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Ruan R, Li Y, Yue H, Ye H, Jin J, Wu J, Du H, Li C. Transcriptome Analyses Reveal Expression Profiles of Morphologically Undifferentiated and Differentiated Gonads of Yangtze Sturgeon Acipenser dabryanus. Genes (Basel) 2023; 14:2058. [PMID: 38003000 PMCID: PMC10671670 DOI: 10.3390/genes14112058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/01/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Sturgeon is known as a primitive fish with the ZZ/ZW sex determination system and is highly prized for its valuable caviar. Exploring the molecular mechanisms underlying gonadal differentiation would contribute to broadening our knowledge on the genetic regulation of sex differentiation of fish, enabling improved artificial breeding and management of sturgeons. However, the mechanisms are still poorly understood in sturgeons. This study aimed to profile expression patterns between female and male gonads at morphologically undifferentiated and early differentiated stages and identify vital genes involved in gonadal sex differentiation of sturgeons. The sexes of Yangtze sturgeon (Acipenser dabryanus) juveniles were identified via the sex-specific DNA marker and histological observation. Transcriptome analyses were carried out on female and male gonads at 30, 80 and 180 days post-hatching. The results showed that there was a total of 17 overlapped DEGs in the comparison groups of between female and male gonads at the three developmental stages, in which there were three DEGs related to ovarian steroidogenesis, including hsd17b1, foxl2 and cyp19a1. The three DEGs were highly expressed in the female gonads, of which the expression levels were gradually increased with the number of days after hatching. No well-known testis-related genes were found in the overlapped DEGs. Additionally, the expression levels of hsd17b1 and cyp19a1 mRNA were decreased with the knockdown of foxl2 mRNA via siRNA. The results further suggested that foxl2 should play a crucial role in the ovarian differentiation of sturgeons. In conclusion, this study showed that more genes involved in ovarian development than testis development emerged with sexually dimorphic expression during early gonadal sex differentiation, and it provided a preliminary understanding of the molecular regulation on gonadal differentiation of sturgeons.
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Affiliation(s)
- Rui Ruan
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (R.R.); (Y.L.); (H.Y.); (H.Y.); (J.J.); (J.W.)
| | - Ying Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (R.R.); (Y.L.); (H.Y.); (H.Y.); (J.J.); (J.W.)
| | - Huamei Yue
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (R.R.); (Y.L.); (H.Y.); (H.Y.); (J.J.); (J.W.)
| | - Huan Ye
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (R.R.); (Y.L.); (H.Y.); (H.Y.); (J.J.); (J.W.)
| | - Jiali Jin
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (R.R.); (Y.L.); (H.Y.); (H.Y.); (J.J.); (J.W.)
| | - Jinping Wu
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (R.R.); (Y.L.); (H.Y.); (H.Y.); (J.J.); (J.W.)
| | - Hao Du
- Laboratory of Freshwater Fish Germplasm Resources and Biotechnology, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Chuangju Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (R.R.); (Y.L.); (H.Y.); (H.Y.); (J.J.); (J.W.)
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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
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Pervasive male-biased expression throughout the germline-specific regions of the sea lamprey genome supports key roles in sex differentiation and spermatogenesis. Commun Biol 2022; 5:434. [PMID: 35538209 PMCID: PMC9090840 DOI: 10.1038/s42003-022-03375-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 04/14/2022] [Indexed: 12/13/2022] Open
Abstract
Sea lamprey undergo programmed genome rearrangement (PGR) in which ∼20% of the genome is jettisoned from somatic cells during embryogenesis. Although the role of PGR in embryonic development has been studied, the role of the germline-specific region (GSR) in gonad development is unknown. We analysed RNA-sequence data from 28 sea lamprey gonads sampled across life-history stages, generated a genome-guided de novo superTranscriptome with annotations, and identified germline-specific genes (GSGs). Overall, we identified 638 GSGs that are enriched for reproductive processes and exhibit 36x greater odds of being expressed in testes than ovaries. Next, while 55% of the GSGs have putative somatic paralogs, the somatic paralogs are not differentially expressed between sexes. Further, putative orthologs of some the male-biased GSGs have known functions in sex determination or differentiation in other vertebrates. We conclude that the GSR of sea lamprey plays an important role in testicular differentiation and potentially sex determination. RNA-sequencing of sea lamprey gonads at different life-history stage identifies germline-specific genes which are highly expressed in males during spermatogenesis. This suggests a link between male-biased germline expression and sex differentiation in the sea lamprey.
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Singh N, Singh D, Modi D. LIM Homeodomain (LIM-HD) Genes and Their Co-Regulators in Developing Reproductive System and Disorders of Sex Development. Sex Dev 2021; 16:147-161. [PMID: 34518474 DOI: 10.1159/000518323] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/01/2021] [Indexed: 11/19/2022] Open
Abstract
LIM homeodomain (LIM-HD) family genes are transcription factors that play crucial roles in a variety of functions during embryonic development. The activities of the LIM-HD proteins are regulated by the co-regulators LIM only (LMO) and LIM domain-binding (LDB). In the mouse genome, there are 13 LIM-HD genes (Lhx1-Lhx9, Isl1-2, Lmx1a-1b), 4 Lmo genes (Lmo1-4), and 2 Ldb genes (Ldb1-2). Amongst these, Lhx1 is required for the development of the müllerian duct epithelium and the timing of the primordial germ cell migration. Lhx8 is necessary for oocyte differentiation and Lhx9 for somatic cell proliferation in the genital ridges and control of testosterone production in the Leydig cells. Lmo4 is involved in Sertoli cell differentiation. Mutations in LHX1 are associated with müllerian agenesis or Mayer-Rokitansky-Kuster-Hauser (MRKH) syndrome. LHX9 gene variants are reported in cases with disorders of sex development (DSD). Mutations in LHX3 and LHX4 are reported in patients with combined pituitary hormone deficiency having absent or delayed puberty. A transcript map of the Lhx, Lmo, and Ldb genes reveal that multiple LIM-HD genes and their co-regulators are expressed in a sexually dimorphic pattern in the developing mouse gonads. Unraveling the roles of LIM-HD genes during development will aid in our understanding of the causes of DSD.
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Affiliation(s)
- Neha Singh
- Molecular and Cellular Biology Laboratory, ICMR-National Institute for Research in Reproductive Health, Indian Council of Medical Research (ICMR-NIRRH), Mumbai, India
| | - Domdatt Singh
- Molecular and Cellular Biology Laboratory, ICMR-National Institute for Research in Reproductive Health, Indian Council of Medical Research (ICMR-NIRRH), Mumbai, India
| | - Deepak Modi
- Molecular and Cellular Biology Laboratory, ICMR-National Institute for Research in Reproductive Health, Indian Council of Medical Research (ICMR-NIRRH), Mumbai, India
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Pan Z, Zhu C, Chang G, Wu N, Ding H, Wang H. Differential expression analysis and identification of sex-related genes by gonad transcriptome sequencing in estradiol-treated and non-treated Ussuri catfish Pseudobagrus ussuriensis. FISH PHYSIOLOGY AND BIOCHEMISTRY 2021; 47:565-581. [PMID: 33523351 DOI: 10.1007/s10695-021-00932-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
The Ussuri catfish (Pseudobagrus ussuriensis) has an XX/XY sex determination system but its sex determination gene(s) remain unknown. To better understand the molecular sex determination mechanism, transcriptome analysis was conducted to obtain sex-related gene expression profiles. Transcriptome analyses were made of male and female developing/differentiating gonads by high-throughput RNA sequencing, including gonads from fish given an estradiol-induced sex reversal treatment. A total of 81,569 unigenes were assembled and 39,904 were significantly matched to known unique proteins by comparison with public databases. Twenty specifically expressed and 142 differentially expressed sex-related genes were extracted from annotated data by comparing the treatment groups. These genes are involved in spermatogenesis (e.g., Dnali1, nectin3, klhl10, mybl1, Katnal1, Eno4, Mns1, Spag6, Tsga10, Septin7), oogenesis (e.g., Lagr5, Fmn2, Npm2, zar1, Fbxo5, Fbxo43, Prdx4, Nrip1, Lfng, Atrip), gonadal development/differentiation (e.g., Cxcr4b, Hmgb2, Cftr, Ch25h, brip1, Prdm9, Tdrd1, Star, dmrt1, Tut4, Hsd17b12a, gdf9, dnd, arf1, Spata22), and estradiol response (e.g., Mmp14, Lhcgr, vtg1, vtg2, esr2b, Piwil1, Aifm1, Hsf1, gdf9). Dmrt1 and gdf9 may play an essential role in sex determination in P. ussuriensis. The expression patterns of six random genes were validated by quantitative real-time PCR, which confirmed the reliability and accuracy of the RNA-seq results. These data provide a valuable resource for future studies of gene expression and for understanding the molecular mechanism of sex determination/differentiation and gonadal development/differentiation (including hormone-induced sexual reversal) in Ussuri catfish. This has the potential to assist in producing monosex Ussuri catfish to increase aquacultural productivity.
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Affiliation(s)
- ZhengJun Pan
- School of Life Sciences, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huaian, 223300, China.
| | - ChuanKun Zhu
- School of Life Sciences, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huaian, 223300, China
| | - GuoLiang Chang
- School of Life Sciences, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huaian, 223300, China
| | - Nan Wu
- School of Life Sciences, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huaian, 223300, China
| | - HuaiYu Ding
- School of Life Sciences, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huaian, 223300, China
| | - Hui Wang
- School of Life Sciences, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huaian, 223300, China
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Klopp C, Cabau C, Greif G, Lasalle A, Di Landro S, Vizziano-Cantonnet D. Siberian sturgeon multi-tissue reference transcriptome database. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:6006229. [PMID: 33238003 PMCID: PMC7687680 DOI: 10.1093/database/baaa082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/25/2020] [Accepted: 09/01/2020] [Indexed: 11/13/2022]
Abstract
Motivation: Siberian sturgeon is a long lived and late maturing fish farmed for caviar production in 50 countries. Functional genomics enable to find genes of interest for fish farming. In the absence of a reference genome, a reference transcriptome is very useful for sequencing based functional studies. Results: We present here a high-quality transcriptome assembly database built using RNA-seq reads coming from brain, pituitary, gonadal, liver, stomach, kidney, anterior kidney, heart, embryonic and pre-larval tissues. It will facilitate crucial research on topics such as puberty, reproduction, growth, food intake and immunology. This database represents a major contribution to the publicly available sturgeon transcriptome reference datasets. Availability: The database is publicly available at http://siberiansturgeontissuedb.sigenae.org Supplementary information: Supplementary data are available at Database online.
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Affiliation(s)
- Christophe Klopp
- SIGENAE, Genotoul Bioinfo, MIAT UR875, INRAe, Chemin de Borde-Rouge - Auzeville BP 52627, 31326 CASTANET-TOLOSAN CEDEX, France
| | - Cédric Cabau
- SIGENAE, GenPhySE, Université de Toulouse, INRAe, ENVT, Chemin de Borde-Rouge - Auzeville BP 52627, 31326 CASTANET-TOLOSAN CEDEX, France
| | - Gonzalo Greif
- Laboratorio de Interacción Hospedero-Patógeno/Unidad de Biología Molecular, Instituto Pasteur de Montevideo, Mataojo 2020, Montevideo 11400, Uruguay
| | - André Lasalle
- Laboratorio de Fisiología de la Reproducción y Ecología de Peces, Instituto de Biología, Facultad de Ciencias, Universidad de la República Oriental del Uruguay, Iguá 4225, Montevideo 11 400, Uruguay
| | - Santiago Di Landro
- Laboratorio de Fisiología de la Reproducción y Ecología de Peces, Instituto de Biología, Facultad de Ciencias, Universidad de la República Oriental del Uruguay, Iguá 4225, Montevideo 11 400, Uruguay
| | - Denise Vizziano-Cantonnet
- Laboratorio de Fisiología de la Reproducción y Ecología de Peces, Instituto de Biología, Facultad de Ciencias, Universidad de la República Oriental del Uruguay, Iguá 4225, Montevideo 11 400, Uruguay
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He S, Du H, Ren P, Leng XQ, Tan QS, Li CJ, Liang XF, Wei QW. Transcriptome analysis of ovarian maturation in a chondrostei Chinese sturgeon Acipenser sinensis. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 334:280-293. [PMID: 32483872 DOI: 10.1002/jez.b.22973] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 03/09/2020] [Accepted: 03/10/2020] [Indexed: 12/21/2022]
Abstract
Chinese sturgeon (Acipenser sinensis) with an evolutionary history of over 200 million years, has a long lifespan, and an extremely late and asynchronous sexual maturation (8-18 years for males and 14-26 years for females), resulting in the difficulty of mature adult culture. However, little is known about the regulatory mechanisms of the transition among ovarian maturation stages in the Chinese sturgeon. We performed de novo transcriptome sequencing of the Chinese sturgeon at different ovarian maturation stages (FII, FIII, and FIV). The number of differentially expressed genes (DEGs) between FII and FIII/FIV (33,517/34,217) was more than that between FIII and FIV (22,123), suggesting that the transition from FII to FIII/FIV is more important than that from FIII to FIV for ovarian maturation. The number of upregulated genes was more than that of the downregulated genes, suggesting that increased gene expression was involved in the transition from FII to FIII/FIV. The representative pathways of DEGs were steroid biosynthesis, fatty acid biosynthesis, fatty acid elongation, glycerolipid metabolism, biosynthesis of unsaturated fatty acid, and α-linolenic acid metabolism. The differential expressions from the transcriptome sequencing were validated with real-time reverse-transcription polymerase chain reaction. We also found 13 genes in sexual development, female sex determination, gonadal development, ovarian maturation, ovarian follicle development, and oocyte development pathways, which were differently expressed among fish at FII, FIII, and FIV. We suggest that enhanced synthesis of steroid, unsaturated fatty acid, and α-linolenic acid may contribute to ovarian maturation of the Chinese sturgeon. These potential determinants provide a glimpse of the molecular architecture of ovary development in sturgeons.
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Affiliation(s)
- Shan He
- Chinese Perch Research Center, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Hao Du
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan, China
| | - Ping Ren
- Chinese Perch Research Center, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Xiao-Qian Leng
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan, China
| | - Qing-Song Tan
- Chinese Perch Research Center, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Chuang-Ju Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan, China
| | - Xu-Fang Liang
- Chinese Perch Research Center, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Qi-Wei Wei
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan, China
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Chen Y, Gong Q, Lai J, Song M, Liu Y, Wu Y, Ai J, Long Z. Transcriptome analysis identifies candidate genes associated with skin color variation in Triplophysa siluroides. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 35:100682. [PMID: 32248074 DOI: 10.1016/j.cbd.2020.100682] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/24/2020] [Accepted: 03/24/2020] [Indexed: 12/18/2022]
Abstract
In vertebrates, skin pigmentation is the most diverse phenotypic trait, and it is produced by a complex biological process that is often genetically controlled. Recently, two different colors (the typical brown and orange varieties) of Triplophysa siluroides, a species restricted to Yellow River drainage in China, were discovered. In the present study, the skin, brain and liver transcriptomes of T. siluroides of both colors were sequenced to search for genes related to skin pigmentation. Transcriptome sequencing generated 1,484,197,774 clean reads, resulting in a total of 222.6 Gb of sequence. The reads were assembled into 470,788 unigenes with a mean length of 1550 bp and an N50 size of 2944 bp. Functional annotation of the unigene dataset showed that 214,507, 304,161, 112,886, 179,074, 180,064, 184,837 and 82,081 unigenes were significantly matched to entries in the Nr protein, Nt, KO, Swiss-Prot, Pfam, GO and KOG databases, respectively. A differential expression analysis revealed that 2774, 3552 and 1529 unigenes were upregulated and 2720, 2663 and 1103 unigenes were downregulated in the skin, brain and liver of orange-skinned T. siluroides, respectively. Several genes that play key roles in pigmentation, i.e., Agouti, Slc45a2, Cbs, Mift and Slc7a11, showed significantly differential expression between brown and orange fish. In addition, we detected 158,863 simple sequence repeats (SSRs) in the T. siluroides transcriptome, and a total of 201,338 single-nucleotide polymorphisms (SNPs) were discovered in the different transcriptomes. The present results will facilitate further study of the molecular mechanisms of skin pigmentation and marker-assisted breeding of fish with valuable skin colors.
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Affiliation(s)
- Yeyu Chen
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
| | - Quan Gong
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
| | - Jiansheng Lai
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China.
| | - Mingjiang Song
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
| | - Ya Liu
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
| | - Yingbin Wu
- Sichuan Juhai Fishery Technology Co., Ltd., Chengdu 610000, China
| | - Jiagui Ai
- Sichuan Juhai Fishery Technology Co., Ltd., Chengdu 610000, China
| | - Zhihai Long
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China.
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Transcriptomic analysis of female and male gonads in juvenile snakeskin gourami (Trichopodus pectoralis). Sci Rep 2020; 10:5240. [PMID: 32251302 PMCID: PMC7090014 DOI: 10.1038/s41598-020-61738-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/19/2020] [Indexed: 01/05/2023] Open
Abstract
The snakeskin gourami (Trichopodus pectoralis) exhibits sexual dimorphism, particularly in body size. Since the snakeskin gourami is usually marketed during sexual maturation, the sexual size dimorphism has become an economically important trait. Sex-biased gene expression plays a key role in phenotypic sexual dimorphism. Therefore, using high-throughput RNA sequencing (RNA-seq) technology, we aimed to explore the differentially expressed genes (DEGs) in ovary and testis during sex differentiation in juvenile snakeskin gourami. Our results revealed a number of DEGs were demonstrated to be overexpressed in ovary (11,625 unigenes) and testis (16,120 unigenes), and the top 10 female-biased (rdh7, dnajc25, ap1s3, zp4, polb, parp12, trim39, gucy2g, rtbs, and fdxr) and male-biased (vamp3, nbl1, dnah2, ccdc11, nr2e3, spats1, pih1d2, tekt3, fbxo36, and mybl2) DEGs were suggested to be mainly associated with ovary and testis differentiation, respectively. Additionally, using real-time reverse transcription polymerase chain reaction (qRT-PCR), validation of the differential expression of 21 genes that were previously shown to be related to gonad development was performed (ar, bHLH, cyp19a1, daz, dead-end, esrb, esrrg, gnrhr, gpa, gsg1l, hsd17B, mospd1, nanos-1, nanos-2, p53, piwi-1, piwi-2, rerg, rps6ka, tgf-beta, and VgR). The results showed a significantly positive correlation (0.84; P < 0.001) between the results of RNA-seq and qRT-PCR. Therefore, RNA-seq analysis in our study identified global genes that were associated with ovary and testis differentiation in the juvenile phase of the snakeskin gourami. Our findings provide valuable transcriptomic bioinformation for further investigation of reproductive biology and applications of sex manipulation.
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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.
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Chen H, Wang B, Yu N, Qi J, Tang N, Wang S, Tian Z, Wang M, Xu S, Zhou B, Long Q, Chen D, Li Z. Transcriptome analysis and the effects of polyunsaturated fatty acids on the immune responses of the critically endangered angtze sturgeon (Acipenser dabryanus). FISH & SHELLFISH IMMUNOLOGY 2019; 94:199-210. [PMID: 31499199 DOI: 10.1016/j.fsi.2019.09.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 09/02/2019] [Accepted: 09/05/2019] [Indexed: 06/10/2023]
Abstract
The poor understanding of nutrition needed has become a significant obstruction to artificial conservation of Yangtze sturgeon (Acipenser dabryanus) and the relationship between ployunsaturated fatty acid nutrition and the immune response of Yangtze sturgeon is remains unclear. To explore this relationship, the immune response was determined by the activities of serum immune-related enzymes and the transcriptome pattern in the spleen after feeding different fat source diets for 7 weeks. In addition, the gene expression pattern after a lipopolysaccharide (LPS) challenge was investigated in the presence of docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA). Long-term feeding of the fish oil diets increased the serum immune-related enzyme activities, including lysozyme, acid phosphatase, and alkaline phosphatase of Yangtze sturgeon. More than 653,999 transcripts with an N50 length of 1047 bp were obtained and a final set of 280,408 unigenes was generated. After annotating the unigenes, 3549 genes were assigned to the immune system and 2839 were identified to participate in the response to the different fat sources. A transcriptome assay showed the fish oil diets moderately upregulated immune-related signaling pathways in the spleen of Yangtze sturgeon, including NLR signaling, platelet activation, Fc gamma R-mediated phagocytosis, Th17 cell differentiation, and Th1 and Th2 cell differentiation. The quantitative polymerase chain reaction (qPCR) results of candidate genes for these pathways showed similar results. The LPS challenge study revealed that DHA and EPA moderately upregulated the candidate immune-related genes and modulated excessive activation of the immune pathway by the pathogen. This study confirmed the immunomodulatory function of unsaturated fatty acids in Yangtze sturgeon. This research will provide a reference for the preparation of artificial diets for Yangtze sturgeon.
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Affiliation(s)
- Hu Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Bin Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Nianye Yu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jingwen Qi
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ni Tang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shuyao Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhengzhi Tian
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mei Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shaoqi Xu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Bo Zhou
- Fisheries Research Institute of Sichuan Academy of Agricultural Sciences, Yibin, 644000, China.
| | - Qiaoling Long
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Defang Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhiqiong Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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Du H, Jian J, Wang B, Liu X, Chen J, Xiao K, Xia J, Yang J, Gao Y, Chen L. Hypothalamus-pituitary-gonad axis transcriptome profiling for sex differentiation in Acipenser sinensis. Sci Data 2019; 6:87. [PMID: 31197171 PMCID: PMC6565624 DOI: 10.1038/s41597-019-0099-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 05/15/2019] [Indexed: 11/24/2022] Open
Abstract
Chinese sturgeon (Acipenser sinensis), a critically endangered Acipenseridae family member, is one of the largest anadromous, native fish in China. Numerous research programmes and protection agencies have focused on breeding and preserving this endangered species. However, available information is limited on the different stages of sex development, especially on the reproductive regulation of the hypothalamus-pituitary-gonad (HPG) axis of A. sinensis. To unravel the mechanism of gene interactions during sex differentiation and gonad development of A. sinensis, we performed transcriptome sequencing using HPG samples from male and female A. sinensis in two developmental stages. In this study, 271.19 Gb high-quality transcriptome data were obtained from 45 samples belonging to 15 individuals (six in stage I, six males and three females in stage II). These transcriptomic data will help us understand the reproductive regulation of the HPG axis in the development stages of A. sinensis and provide important reference data for genomic and genetic studies in A. sinensis and related species.
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Affiliation(s)
- Hejun Du
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang, Hubei, 443100, China.
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, Hubei, 443100, China.
| | - Jianbo Jian
- BGI genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Binzhong Wang
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang, Hubei, 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, Hubei, 443100, China
| | - Xueqing Liu
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang, Hubei, 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, Hubei, 443100, China
| | - Jianwei Chen
- BGI genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong, 266555, China
| | - Kan Xiao
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang, Hubei, 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, Hubei, 443100, China
| | - Jinquan Xia
- BGI genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Jing Yang
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang, Hubei, 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, Hubei, 443100, China
| | - Yong Gao
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang, Hubei, 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, Hubei, 443100, China
| | - Lei Chen
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang, Hubei, 443100, China.
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, Hubei, 443100, China.
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13
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Gonadal transcriptomic analysis and identification of candidate sex-related genes in Mesocentrotus nudus. Gene 2019; 698:72-81. [DOI: 10.1016/j.gene.2019.02.054] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 02/18/2019] [Accepted: 02/20/2019] [Indexed: 12/14/2022]
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Chen Y, Gong Q, Song M, Lai J, Sun J, Liu Y. Identification and characterization of three novel antimicrobial peptides from Acipenser dabryanus. FISH & SHELLFISH IMMUNOLOGY 2019; 88:207-216. [PMID: 30807859 DOI: 10.1016/j.fsi.2019.02.050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/18/2019] [Accepted: 02/22/2019] [Indexed: 06/09/2023]
Abstract
Antimicrobial peptides (AMPs) play essential roles in the innate immune system to protect against a wide variety of pathogens in aquatic environments. In this study, three very important AMPs, cathelicidin, hepcidin and defensin, were identified in the critically endangered Acipenser dabryanus. The full-length cDNA sequences of these three AMPs were identified from transcriptome sequencing and the rapid amplification of cDNA ends (RACE) technique. Phylogenetic analysis showed that cathelicidin formed a clade with the other members of the cathelicidin family, and similar results were obtained for hepcidin. The A. dabryanus β-defensin belonged to the fish class 2 β-defensins. A tissue distribution study showed that the three AMP transcripts could be detected constitutively in various tissues. The highest expression levels of cathelicidin and hepcidin were found in the liver, while defensin was primarily expressed in the skin. Bacterial challenge in vivo revealed significant changes in the gene expression of the three AMPs at both mucosal sites and systemic sites. Striking upregulation of cathelicidin and hepcidin was observed in the skin at 12 h post-challenge, with increases of more than 7000-fold and 1000-fold, respectively, compared to the control, and the expression of defensin mRNA was remarkably elevated in the hindgut (by 230-fold at 6 h post-challenge). Moreover, according to the expression profiles of the AMPs post-challenge, we found that the mucosal immune response occurred earlier than the systemic immune response following bacterial infection. Our results suggest that these three novel AMPs may play important roles in the innate immune system of A. dabryanus to protect against invading pathogens, especially during the mucosal immune response.
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Affiliation(s)
- Yeyu Chen
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China
| | - Quan Gong
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China
| | - Mingjiang Song
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China
| | - Jiansheng Lai
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China
| | - Jiahua Sun
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China
| | - Ya Liu
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China.
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