of ovaries and testes reveals sex-biased genes and pathways in zebrafish. Gene 2024; 901:148176. [PMID: 38242380 DOI: 10.1016/j.gene.2024.148176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/07/2024] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
Zebrafish (Danio rerio) is a widely recognized and extensively studied model organism in scientific research. The regulatory mechanism of gonadal development and differentiation of this species has aroused considerable attention. Nonetheless, the major sex-biased genes and pathways associated with gonadal development remain elusive. Therefore, to comprehend this intricate process, gonadal transcriptome sequencing was carried out to identify differentially expressed genes (DEGs) between the testes and ovaries of adult zebrafish. The preliminary assessment yielded a total of 23,529,272 and 23,521,368 clean reads from the cDNA libraries of ovaries and testes. Afterward, a comparative analysis of the transcriptome revealed 3,604 upregulated and 11,371 downregulated DEGs in the ovaries compared to the testes. Of these genes, 428 were exclusively expressed in females, while 3,516 were exclusively expressed in males. Additionally, further assessments were conducted to explore the functions associated with these DEGs in various biological processes. The data revealed their involvement in sex-biased pathways, such as progesterone-mediated oocyte maturation, oocyte meiosis, cytokine-cytokine receptor interaction, and cardiac muscle contraction. Finally, the expression levels of 14 sex-biased DEGs (cdc20, ccnb1, ypel3, chn1, bmp15, rspo1, tnfsf10, egfra, acta2, cox8a, gsdf, dmrt1, star, and cyp17a1) associated with the enriched pathways were subjected to further validation through qRT-PCR. The data acquired from these investigations offer valuable resources to support further exploration of the mechanisms governing sexual dimorphism and gonadal development in zebrafish.
Collapse
Affiliation(s)
- Cong Li
- Department of Hematology, The Second Affiliated Hospital of Anhui Medical University, Hefei 230032, China
| | - Rui Cai
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Wenhui Shi
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Hao Zhang
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Zhuang Liu
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Fenfen Xie
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China.
| | - Yuanhua Chen
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China.
| | - Qiang Hong
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China.
| |
Collapse
|
3
|
Wang L, Guan T, Gu J, Zhu C, Pan Z, Wang H, Li J. Comparative transcriptome analysis of gonads in male and female Pseudobagrus ussuriensis (Bagridae, Siluriformes). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 47:101105. [PMID: 37354751 DOI: 10.1016/j.cbd.2023.101105] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 06/26/2023]
Abstract
As an important aquaculture fish in the Heilongjiang River Basin, Pseudobagrus ussuriensis has high economic value, and all-male culture is beneficial to the economic development of this fish. In this study, the transcriptomes of gonads in males and females were analyzed, and some genes related to gonad development were found. A total of 82,931 unigenes were found (average length 1504 bp, N50 1829 bp). In addition, 4689 differentially expressed genes (DEGs; including 1424 genes upregulated and 3265 genes downregulated in males) were identified. Some genes associated with testis development (such as Dmrt1 and Ropn1l) were significantly upregulated in males, while genes related to ovary development (such as Wnt2, PLC, Cyp19a, ZP3) were significantly downregulated in males, demonstrating that these genes have a crucial influence on gonad development in P. ussuriensis. Some signaling pathways related to gonad development were found, such as the Wnt pathway and oocyte meiosis. The results of RNA-seq obtained in this study provide theoretical data for elucidating the potential mechanism of gonad development of P. ussuriensis and reliable genomic data for the establishment of mono-sex breeding of P. ussuriensis.
Collapse
Affiliation(s)
- Long Wang
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huai'yin Normal University, Huai'an 223300, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China
| | - Tianyu Guan
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huai'yin Normal University, Huai'an 223300, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China
| | - Jieyi Gu
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huai'yin Normal University, Huai'an 223300, China
| | - Chuankun Zhu
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huai'yin Normal University, Huai'an 223300, China
| | - Zhengjun Pan
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huai'yin Normal University, Huai'an 223300, China
| | - Hui Wang
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huai'yin Normal University, Huai'an 223300, China.
| | - Jiale Li
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
Yang YH, Wang R, Li M, Yang HZ, Huang GH, Ma KY, Qiu GF, Lin Y. Comparative transcriptomes analysis of the ovary reveals potential ovarian development-related genes and pathways in Macrobrachium rosenbergii. INVERTEBR REPROD DEV 2022. [DOI: 10.1080/07924259.2022.2156822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Yan-Hao Yang
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, MiMinistry of Agriculture (Shanghai Ocean University), Shanghai Engineering Research Center of Aquaculture (Shanghai Ocean University)ministry of Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai 201306, China
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Institute of Fisheries, 530021, Nanning, Guangxi, China
| | - Rui Wang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Institute of Fisheries, 530021, Nanning, Guangxi, China
| | - Ming Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Institute of Fisheries, 530021, Nanning, Guangxi, China
| | - Hui-Zan Yang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Institute of Fisheries, 530021, Nanning, Guangxi, China
| | - Guang-Hua Huang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Institute of Fisheries, 530021, Nanning, Guangxi, China
| | - Ke-Yi Ma
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, MiMinistry of Agriculture (Shanghai Ocean University), Shanghai Engineering Research Center of Aquaculture (Shanghai Ocean University)ministry of Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai 201306, China
| | - Gao-Feng Qiu
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, MiMinistry of Agriculture (Shanghai Ocean University), Shanghai Engineering Research Center of Aquaculture (Shanghai Ocean University)ministry of Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai 201306, China
| | - Yong Lin
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Institute of Fisheries, 530021, Nanning, Guangxi, China
| |
Collapse
|
6
|
Dechaud C, Miyake S, Martinez-Bengochea A, Schartl M, Volff JN, Naville M. Clustering of Sex-Biased Genes and Transposable Elements in the Genome of the Medaka Fish Oryzias latipes. Genome Biol Evol 2021; 13:6384576. [PMID: 34623422 PMCID: PMC8633743 DOI: 10.1093/gbe/evab230] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2021] [Indexed: 12/17/2022] Open
Abstract
Although genes with similar expression patterns are sometimes found in the same genomic regions, almost nothing is known about the relative organization in genomes of genes and transposable elements (TEs), which might influence each other at the regulatory level. In this study, we used transcriptomic data from male and female gonads of the Japanese medaka Oryzias latipes to define sexually biased genes and TEs and analyze their relative genomic localization. We identified 20,588 genes expressed in the adult gonads of O. latipes. Around 39% of these genes are differentially expressed between male and female gonads. We further analyzed the expression of TEs using the program SQuIRE and showed that more TE copies are overexpressed in testis than in ovaries (36% vs. 10%, respectively). We then developed a method to detect genomic regions enriched in testis- or ovary-biased genes. This revealed that sex-biased genes and TEs are not randomly distributed in the genome and a part of them form clusters with the same expression bias. We also found a correlation of expression between TE copies and their closest genes, which increases with decreasing intervening distance. Such a genomic organization suggests either that TEs hijack the regulatory sequences of neighboring sexual genes, allowing their expression in germ line cells and consequently new insertions to be transmitted to the next generation, or that TEs are involved in the regulation of sexual genes, and might therefore through their mobility participate in the rewiring of sex regulatory networks.
Collapse
Affiliation(s)
- Corentin Dechaud
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, Lyon, France
| | - Sho Miyake
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, Lyon, France
| | | | - Manfred Schartl
- Entwicklungsbiochemie, Biozentrum, Universität Würzburg, Würzburg, Germany.,Department of Chemistry and Biochemistry, The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, USA
| | - Jean-Nicolas Volff
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, Lyon, France
| | - Magali Naville
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, Lyon, France
| |
Collapse
|
7
|
Senthilkumaran B, Kar S. Advances in Reproductive Endocrinology and Neuroendocrine Research Using Catfish Models. Cells 2021; 10:2807. [PMID: 34831032 PMCID: PMC8616529 DOI: 10.3390/cells10112807] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/09/2021] [Accepted: 10/11/2021] [Indexed: 12/12/2022] Open
Abstract
Catfishes, belonging to the order siluriformes, represent one of the largest groups of freshwater fishes with more than 4000 species and almost 12% of teleostean population. Due to their worldwide distribution and diversity, catfishes are interesting models for ecologists and evolutionary biologists. Incidentally, catfish emerged as an excellent animal model for aquaculture research because of economic importance, availability, disease resistance, adaptability to artificial spawning, handling, culture, high fecundity, hatchability, hypoxia tolerance and their ability to acclimate to laboratory conditions. Reproductive system in catfish is orchestrated by complex network of nervous, endocrine system and environmental factors during gonadal growth as well as recrudescence. Lot of new information on the molecular mechanism of gonadal development have been obtained over several decades which are evident from significant number of scientific publications pertaining to reproductive biology and neuroendocrine research in catfish. This review aims to synthesize key findings and compile highly relevant aspects on how catfish can offer insight into fundamental mechanisms of all the areas of reproduction and its neuroendocrine regulation, from gametogenesis to spawning including seasonal reproductive cycle. In addition, the state-of-knowledge surrounding gonadal development and neuroendocrine control of gonadal sex differentiation in catfish are comprehensively summarized in comparison with other fish models.
Collapse
Affiliation(s)
- Balasubramanian Senthilkumaran
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, Telangana, India;
| | | |
Collapse
|
8
|
Wan ZY, Lin VCL, Hua YG. Pomc Plays an Important Role in Sexual Size Dimorphism in Tilapia. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2021; 23:201-214. [PMID: 33580373 DOI: 10.1007/s10126-020-10015-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/27/2020] [Indexed: 06/12/2023]
Abstract
Sexual dimorphism is common across the animal kingdom. Knowledge of the mechanisms of sexual size dimorphism is limited although it is important in biology and aquaculture. Tilapia is the common name for ~ 100 species of cichlid fish. Some are important aquaculture species and males outgrow females. To gain novel insights into the mechanisms underlying sexual size dimorphism, we analyzed the differences of brain transcriptomes between males and females in Mozambique tilapia and studied the function of the pro-opiomelanocortin (Pomc) gene in tilapia and zebrafish. The transcriptome analysis identified 123, 55, and 2706 sex-biased genes at 5, 30, and 90 dph (days post-hatch), respectively, indicating sexual dimorphism of gene expressions in the brain. The expression of Pomc in the tilapia brain was a female-biased at 30, 90, and 120 dph. An analysis of the DNA sequence located upstream of the tilapia Pomc transcriptional start site identified two estrogenic response elements. In vitro luciferase assay of the two elements revealed that β-estradiol significantly enhanced the expression of luciferase activity, suggesting that the expression of Pomc is mediated by estrogen. We knocked out Pomc in zebrafish using Crispr/Cas-9. The Pomc-knockout zebrafish showed faster growth and higher sensitivity to feeding as compared to the wild-type fish. Taken together, our results indicate that Pomc contributes to sexual size dimorphism and suggest that the high estrogen level in females promotes the expression of Pomc and suppresses feeding in female tilapias, which leads to the slower growth of female tilapias.
Collapse
Affiliation(s)
- Z Y Wan
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - V C L Lin
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
| | - Yue Gen Hua
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore.
| |
Collapse
|
9
|
Li J, Zhou Y, Zhou Z, Lin C, Wei J, Qin Y, Xiang Z, Ma H, Zhang Y, Zhang Y, Yu Z. Comparative transcriptome analysis of three gonadal development stages reveals potential genes involved in gametogenesis of the fluted giant clam (Tridacna squamosa). BMC Genomics 2020; 21:872. [PMID: 33287701 PMCID: PMC7720611 DOI: 10.1186/s12864-020-07276-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 11/24/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Gonad development and differentiation is an essential function for all sexually reproducing species, and many aspects of these developmental processes are highly conserved among the metazoa. However, the mechanisms underlying gonad development and gametogenesis remain unclear in Tridacna squamosa, a large-size bivalve of great ecological value. They are protandrous simultaneous hermaphrodites, with the male gonad maturing first, eventually followed by the female gonads. In this study, nine gonad libraries representing resting, male and hermaphrodite stages in T. squamosa were performed to identify the molecular mechanisms. RESULTS Sixteen thousand four hundred ninety-one unigenes were annotated in the NCBI non-redundant protein database. Among the annotated unigenes, 5091 and 7328 unigenes were assigned to Gene Ontology categories and the Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway database, respectively. A total of 4763 differentially expressed genes (DEGs) were identified by comparing male to resting gonads, consisting of 3499 which were comparatively upregulated in males and 1264 which were downregulated in males. Six hundred-ninteen DEGs between male and hermaphroditic gonads were identified, with 518 DEGs more strongly expressed in hermaphrodites and 101 more strongly expressed in males. GO (Gene Ontology) and KEGG pathway analyses revealed that various biological functions and processes, including functions related to the endocrine system, oocyte meiosis, carbon metabolism, and the cell cycle, were involved in regulating gonadal development and gametogenesis in T. squamosa. Testis-specific serine/threonine kinases 1 (TSSK1), TSSK4, TSSK5, Doublesex- and mab-3-related transcription factor 1 (DMRT1), SOX, Sperm surface protein 17 (SP17) and other genes were involved in male gonadal development in Tridacna squamosal. Both spermatogenesis- (TSSK4, spermatogenesis-associated protein 17, spermatogenesis-associated protein 8, sperm motility kinase X, SP17) and oogenesis-related genes (zona pellucida protein, Forkhead Box L2, Vitellogenin, Vitellogenin receptor, 5-hydroxytryptamine, 5-hydroxytryptamine receptor) were simultaneously highly expressed in the hermaphroditic gonad to maintain the hermaphroditism of T. squamosa. CONCLUSION All these results from our study will facilitate better understanding of the molecular mechanisms underlying giant clam gonad development and gametogenesis, which can provided a base on obtaining excellent gametes during the seed production process for giant clams.
Collapse
Affiliation(s)
- Jun Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301, China
- Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya Institute of Oceanology Chinese Academy of Sciences, Sanya, 572024, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Yinyin Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301, China
- Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya Institute of Oceanology Chinese Academy of Sciences, Sanya, 572024, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zihua Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301, China
- Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya Institute of Oceanology Chinese Academy of Sciences, Sanya, 572024, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chuanxu Lin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China
| | - Jinkuan Wei
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301, China
- Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya Institute of Oceanology Chinese Academy of Sciences, Sanya, 572024, China
| | - Yanpin Qin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301, China
- Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya Institute of Oceanology Chinese Academy of Sciences, Sanya, 572024, China
| | - Zhiming Xiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301, China
- Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya Institute of Oceanology Chinese Academy of Sciences, Sanya, 572024, China
| | - Haitao Ma
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301, China
- Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya Institute of Oceanology Chinese Academy of Sciences, Sanya, 572024, China
| | - Yang Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301, China
- Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya Institute of Oceanology Chinese Academy of Sciences, Sanya, 572024, China
| | - Yuehuan Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301, China.
- Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya Institute of Oceanology Chinese Academy of Sciences, Sanya, 572024, China.
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China.
| | - Ziniu Yu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301, China.
- Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya Institute of Oceanology Chinese Academy of Sciences, Sanya, 572024, China.
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
10
|
Comparative Transcriptome Analysis of Gonads for the Identification of Sex-Related Genes in Giant Freshwater Prawns ( Macrobrachium Rosenbergii) Using RNA Sequencing. Genes (Basel) 2019; 10:genes10121035. [PMID: 31835875 PMCID: PMC6947849 DOI: 10.3390/genes10121035] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 11/26/2019] [Accepted: 12/02/2019] [Indexed: 12/18/2022] Open
Abstract
The giant freshwater prawn (Macrobrachium rosenbergii) exhibits sex dimorphism between the male and female individuals. To date, the molecular mechanism governing gonadal development was unclear, and limited data were available on the gonad transcriptome of M. rosenbergii. Here, we conducted comprehensive gonadal transcriptomic analysis of female (ZW), super female (WW), and male (ZZ) M. rosenbergii for gene discovery. A total of 70.33 gigabases (Gb) of sequences were generated. There were 115,338 unigenes assembled with a mean size of 1196 base pair (bp) and N50 of 2195 bp. Alignment against the National Center for Biotechnology Information (NCBI) non-redundant nucleotide/protein sequence database (NR and NT), the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, SwissProt database, Protein family (Pfam), Gene ontology (GO), and the eukaryotic orthologous group (KOG) database, 36,282 unigenes were annotated at least in one database. Comparative transcriptome analysis observed that 10,641, 16,903, and 3393 genes were significantly differentially expressed in ZW vs. ZZ, WW vs. ZZ, and WW vs. ZW samples, respectively. Enrichment analysis of differentially expressed genes (DEGs) resulted in 268, 153, and 42 significantly enriched GO terms, respectively, and a total of 56 significantly enriched KEGG pathways. Additionally, 23 putative sex-related genes, including Gtsf1, IR, HSP21, MRPINK, Mrr, and other potentially promising candidate genes were identified. Moreover, 56,241 simple sequence repeats (SSRs) were identified. Our findings provide a valuable archive for further functional analyses of sex-related genes and future discoveries of underlying molecular mechanisms of gonadal development and sex determination.
Collapse
|
11
|
Zhang X, Li W, Liu M, Zhang X, Yin X, Xu Z, Liu J. Transcriptomic Analysis of the Cold-Pretreated Larimichthys crocea Showing Enhanced Growth Fitness in Cold Water. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:791-805. [PMID: 31741169 DOI: 10.1007/s10126-019-09924-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 09/24/2019] [Indexed: 06/10/2023]
Abstract
The large yellow croaker Larimichthys crocea is an economically important marine fish species endemic to China and East Asia. Ningde area of Fujian Province is a major L. crocea aquaculture and spawning center in China. L. crocea cultivated at the Zhoushan area appears to be popular but suffered high mortality in cold water during winter seasons. To reduce the mortality rate, we pretreated fish with cold shocks prior to shift to cold water. In this study, we show that cold-pretreated L. crocea 12 days after shift to cold water increase the viability by 5.77-fold compared to the unpretreated (live fish 75 versus 13, p value = 1.775e-06, n = 100). The highest loss of 31 out of 100 fish in the unpretreated group occurred in day 3 after temperature shift. To identify the pretreatment-induced transcriptional changes that may be attributed to cold-resistance and survival, we performed RNA-seq analysis of a total of 48 fish that were prior to and 48 h, 54 h, and 72 h after temperature shift in pretreated and unpretreated groups in sextuplicate. Transcriptomic profiling analysis indicates that pretreatment-induced transcriptional alterations of enzymes involved in FASI, β-oxidation, PUFA synthesis, oxidative phosphorylation, and molecular chaperones persisted after temperature shift, suggesting that these metabolic pathways may play a role in L. crocea cold-resistance and survival. Our study provides insights on how the pretreatment enhances the L. crocea growth fitness in cold water.
Collapse
Affiliation(s)
- Xiaolin Zhang
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Weiye Li
- Fishery Research Institute of Zhoushan, Zhoushan, 316003, China
- School of Marine Sciences, Ningbo University, Ningbo, 315823, China
| | - Minhai Liu
- Fishery Research Institute of Zhoushan, Zhoushan, 316003, China
| | - Xia Zhang
- Fishery Research Institute of Zhoushan, Zhoushan, 316003, China
| | - Xiaolong Yin
- Fishery Research Institute of Zhoushan, Zhoushan, 316003, China
| | - Zhijing Xu
- Fishery Research Institute of Zhoushan, Zhoushan, 316003, China.
- Zhejiang Huaxing Aquatic Technology Co. Ltd., Zhoushan, 316100, China.
| | - Jianhua Liu
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China.
- School of Marine Science and Technology, Zhejiang Ocean University, Marine Science Building #106, 1 South Haida Road, Lincheng-Changzhi Island,, Zhoushan, 316022, Zhejiang, China.
| |
Collapse
|
12
|
Wei P, He P, Zhang X, Li W, Zhang L, Guan J, Chen X, Lin Y, Zhuo X, Li Q, Peng J. Identification and characterization of microRNAs in the gonads of Crassostrea hongkongensis using high-throughput sequencing. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 31:100606. [PMID: 31325756 DOI: 10.1016/j.cbd.2019.100606] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/29/2019] [Accepted: 07/03/2019] [Indexed: 12/14/2022]
Abstract
Crassostrea hongkongensis is one of the three most-commonly cultivated oyster species in China. Although microRNAs (miRNAs) expression in the gonads have been widely investigated, few studies of miRNAs in mollusk gonads are available, particularly in oyster. In the present study, we analyzed the miRNAs expressed in the ovaries and testes of C. hongkongensis. We obtained 14,166,409 and 15,133,900 raw reads from the ovaries and testes, respectively, yielding 13,634,997 (ovarian) and 14,494,149 (testicular) 18-35-nt sequences. We mapped these sequences to the C. hongkongensis genome reference sequence, and identified 8,771,717 (ovarian) and 9,926,014 (testicular) sequences corresponding to miRNAs in the Rfam database. After blasting the miRNA sequences against the miRBase database, we identified 50 known mature miRNAs and 53 novel miRNAs. Of these, 27 miRNAs were significantly upregulated in ovaries as compared to the testes, and 43 miRNAs were significantly upregulated in the testes as compared to the ovaries. To validate the differential expression results generated by Illumina sequencing, we used RT-real-time quantitative PCR (RT-qPCR) to characterize the expression patterns of the six most differently expressed miRNAs (lgi-miR-1990, lgi-miR-1986, lgi-miR-263b, lgi-miR-279, lgi-miR-1992, and novel_98) as well as two miRNAs associated with gonad development (lgi-miR-29 and lgi-miR-8). Most of the RT-qPCR miRNA expression patterns were similar to those recovered by high-throughput sequencing with the exceptions of novel_98 and lgi-miR-1992. Gene Ontology (GO) annotations indicated that the multi-organism cellular process GO category was enriched with the target genes of the differentially expressed miRNAs. Additionally, the target genes were enriched in several KEGG pathways, including the ECM-receptor interaction, galactose metabolism, phagosome, and notch signaling pathway. These pathways are involved in gonadal differentiation and the maintenance of gonad function. This identification and characterization of the miRNAs differentially expressed between the ovaries and testes of C. hongkongensis will increase our understanding of the role of miRNAs in gonad differentiation in the oyster.
Collapse
Affiliation(s)
- Pinyuan Wei
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Academy of Fisheries Sciences, Nanning, Guangxi 530021, China
| | - Pingping He
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Academy of Fisheries Sciences, Nanning, Guangxi 530021, China
| | - Xingzhi Zhang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Academy of Fisheries Sciences, Nanning, Guangxi 530021, China
| | - Wei Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Academy of Fisheries Sciences, Nanning, Guangxi 530021, China
| | - Li Zhang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Academy of Fisheries Sciences, Nanning, Guangxi 530021, China
| | - Junliang Guan
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Academy of Fisheries Sciences, Nanning, Guangxi 530021, China
| | - Xiaohan Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Academy of Fisheries Sciences, Nanning, Guangxi 530021, China
| | - Yong Lin
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Academy of Fisheries Sciences, Nanning, Guangxi 530021, China
| | - Xiaofei Zhuo
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Academy of Fisheries Sciences, Nanning, Guangxi 530021, China
| | - Qiongzhen Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Academy of Fisheries Sciences, Nanning, Guangxi 530021, China.
| | - Jinxia Peng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Academy of Fisheries Sciences, Nanning, Guangxi 530021, China.
| |
Collapse
|