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Żelazowska M, Pšenička M. Secondary growth ovarian follicles of the pigmented sterlet sturgeon Acipenser ruthenus L. 1758 (Acipenseriformes, Chondrostei, Actinopterygii, Osteichthyes) - Microscopic study of oocytes, egg envelope and diversification of follicular cells. Micron 2024; 186:103701. [PMID: 39128200 DOI: 10.1016/j.micron.2024.103701] [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: 06/24/2024] [Revised: 07/29/2024] [Accepted: 08/01/2024] [Indexed: 08/13/2024]
Abstract
The individual ovarian follicle of sturgeons (Acipenseriformes, Acipenseridae) contains an oocyte surrounded by follicular cells (FCs), basal lamina, and thecal cells. The late stages of the secondary growth of follicles (mid- and advanced vitellogenic) are not fully explained in Acipenseriformes. To explore and discuss the ultrastructure of oocytes, FCs, an egg envelope, and explain how micropylar cells differentiate and the canals of a multiple micropyle are formed, the samples of ovaries of the mature sterlet sturgeon Acipenser ruthenus were examined. The oocytes are polarized, the nucleus is located in the animal hemisphere, contains lampbrush chromosomes and multiple nucleoli. In the ooplasm three regions are present: a perinuclear (contains the mitochondria), an endoplasm (contains the lipid droplets and yolk platelets), and a periplasm (contains the cortical granules, melanosomes, endocytotic and exocytotic vesicles). The melanosomes in animal hemisphere form two concentric rings separated by a lighter region between them. The FCs are differentiated into bright and dark cells that are both translationally and secretory active. Diversification of FCs involves repeated and cytoskeleton-dependent change of shape. In the advanced follicles the FCs are diversified into micropylar, the animal and vegetal regions cells, and the cells that delaminated from the epithelium in the animal region. The egg envelope is present in the perioocytic space and consists of three layers: (1) an inner layer or vitelline envelope, (2) a middle layer, and (3) an outer layer. The inner layer consists of four sublayers: (a) a filamentous sublayer composed of filaments released from the oocytes, (b) a trabecular 1 sublayer and (c) a trabecular 2 sublayer named due to the sequence of the deposition, and composed of filaments, fibres and trabecules, (d) a homogeneous sublayer located between the trabecular 1 and trabecular 2 sublayers composed of filaments that adhere to each other closely. The middle layer contains two sublayers: a porous 1 and a porous 2 (composed of granular material) which are released by the oocyte and FCs. The outer layer consists of fibrillar material released by the FCs. The egg envelope is pierced by radial canals formed around the microvilli of the oocyte and the microvilli-like processes of FCs. A micropylar field in the egg envelope that covers the animal pole of the oocyte contains 1 - 4 micropylar canals. Micropylar cells are involved in their formation. The shape of these cells is icicle-like and the cytoplasm is differentiated into two regions (a basal and apical bearing a projection) equipped with different sets of organelles.
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Affiliation(s)
- Monika Żelazowska
- Department of Developmental Biology and Invertebrate Morphology, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Kraków, Poland.
| | - Martin Pšenička
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Vodňany, Czechia
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Yue H, Ye H, Ruan R, Du H, Li C. Identification of ActivinβA and Gonadotropin Regulation of the Activin System in the Ovary of Chinese Sturgeon Acipenser sinensis. Animals (Basel) 2024; 14:2314. [PMID: 39199851 PMCID: PMC11350771 DOI: 10.3390/ani14162314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 08/02/2024] [Accepted: 08/07/2024] [Indexed: 09/01/2024] Open
Abstract
Activin is a dimeric growth factor with diverse biological activities in vertebrates. This study aimed to investigate the regulatory role of the activin signaling pathway in the ovary of the endangered, cultured sturgeon species Acipenser sinensis. One activinβA subunit was identified, with a full-length complementary DNA (cDNA) sequence of 1572 base pairs. Multiple sequence alignment suggested that ActivinβA shared high sequence identities with its counterparts in four other sturgeon species. Phylogenetic analysis indicated the conserved evolution of ActivinβA among vertebrates from mammals to fish species. Transcripts of activinβA were distributed ubiquitously in the liver, kidney, intestine, ovary, midbrain, hypothalamus, and pituitary, with the highest transcription found in the pituitary. In Chinese sturgeon ovarian cells, in vitro human recombinant Activin A incubation stimulated the activin system-related gene transcriptions of activinβA, follistatin, its receptors -activinRIIA and activinRIIB, and drosophila mothers against decapentaplegic proteins (smads) smad2, smad3, and smad4. Ovary development-related mRNA levels of cyp19a1a and aromatase receptors of erα and erβ were enhanced by Activin A or human chorionic gonadotropin (hCG) incubation. Furthermore, 15 IU/mL hCG treatment increased the transcription levels of activinβA, follistatin, activinRIIA, and smad2. This suggested that the activin system was functional for the regulation of ovary development in Chinese sturgeon, possibly under the regulation of gonadotropin, by recruiting activinβA, follistatin, activinRIIA, and smad2. These results were helpful for the molecular exploration of activin signaling in fish species, as well as the ovarian maturation regulation of A. sinensis.
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Affiliation(s)
| | | | | | | | - 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; (H.Y.)
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Park JE, Patnaik BB, Sang MK, Song DK, Jeong JY, Hong CE, Kim YT, Shin HJ, Ziwei L, Patnaik HH, Hwang HJ, Park SY, Kang SW, Ko JH, Lee JS, Park HS, Jo YH, Han YS, Lee YS. Transcriptome sequencing of the endangered land snail Karaftohelix adamsi from the Island Ulleung: De novo assembly, annotation, valuation of fitness genes and SSR markers. Genes Genomics 2024; 46:851-870. [PMID: 38809491 DOI: 10.1007/s13258-024-01511-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: 06/12/2023] [Accepted: 03/08/2024] [Indexed: 05/30/2024]
Abstract
BACKGROUND The Bradybaenidae snail Karaftohelix adamsi is endemic to Korea, with the species tracked from Island Ulleung in North Gyeongsang Province of South Korea. K. adamsi has been classified under the Endangered Wildlife Class II species of Korea and poses a severe risk of extinction following habitat disturbances. With no available information at the DNA (genome) or mRNA (transcriptome) level for the species, conservation by utilizing informed molecular resources seems difficult. OBJECTIVE In this study, we used the Illumina short-read sequencing and Trinity de novo assembly to draft the reference transcriptome of K. adamsi. RESULTS After assembly, 13,753 unigenes were obtained of which 10,511 were annotated to public databases (a maximum of 10,165 unigenes found homologs in PANM DB). A total of 6,351, 3,535, 358, and 3,407 unigenes were ascribed to the functional categories under KOG, GO, KEGG, and IPS, respectively. The transcripts such as the HSP 70, aquaporin, TLR, and MAPK, among others, were screened as putative functional resources for adaptation. DNA transposons were found to be thickly populated in comparison to retrotransposons in the assembled unigenes. Further, 2,164 SSRs were screened with the promiscuous presence of dinucleotide repeats such as AC/GT and AG/CT. CONCLUSION The transcriptome-guided discovery of molecular resources in K. adamsi will not only serve as a basis for functional genomics studies but also provide sustainable tools to be utilized for the protection of the species in the wild. Moreover, the development of polymorphic SSRs is valuable for the identification of species from newer habitats and cross-species genotyping.
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Affiliation(s)
- Jie Eun Park
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Chungnam, 31, Asan, South Korea
| | - Bharat Bhusan Patnaik
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
- PG Department of Biosciences and Biotechnology, Fakir Mohan University, Nuapadhi, Balasore, Odisha, 756089, India
| | - Min Kyu Sang
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Chungnam, 31, Asan, South Korea
| | - Dae Kwon Song
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Chungnam, 31, Asan, South Korea
| | - Jun Yang Jeong
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - Chan Eui Hong
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - Yong Tae Kim
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - Hyeon Jun Shin
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - Liu Ziwei
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - Hongray Howrelia Patnaik
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- PG Department of Zoology, BJB Autonomous College, Bhubaneswar, Odisha, 751014, India
| | - Hee Ju Hwang
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - So Young Park
- Biodiversity Research Team, Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Gyeongbuk, South Korea
| | - Se Won Kang
- Biological Resource Center (BRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeonbuk, South Korea
| | - Jung Ho Ko
- Police Science Institute, Korean National Police University, Asan, 31539, Chungnam, Korea
| | - Jun Sang Lee
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
| | - Hong Seog Park
- Research Institute, GnC BIO Co., LTD, 621-6 Banseok-Dong, Yuseong-Gu, Daejeon, 34069, Korea
| | - Yong Hun Jo
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - Yeon Soo Han
- College of Agriculture and Life Science, Chonnam National University, 77 Yongbong-Ro, Buk-Gu, Gwangju, 61186, South Korea
| | - Yong Seok Lee
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea.
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Chungnam, 31, Asan, South Korea.
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea.
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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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Rather MA, Agarwal D, Bhat TA, Khan IA, Zafar I, Kumar S, Amin A, Sundaray JK, Qadri T. Bioinformatics approaches and big data analytics opportunities in improving fisheries and aquaculture. Int J Biol Macromol 2023; 233:123549. [PMID: 36740117 DOI: 10.1016/j.ijbiomac.2023.123549] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
Aquaculture has witnessed an excellent growth rate during the last two decades and offers huge potential to provide nutritional as well as livelihood security. Genomic research has contributed significantly toward the development of beneficial technologies for aquaculture. The existing high throughput technologies like next-generation technologies generate oceanic data which requires extensive analysis using appropriate tools. Bioinformatics is a rapidly evolving science that involves integrating gene based information and computational technology to produce new knowledge for the benefit of aquaculture. Bioinformatics provides new opportunities as well as challenges for information and data processing in new generation aquaculture. Rapid technical advancements have opened up a world of possibilities for using current genomics to improve aquaculture performance. Understanding the genes that govern economically relevant characteristics, necessitates a significant amount of additional research. The various dimensions of data sources includes next-generation DNA sequencing, protein sequencing, RNA sequencing gene expression profiles, metabolic pathways, molecular markers, and so on. Appropriate bioinformatics tools are developed to mine the biologically relevant and commercially useful results. The purpose of this scoping review is to present various arms of diverse bioinformatics tools with special emphasis on practical translation to the aquaculture industry.
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Affiliation(s)
- Mohd Ashraf Rather
- Division of Fish Genetics and Biotechnology, Faculty of Fisheries Ganderbal, Sher-e- Kashmir University of Agricultural Science and Technology, Kashmir, India.
| | - Deepak Agarwal
- Institute of Fisheries Post Graduation Studies OMR Campus, Vaniyanchavadi, Chennai, India
| | | | - Irfan Ahamd Khan
- Division of Fish Genetics and Biotechnology, Faculty of Fisheries Ganderbal, Sher-e- Kashmir University of Agricultural Science and Technology, Kashmir, India
| | - Imran Zafar
- Department of Bioinformatics and Computational Biology, Virtual University Punjab, Pakistan
| | - Sujit Kumar
- Department of Bioinformatics and Computational Biology, Virtual University Punjab, Pakistan
| | - Adnan Amin
- Postgraduate Institute of Fisheries Education and Research Kamdhenu University, Gandhinagar-India University of Kurasthra, India; Department of Aquatic Environmental Management, Faculty of Fisheries Rangil- Ganderbel -SKUAST-K, India
| | - Jitendra Kumar Sundaray
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha 751002, India
| | - Tahiya Qadri
- Division of Food Science and Technology, SKUAST-K, Shalimar, India
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Transcript annotation of Chinese sturgeon (Acipenser sinensis) using Iso-seq and RNA-seq data. Sci Data 2023; 10:105. [PMID: 36823216 PMCID: PMC9950146 DOI: 10.1038/s41597-023-02014-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 02/10/2023] [Indexed: 02/25/2023] Open
Abstract
Chinese sturgeon (Acipenser sinensis) is a critically endangered fish inhabiting the Yangtze River and Chinese coastal waters. Numerous research projects and conservation efforts have focused on artificial propagation and release to restore this endangered species. However, genomic and full-length transcriptomic sequencing of Chinese sturgeon has rarely been reported. In this study, a total of 10 Chinese sturgeon tissues were used for PacBio Iso-seq and RNA-seq analyses. A total of 19,538 full-length transcripts were obtained with sizes from 51 bp to 7,033 bp. Moreover, cluster analysis of gene families and phylogenetic analysis of 14 species were performed. Furthermore, lncRNAs and coding sequence (CDS) were identified in all Chinese sturgeon tissues. Finally, gene expression profiles and differentially expressed genes (DEGs) were analyzed among 10 tissues in Chinese sturgeon. Taken together, full-length transcripts and the gene expression profile from Chinese sturgeon tissues will provide gene sequences and expression information for future functional genomic study and be very helpful for comprehensive understanding of the genetic mechanism of endangerment in Chinese sturgeon.
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Boscari E, Wu J, Jiang T, Zhang S, Cattelan S, Wang C, Du H, Li C, Li J, Ruan R, Xu J, Zheng Y, Palle SD, Yang J, Congiu L, Wei Q. The last giants of the Yangtze River: A multidisciplinary picture of what remains of the endemic Chinese sturgeon. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 843:157011. [PMID: 35772549 DOI: 10.1016/j.scitotenv.2022.157011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/09/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
The Chinese sturgeon, an important endemism of the Yangtze River, belongs to 'the most critically endangered group of species' worldwide, with overfishing and habitat destruction being the main drivers towards extinction. Newly obtained microchemical comparisons between animals and water from different river locations revealed a probable shifting of the spawning ground few kilometers downstream compared to the only previously known site, located under the Gezhouba Dam. This offers a glimmer of hope for an adaptive response to habitat perturbation caused by the recently built Three Gorges dam on the Yangtze River. On the other hand, genetic data provide an estimate of about 20 breeders participating in the only significant breeding event of the past 10 years. This warns of a near species extinction forecast if no in situ and ex situ conservation efforts occur promptly. Given these results we propose a list of priority conservation actions that urgently need to be promoted, supported, and put into practice.
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Affiliation(s)
- Elisa Boscari
- 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; Ecology Research Unit, Department of Biology, University of Padua, Padova 35131, Italy
| | - Jinming 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
| | - Tao Jiang
- Key Laboratory of Fishery Ecological Environment Assessment and Resource Conservation in Middle and Lower Reaches of the Yangtze River, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi City, Jiangsu Province 214081, China
| | - Shuhuan Zhang
- Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China
| | - Silvia Cattelan
- Ecology Research Unit, Department of Biology, University of Padua, Padova 35131, Italy
| | - Chengyou Wang
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Hao Du
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - 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
| | - Junyi 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
| | - 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
| | - Junmin Xu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Yueping Zheng
- Shanghai Aquatic Wildlife Conservation and Research Center, Chongming, Shanghai 200003, China
| | - Stefano Dalle Palle
- Ecology Research Unit, Department of Biology, University of Padua, Padova 35131, Italy
| | - Jian Yang
- Key Laboratory of Fishery Ecological Environment Assessment and Resource Conservation in Middle and Lower Reaches of the Yangtze River, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi City, Jiangsu Province 214081, China
| | - Leonardo Congiu
- Ecology Research Unit, Department of Biology, University of Padua, Padova 35131, Italy.
| | - Qiwei Wei
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China
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Castro-Arnau J, Chauvigné F, Gómez-Garrido J, Esteve-Codina A, Dabad M, Alioto T, Finn RN, Cerdà J. Developmental RNA-Seq transcriptomics of haploid germ cells and spermatozoa uncovers novel pathways associated with teleost spermiogenesis. Sci Rep 2022; 12:14162. [PMID: 35986060 PMCID: PMC9391476 DOI: 10.1038/s41598-022-18422-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 08/10/2022] [Indexed: 12/18/2022] Open
Abstract
AbstractIn non-mammalian vertebrates, the molecular mechanisms involved in the transformation of haploid germ cells (HGCs) into spermatozoa (spermiogenesis) are largely unknown. Here, we investigated this process in the marine teleost gilthead seabream (Sparus aurata) through the examination of the changes in the transcriptome between cell-sorted HGCs and ejaculated sperm (SPZEJ). Samples were collected under strict quality controls employing immunofluorescence microscopy as well as by determining the sperm motion kinematic parameters by computer-assisted sperm analysis. Deep sequencing by RNA-seq identified a total of 7286 differentially expressed genes (DEGs) (p-value < 0.01) between both cell types, of which nearly half were upregulated in SPZEJ compared to HCGs. In addition, approximately 9000 long non-coding RNAs (lncRNAs) were found, of which 56% were accumulated or emerged de novo in SPZEJ. The upregulated transcripts are involved in transcriptional and translational regulation, chromatin and cytoskeleton organization, metabolic processes such as glycolysis and oxidative phosphorylation, and also include a number of ion and water channels, exchangers, transporters and receptors. Pathway analysis conducted on DEGs identified 37 different signaling pathways enriched in SPZEJ, including 13 receptor pathways, from which the most predominant correspond to the chemokine and cytokine, gonadotropin-releasing hormone receptor and platelet derived growth factor signaling pathways. Our data provide new insight into the mRNA and lncRNA cargos of teleost spermatozoa and uncover the possible involvement of novel endocrine mechanisms during the differentiation and maturation of spermatozoa.
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Zhao C, Li Y, Liang Z, Gao L, Han C, Wu X. Molecular Mechanisms Associated with the Resistance of Rhizoctonia solani AG-4 Isolates to the Succinate Dehydrogenase Inhibitor Thifluzamide. PHYTOPATHOLOGY 2022; 112:567-578. [PMID: 34615378 DOI: 10.1094/phyto-06-21-0266-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Thifluzamide, a succinate dehydrogenase (SDH) inhibitor, possesses high activity against Rhizoctonia. In this study, 144 Rhizoctonia solani AG-4 (4HGI, 4HGII, and 4HGIII) isolates, the predominate pathogen associated with sugar beet seedling damping-off, were demonstrated to be sensitive to thifluzamide with a calculated mean median effective concentration of 0.0682 ± 0.0025 μg/ml. Thifluzamide-resistant isolates were generated using fungicide-amended media, resulting in four AG-4HGI isolates and eight AG-4HGII isolates with stable resistance and almost no loss in fitness. Evaluation of cross-resistance of the 12 thifluzamide-resistant isolates and their corresponding parental-sensitive isolates revealed a moderately positive correlation between thifluzamide resistance and the level of resistance to eight other fungicides from three groups, the exception being fludioxonil. An active efflux of fungicide through ATP-binding cassette and major facilitator superfamily transporters was found to be correlated to the resistance of R. solani AG-4HGII isolates to thifluzamide based on RNA-sequencing and quantitative reverse transcription-PCR analyses. Sequence analysis of sdhA, sdhB, sdhC, and sdhD revealed replacement of isoleucine by phenylalanine at position 61 in SDHC in 9 of the 12 generated thifluzamide-resistant isolates. No other mutations were found in any of the other genes. Collectively, the data indicate that the active efflux of fungicide and a point mutation in sdhC may contribute to the resistance of R. solani AG-4HGI and AG-4HGII isolates to thifluzamide in vitro. This is the first characterization of the potential molecular mechanism associated with the resistance of R. solani AG-4 isolates to thifluzamide and provides practical guidance for the use of this fungicide.
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Affiliation(s)
- Can Zhao
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
- College of Horticulture, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
| | - Yuting Li
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
| | - Zhijian Liang
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
| | - Lihong Gao
- College of Horticulture, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
| | - Chenggui Han
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
| | - Xuehong Wu
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
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10
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Aversa-Marnai M, Castellano M, Quartiani I, Conijesky D, Perretta A, Villarino A, Silva-Álvarez V, Ferreira AM. Different response of Acipenser gueldenstaedtii CRP/SAP and SAA to bacterial challenge and chronic thermal stress sheds light on the innate immune system of sturgeons. FISH & SHELLFISH IMMUNOLOGY 2022; 121:404-417. [PMID: 34971737 DOI: 10.1016/j.fsi.2021.12.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/16/2021] [Accepted: 12/18/2021] [Indexed: 06/14/2023]
Abstract
Sturgeons are chondrostean fish critically endangered due to anthropogenic loss and degradation of natural habitat and overfishing for meat and caviar production. Consequently, sturgeon aquaculture has extensively developed lately, being Russian sturgeon (Acipenser gueldenstaedtii) the second most important species reared for caviar production. However, Russian sturgeon aquaculture in subtropical countries, such as Uruguay, confronts difficulties because fish have to endure excessive summertime warm temperatures, which weaken their innate defences facilitating opportunistic infections. To address this problem, we look for identifying putative acute phase proteins (APPs), which might be robust serum biomarkers of both infection and chronic thermal stress, applied to monitoring Russian sturgeon health status in farms. We focused on the C-Reactive Protein/Serum Amyloid P (CRP/SAP) pentraxin since the pentraxin family includes well-known APPs, better characterised in mammals than fish. We identified A.gueldenstaedtii CRP/SAP (AgCRP/SAP), as a member of the universal CRP/SAP pentraxin sub-family, and studied AgCRP/SAP involvement in sturgeon response to bacterial challenge and chronic thermal stress, in comparison with A. gueldenstaedtii Serum Amyloid A (AgSAA), a previously described positive APP. Results showed that AgCRP/SAP is a constitutive serum component that remained constant upon Aeromonas hydrophila challenge and chronic thermal stress. Contrastingly, serum AgSAA was subjected to regulation by bacterial and thermal stress challenges, showing a 50-fold increase and 3-fold decline in serum levels, respectively. Overall, results highlight the potential value of AgSAA, but not of AgCRP/SAP, as a biomarker of bacterial infection and the need to continue searching for robust chronic thermal stress biomarkers in sturgeons.
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Affiliation(s)
- Marcio Aversa-Marnai
- Unidad de Inmunología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, CP 11600, Montevideo, Uruguay; Área Inmunología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, CP 11600, Montevideo, Uruguay
| | - Mauricio Castellano
- Unidad de Inmunología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, CP 11600, Montevideo, Uruguay; Área Inmunología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, CP 11600, Montevideo, Uruguay; Sección Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de la República, CP 11400, Montevideo, Uruguay
| | - Ignacio Quartiani
- Unidad de Patología, Biología y Cultivo de Organismos Acuáticos, Departamento de Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad de la República, CP 11300, Montevideo, Uruguay
| | | | - Alejandro Perretta
- Unidad de Patología, Biología y Cultivo de Organismos Acuáticos, Departamento de Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad de la República, CP 11300, Montevideo, Uruguay
| | - Andrea Villarino
- Sección Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de la República, CP 11400, Montevideo, Uruguay
| | - Valeria Silva-Álvarez
- Unidad de Inmunología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, CP 11600, Montevideo, Uruguay; Área Inmunología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, CP 11600, Montevideo, Uruguay.
| | - Ana María Ferreira
- Unidad de Inmunología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, CP 11600, Montevideo, Uruguay; Área Inmunología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, CP 11600, Montevideo, Uruguay.
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Xie X, Tichopád T, Kislik G, Langerová L, Abaffy P, Šindelka R, Franěk R, Fučíková M, Steinbach C, Shah MA, Šauman I, Chen F, Pšenička M. Isolation and Characterization of Highly Pure Type A Spermatogonia From Sterlet ( Acipenser ruthenus) Using Flow-Cytometric Cell Sorting. Front Cell Dev Biol 2021; 9:772625. [PMID: 34957105 PMCID: PMC8708567 DOI: 10.3389/fcell.2021.772625] [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: 09/08/2021] [Accepted: 11/08/2021] [Indexed: 12/17/2022] Open
Abstract
Sturgeons are among the most ancient linages of actinopterygians. At present, many sturgeon species are critically endangered. Surrogate production could be used as an affordable and a time-efficient method for endangered sturgeons. Our study established a method for identifying and isolating type A spermatogonia from different developmental stages of testes using flow cytometric cell sorting (FCM). Flow cytometric analysis of a whole testicular cell suspension showed several well-distinguished cell populations formed according to different values of light scatter parameters. FCM of these different cell populations was performed directly on glass slides for further immunocytochemistry to identify germ cells. Results showed that the cell population in gate P1 on a flow cytometry plot (with high forward scatter and high side scatter parameter values) contains the highest amount of type A spermatogonia. The sorted cell populations were characterized by expression profiles of 10 germ cell specific genes. The result confirmed that setting up for the P1 gate could precisely sort type A spermatogonia in all tested testicular developmental stages. The P2 gate, which was with lower forward scatter and side scatter values mostly, contained type B spermatogonia at a later maturing stage. Moreover, expressions of plzf, dnd, boule, and kitr were significantly higher in type A spermatogonia than in later developed germ cells. In addition, plzf was firstly found as a reliable marker to identify type A spermatogonia, which filled the gap of identification of spermatogonial stem cells in sterlet. It is expected to increase the efficiency of germ stem cell culture and transplantation with plzf identification. Our study thus first addressed a phenotypic characterization of a pure type A spermatogonia population in sterlet. FCM strategy can improve the production of sturgeons with surrogate broodstock and further the analysis of the cellular and molecular mechanisms of sturgeon germ cell development.
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Affiliation(s)
- Xuan Xie
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, Research Institute of Fish Culture and Hydrobiology, University of South Bohemia in České Budějovice, Vodňany, Czechia
| | - Tomáš Tichopád
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, Research Institute of Fish Culture and Hydrobiology, University of South Bohemia in České Budějovice, Vodňany, Czechia
| | - Galina Kislik
- Imaging Methods Core Facility at BIOCEV, Operated by Faculty of Science, Charles University in Prague, Vestec, Czechia
| | - Lucie Langerová
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
| | - Pavel Abaffy
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
| | - Radek Šindelka
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
| | - Roman Franěk
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, Research Institute of Fish Culture and Hydrobiology, University of South Bohemia in České Budějovice, Vodňany, Czechia
| | - Michaela Fučíková
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, Research Institute of Fish Culture and Hydrobiology, University of South Bohemia in České Budějovice, Vodňany, Czechia
| | - Christoph Steinbach
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, Research Institute of Fish Culture and Hydrobiology, University of South Bohemia in České Budějovice, Vodňany, Czechia
| | - Mujahid Ali Shah
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, Research Institute of Fish Culture and Hydrobiology, University of South Bohemia in České Budějovice, Vodňany, Czechia
| | - Ivo Šauman
- Biology Center of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czechia.,University of South Bohemia, Faculty of Science, České Budějovice, Czechia
| | - Fan Chen
- Department of Pharmacology, C_DAT, University Medicine Greifswald, Greifswald, Germany
| | - Martin Pšenička
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, Research Institute of Fish Culture and Hydrobiology, University of South Bohemia in České Budějovice, Vodňany, Czechia
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12
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Zhong Z, Ao L, Wang Y, Wang S, Zhao L, Ma S, Jiang Y. Comparison of differential expression genes in ovaries and testes of Pearlscale angelfish Centropyge vrolikii based on RNA-Seq analysis. FISH PHYSIOLOGY AND BIOCHEMISTRY 2021; 47:1565-1583. [PMID: 34415453 DOI: 10.1007/s10695-021-00977-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 06/20/2021] [Indexed: 06/13/2023]
Abstract
Pearlscale angelfish Centropyge vrolikii is a kind of protogynous hermaphrodite fish with a natural sexual reversion. Under appropriate social conditions, a female fish can transform into a male fish spontaneously. It is an important prerequisite for artificial breeding to understand the process of its gonadal development and sexual reversion. Gonadal development is regulated by many sex-related genes. In this study, we used unreferenced RNA-Seq technology to sequence the ovary at the perinucleolus stage (OII), ovary at the yolk vesicle stage (OIV),IV and testis (T), respectively; screened the gonadal differential expression genes (DEGs); and analyzed the expression of these genes in different developmental stages of ovary and different sex gonads. The results showed that a total of 142,589 all-unigene samples were assembled, and gene annotation was performed by COG, GO, KEGG, KOG, Pfam, Swissprot, eggNOG, and NR functional database. Comparative analysis revealed that there were 1919 genes that were up-regulated and 1289 genes were down-regulated in comparison to OIV vs OII, while there were 3653 genes that were up-regulated and 2874 genes were down-regulated in comparison of OIV vs T, there were 3345 genes that were up-regulated and 2995 genes were down-regulated in comparison of the OII vs the T. At the same time, the results verified by RT-qPCR were consistent with the variation trend of transcriptome data. Among the results, amh, sox9b, dmrt1, dmrt2, cyp11a, cyp17a, and cyp19a were significantly expressed in the testes, while sox3, sox4, sox11, sox17, and hsd3b7 were significantly expressed in the ovaries. And, the expression of the amh, sox9b, dmrt2, and dmrt1 were low in the OII and OIV, while significantly increased during the ovotestis in the hermaphroditic period (OT), and finally reached the highest level in pure testis after sex reversal. The expression of sox3, sox4, hsd3b7, sox11, and sox17 was significantly reduced during the hermaphroditic period (OT). These results suggested that these genes may play an important role in the process of sex reversal. This study is helpful to further understand the molecular regulation mechanism of gonadal development and sexual reversion in Pearlscale angelfish and also provide important clues for future studies.
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Affiliation(s)
- Zhaowei Zhong
- Key Laboratory of Healthy Mariculture for East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, 361021, China
| | - Lulu Ao
- Key Laboratory of Healthy Mariculture for East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, 361021, China
| | - Yilei Wang
- Key Laboratory of Healthy Mariculture for East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, 361021, China
- National Demonstration Center for Experimental Aquatic Science and Technology Education, Jimei University), Xiamen, 361021, China
| | - Shuhong Wang
- Key Laboratory of Healthy Mariculture for East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, 361021, China
- National Demonstration Center for Experimental Aquatic Science and Technology Education, Jimei University), Xiamen, 361021, China
| | - Liping Zhao
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Senwei Ma
- Key Laboratory of Healthy Mariculture for East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, 361021, China
| | - Yonghua Jiang
- Key Laboratory of Healthy Mariculture for East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, 361021, China.
- National Demonstration Center for Experimental Aquatic Science and Technology Education, Jimei University), Xiamen, 361021, China.
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13
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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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14
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De Novo Transcriptomic Characterization Enables Novel Microsatellite Identification and Marker Development in Betta splendens. Life (Basel) 2021; 11:life11080803. [PMID: 34440547 PMCID: PMC8400612 DOI: 10.3390/life11080803] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/05/2021] [Accepted: 08/07/2021] [Indexed: 01/10/2023] Open
Abstract
The wild populations of the commercially valuable ornamental fish species, Betta splendens, and its germplasm resources have long been threatened by habitat degradation and contamination with artificially bred fish. Because of the lack of effective marker resources, population genetics research projects are severely hampered. To generate genetic data for developing polymorphic simple sequence repeat (SSR) markers and identifying functional genes, transcriptomic analysis was performed. Illumina paired-end sequencing yielded 105,505,486 clean reads, which were then de novo assembled into 69,836 unigenes. Of these, 35,751 were annotated in the non-redundant, EuKaryotic Orthologous Group, Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology databases. A total of 12,751 SSR loci were identified from the transcripts and 7970 primer pairs were designed. One hundred primer pairs were randomly selected for PCR validation and 53 successfully generated target amplification products. Further validation demonstrated that 36% (n = 19) of the 53 amplified loci were polymorphic. These data could not only enrich the genetic information for the identification of functional genes but also effectively facilitate the development of SSR markers. Such knowledge would accelerate further studies on the genetic variation and evolution, comparative genomics, linkage mapping and molecular breeding in B. splendens.
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15
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Jeffries KM, Teffer A, Michaleski S, Bernier NJ, Heath DD, Miller KM. The use of non-lethal sampling for transcriptomics to assess the physiological status of wild fishes. Comp Biochem Physiol B Biochem Mol Biol 2021; 256:110629. [PMID: 34058376 DOI: 10.1016/j.cbpb.2021.110629] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 05/19/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022]
Abstract
Fishes respond to different abiotic and biotic stressors through changes in gene expression as a part of an integrated physiological response. Transcriptomics approaches have been used to quantify gene expression patterns as a reductionist approach to understand responses to environmental stressors in animal physiology and have become more commonly used to study wild fishes. We argue that non-lethal sampling for transcriptomics should become the norm for assessing the physiological status of wild fishes, especially when there are conservation implications. Processes at the level of the transcriptome provide a "snapshot" of the cellular conditions at a given time; however, by using a non-lethal sampling protocol, researchers can connect the transcriptome profile with fitness-relevant ecological endpoints such as reproduction, movement patterns and survival. Furthermore, telemetry is a widely used approach in fisheries to understand movement patterns in the wild, and when combined with transcriptional profiling, provides arguably the most powerful use of non-lethal sampling for transcriptomics in wild fishes. In this review, we discuss the different tissues that can be successfully incorporated into non-lethal sampling strategies, which is particularly useful in the context of the emerging field of conservation transcriptomics. We briefly describe different methods for transcriptional profiling in fishes from high-throughput qPCR to whole transcriptome approaches. Further, we discuss strategies and the limitations of using transcriptomics for non-lethally studying fishes. Lastly, as 'omics' technology continues to advance, transcriptomics paired with different omics approaches to study wild fishes will provide insight into the factors that regulate phenotypic variation and the physiological responses to changing environmental conditions in the future.
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Affiliation(s)
- Ken M Jeffries
- Department of Biological Sciences, University of Manitoba, 50 Sifton Road, Winnipeg, Manitoba R3T 2N2, Canada.
| | - Amy Teffer
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA 01003, United States of America
| | - Sonya Michaleski
- Department of Biological Sciences, University of Manitoba, 50 Sifton Road, Winnipeg, Manitoba R3T 2N2, Canada
| | - Nicholas J Bernier
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Daniel D Heath
- Department of Integrative Biology, Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC V9T 6N7, Canada
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Liu QN, Tang YY, Zhou MJ, Luo S, Li YT, Wang G, Zhang DZ, Yang H, Tang BP, He WF. Differentially expressed genes involved in immune pathways from yellowhead catfish (Tachysurus fulvidraco) after poly (I:C) challenge. Int J Biol Macromol 2021; 183:340-345. [PMID: 33932411 DOI: 10.1016/j.ijbiomac.2021.04.167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/23/2021] [Accepted: 04/24/2021] [Indexed: 01/11/2023]
Abstract
Yellowhead catfish (Tachysurus fulvidraco) is an important aquaculture fish species in China with a high market value. Infectious diseases pose serious threats in farmed fish species, and although vaccines can prevent certain infections, they rely on potent adjuvants. In this study, we analyzed the transcriptomic profiles of spleens from poly (I:C)-treated T. fulvidraco. We obtained 46,362,922 reads corresponding to 490,926 transcripts and 318,059 genes. Gene annotation using different databases and subsequent differential gene expression analyses led to the identification of 5587 differentially expressed genes (DEGs), of which 2473 were up-regulated and 3114 were down-regulated in poly (I:C)-treated fish. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of DEGs revealed the significant dysregulation of immune- and cancer-related genes in the spleens of poly (I:C)-treated fish. Notably, several components of JAK-STAT, MAPK, and p53 signaling pathways were significantly dysregulated in response to poly (I:C) treatment. Quantitative real-time PCR (qRT-PCR) analysis of 11 randomly selected immune response genes confirmed the reliability of our findings. In conclusion, our findings provide novel insight into the immune responses of T. fulvidraco and suggest that poly (I:C) may represent a promising adjuvant of fish vaccines.
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Affiliation(s)
- Qiu-Ning Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224007, People's Republic of China; School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, People's Republic of China
| | - Ying-Yu Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224007, People's Republic of China; College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing 210009, People's Republic of China
| | - Meng-Jiao Zhou
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224007, People's Republic of China
| | - Sha Luo
- Institute of Life Sciences, Wenzhou University, Wenzhou 325035, People's Republic of China
| | - Yue-Tian Li
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224007, People's Republic of China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Aquaculture and Life Science, Shanghai Ocean University, Shanghai 201306, People's Republic of China
| | - Gang Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224007, People's Republic of China
| | - Dai-Zhen Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224007, People's Republic of China
| | - Hui Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, People's Republic of China.
| | - Bo-Ping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224007, People's Republic of China.
| | - Wen-Fei He
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, People's Republic of China.
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17
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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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Development of EST-Molecular Markers from RNA Sequencing for Genetic Management and Identification of Growth Traits in Potato Grouper ( Epinephelus tukula). BIOLOGY 2021; 10:biology10010036. [PMID: 33430356 PMCID: PMC7825770 DOI: 10.3390/biology10010036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 12/25/2020] [Accepted: 01/05/2021] [Indexed: 12/16/2022]
Abstract
Simple Summary The potato grouper is a novel aquaculture species in Taiwan. Due to the lack of genetic information concerning this species, we have developed molecular markers based on transcriptome sequencing and further characterized their association with gene diversity and growth traits of this species. Ultimately, these markers could be utilized as accurate and efficient tools for genetic management and marker-assisted selection of potato grouper with distinct growth traits. Abstract The accuracy and efficiency of marker-assisted selection (MAS) has been proven for economically critical aquaculture species. The potato grouper (Epinephelus tukula), a novel cultured grouper species in Taiwan, shows large potential in aquaculture because of its fast growth rate among other groupers. Because of the lack of genetic information for the potato grouper, the first transcriptome and expressed sequence tag (EST)-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were developed. Initially, the transcriptome was obtained from seven cDNA libraries by using the Illumina platform. De novo transcriptome of the potato grouper yielded 51.34 Gb and 111,490 unigenes. The EST-derived SSR and SNP markers were applied in genetic management, in parentage analysis, and to discover the functional markers of economic traits. The F1 juveniles were identified as siblings from one pair of parents (80 broodstocks). Fast- and slow-growth individuals were analyzed using functional molecular markers and through their association with growth performance. The results revealed that two SNPs were correlated with growth traits. The transcriptome database obtained in this study and its derived SSR and SNP markers may be applied not only for MAS but also to maintain functional gene diversity in the novel cultured grouper.
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Serum amyloid A is a positive acute phase protein in Russian sturgeon challenged with Aeromonas hydrophila. Sci Rep 2020; 10:22162. [PMID: 33335147 PMCID: PMC7746741 DOI: 10.1038/s41598-020-79065-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/02/2020] [Indexed: 11/23/2022] Open
Abstract
The immune system of sturgeons, one of the most ancient and economically valuable fish worldwide, is poorly understood. The lack of molecular tools and data about infection biomarkers hinders the possibility to monitor sturgeon health during farming and detect infection outbreaks. To tackle this issue, we mined publicly available transcriptomic datasets and identified putative positive acute-phase proteins (APPs) of Russian sturgeons that could be induced by a bacterial infection and monitored using non-invasive methods. Teleost literature compelled us to focus on five promising candidates: hepcidin, a warm acclimation associated hemopexin, intelectin, serum amyloid A protein (SAA) and serotransferrin. Among them, SAA was the most upregulated protein at the mRNA level in the liver of sturgeons challenged with heat-inactivated or live Aeromonas hydrophila. To assess whether this upregulation yielded increasing SAA levels in circulation, we developed an in-house ELISA to quantify SAA levels in sturgeon serum. Circulating SAA rose upon bacterial challenge and positively correlated with hepatic saa expression. This is the first time serum SAA has been quantified in an Actinopterygii fish. Since APPs vary across different fish species, our work sheds light on sturgeon acute-phase response, revealing that SAA is a positive APP with potential value as infection biomarker.
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20
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Wang J, Lu C, Zhao Y, Tang Z, Song J, Fan C. Transcriptome profiles of sturgeon lateral line electroreceptor and mechanoreceptor during regeneration. BMC Genomics 2020; 21:875. [PMID: 33287707 PMCID: PMC7720607 DOI: 10.1186/s12864-020-07293-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/28/2020] [Indexed: 11/10/2022] Open
Abstract
Background The electrosensory ampullary organs (AOs) and mechanosensory neuromasts (NMs) found in sturgeon and some other non-neopterygian fish or amphibians are both originated from lateral line placodes. However, these two sensory organs have characteristic morphological and physiological differences. The molecular mechanisms for the specification of AOs and NMs are not clearly understood. Results We sequenced the transcriptome for neomycin treated sturgeon AOs and NMs in the early regeneration stages, and de novo assembled a sturgeon transcriptome. By comparing the gene expression differences among untreated AOs, NMs and general epithelia (EPs), we located some specific genes for these two sensory organs. In sturgeon lateral line, the voltage-gated calcium channels and voltage-gated potassium channels were predominant calcium and potassium channel subtypes, respectively. And by correlating gene expression with the regeneration process, we predicated several candidate key transcriptional regulation related genes might be involved in AOs and NMs regeneration. Conclusions Genes with specific expression in the two lateral line sensory organs suggests their important roles in mechanoreceptor and electroreceptor formation. The candidate transcriptional regulation related genes may be important for mechano- and electro- receptor specification, in a “dosage-related” manner. These results suggested the molecular basis for specification of these two sensory organs in sturgeon.
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Affiliation(s)
- Jian Wang
- International Joint Center for Marine Biological Sciences Research, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Chengcheng Lu
- International Joint Center for Marine Biological Sciences Research, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China.,Institute for Marine Biosystem and Neuroscience, International Center for Marine Studies, Shanghai Ocean University, Shanghai, China
| | - Yifan Zhao
- International Joint Center for Marine Biological Sciences Research, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China.,Institute for Marine Biosystem and Neuroscience, International Center for Marine Studies, Shanghai Ocean University, Shanghai, China
| | - Zhijiao Tang
- Institute for Marine Biosystem and Neuroscience, International Center for Marine Studies, Shanghai Ocean University, Shanghai, China
| | - Jiakun Song
- Institute for Marine Biosystem and Neuroscience, International Center for Marine Studies, Shanghai Ocean University, Shanghai, China
| | - Chunxin Fan
- International Joint Center for Marine Biological Sciences Research, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China. .,Institute for Marine Biosystem and Neuroscience, International Center for Marine Studies, Shanghai Ocean University, Shanghai, China.
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21
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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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22
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Jiang N, Ni Q, Fan Y, Wu S, Zhou Y, Liu W, Si K, Zhang H, Robert J, Zeng L. Characterization and expression of macrophage migration inhibitory factor (mif) in Chinese sturgeon (Acipenser sinensis). FISH & SHELLFISH IMMUNOLOGY 2020; 103:9-16. [PMID: 32344024 DOI: 10.1016/j.fsi.2020.04.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/21/2020] [Accepted: 04/23/2020] [Indexed: 06/11/2023]
Abstract
The Chinese sturgeon (Acipenser sinensis) is one of the critically endangered aquatic species in China. It is also among the oldest extant actinopterygian fish species. To advance the characterization of the Chinese sturgeon immune system, we identified the gene encoding the macrophage migration inhibitory factor (MIF), a multifunctional cytokine that contributes to both innate and adaptive immune responses. Molecular and phylogenic analysis indicates the Chinese sturgeon (cs) MIF share a high degree of structural conservation with other MIF sequences and is closely related to other bony fish MIF. At steady state, cs-mif gene is expressed at relatively high levels in the brain, and to a lesser but significant level in liver, spleen, kidney, gut and skin. The spatial expression patterns determined by in situ hybridization indicates a preferential distribution of cs-mif transcripts in the cerebral cortex, the gut epithelium, hematopoietic tissues of kidney, spleen and liver parenchyma, and skin epidermis. Marked increase of cs-mif gene expression was induced by lipopolysaccharide (LPS) stimulation and Aeromonas hydrophila infection in all tested tissues. Furthermore, higher cs-mif transcript levels were detected in the liver, spleen, kidney, gut and skin during stress response resulting from hyperthermia. These results are not only consistent with the expected role of cs-mif gene in innate immunity but also suggest a potential role of this gene in stress response to hyperthermia in the Chinese sturgeon.
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Affiliation(s)
- Nan Jiang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, 430223, PR China; Department of Microbiology and Immunology, University of Rochester Medical Center, New York, 14642, USA
| | - Qi Ni
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200092, PR China
| | - Yuding Fan
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, 430223, PR China
| | - Shuwang Wu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, 430223, PR China
| | - Yong Zhou
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, 430223, PR China
| | - Wenzhi Liu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, 430223, PR China
| | - Kaige Si
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, 430223, PR China
| | - Haigeng Zhang
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200092, PR China
| | - Jacques Robert
- Department of Microbiology and Immunology, University of Rochester Medical Center, New York, 14642, USA.
| | - Lingbing Zeng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, 430223, PR China.
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Rahdari A, Khoshkholgh M, Yarmohammadi M, Ortiz-Zarragoitia M, Lokman PM, Akhavan SR, de Cerio OD, Cancio I, Falahatkar B. The effects of 11-ketotestosterone implants on transcript levels of gonadotropin receptors, and foxl2 and dmrt1 genes in the Previtellogenic ovary of cultured beluga (Huso huso). JOURNAL OF FISH BIOLOGY 2020; 97:374-382. [PMID: 32388872 DOI: 10.1111/jfb.14366] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 04/22/2020] [Accepted: 05/01/2020] [Indexed: 06/11/2023]
Abstract
The in vivo effect of 11-ketotestosterone (11KT) on transcript levels of the gonadotropin receptors (fshr and lhr) and sex differentiation-related genes (dmrt1 and foxl2) was examined in the ovaries of immature female beluga. For this purpose, six fish were treated with implants containing 2.5 mg 11KT and a placebo group of six females of the same age and gametogenic stage were given a blank implant. The implants were intraperitoneally inserted into 4-year-old females at the previtellogenic stage (mean body weight 5580 ± 165 g) and maintained under culture conditions for 8 weeks. Ovary samples for gene expression analysis of lhr, fshr, dmrt1 and foxl2 were collected by biopsy at 3 and 8 weeks post implantation. Diameters of oocytes increased in response to 11KT treatment, both at 3 and at 8 weeks post implantation, but no obvious changes were evident in cytology. Three weeks of 11KT treatment did not affect target gene expression, but a tendency for a time-dependent decrease of lhr and dmrt1 mRNA levels was observed in both treatment and placebo groups. By 8 weeks of treatment, however, 11KT implants provoked the upregulation of fshr and foxl2 transcript levels. Furthermore, lhr and dmrt1 transcript abundances recovered by 8 weeks of exposure in both blank- and 11KT-implanted beluga. These results suggest that 11KT, either directly or indirectly, may affect gametogenesis and regulate some key components of the reproductive axis in female beluga.
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Affiliation(s)
- Abdolali Rahdari
- Fisheries Department, Faculty of Natural Resources, University of Guilan, Sowmeh Sara, Iran
- Department of Fisheries, Hamoun International Wetland Research Institute, University of Zabol, Zabol, Iran
| | - Majidreza Khoshkholgh
- Fisheries Department, Faculty of Natural Resources, University of Guilan, Sowmeh Sara, Iran
| | - Mahtab Yarmohammadi
- International Sturgeon Research Institute, Agricultural Research Education and Extension Organization, Rasht, Iran
| | - Maren Ortiz-Zarragoitia
- Cell Biology in Environmental Toxicology Research Group, Department of Zoology and Animal Cell Biology, Faculty of Science and Technology and Research Centre for Experimental Marine Biology and Biotechnology, University of the Basque Country, Basque Country, Spain
| | | | - Sobhan R Akhavan
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Oihane Diaz de Cerio
- Cell Biology in Environmental Toxicology Research Group, Department of Zoology and Animal Cell Biology, Faculty of Science and Technology and Research Centre for Experimental Marine Biology and Biotechnology, University of the Basque Country, Basque Country, Spain
| | - Ibon Cancio
- Cell Biology in Environmental Toxicology Research Group, Department of Zoology and Animal Cell Biology, Faculty of Science and Technology and Research Centre for Experimental Marine Biology and Biotechnology, University of the Basque Country, Basque Country, Spain
| | - Bahram Falahatkar
- Fisheries Department, Faculty of Natural Resources, University of Guilan, Sowmeh Sara, Iran
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Xu R, Pan L, Yang Y, Zhou Y. Characterizing transcriptome in female scallop Chlamys farreri provides new insights into the molecular mechanisms of reproductive regulation during ovarian development and spawn. Gene 2020; 758:144967. [PMID: 32707299 DOI: 10.1016/j.gene.2020.144967] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 07/06/2020] [Accepted: 07/17/2020] [Indexed: 10/23/2022]
Abstract
Bivalve mollusks are descendants of an early-Cambrian lineage and have successfully evolved unique strategies for reproduction. Nonetheless, the molecular mechanisms underlying reproductive regulation in mollusks remain to be elucidated. In this study, transcriptomes of ovary at four reproductive stages in female Chlamys farreri were characterized by RNA-Seq. Regarding signaling pathways, ECM-receptor interaction pathway, mTOR signaling pathway, Fanconi anemia pathway, FoxO signaling pathway, Wnt signaling pathway and Hedgehog signaling pathway were enriched during ovarian development processes. In addition, pathways related to energy metabolism such as Nitrogen metabolism and Arachidonic acid metabolism were enriched at spawn stage. Interestingly, Neuroactive ligand-receptor interaction was significantly enriched involved in ovarian development and spawn, and indicated the potential functions of nervous system on reproductive regulation in C. farreri. What's more, this study identified and characterized fourteen genes involved in "sex hormones synthesis and regulation", "ovarian development and spawn" and "maternal immunity" during the four reproductive stages in C. farreri. We determined that CYP17 uniquely affected gamete release by influencing the physiological balance among the steroid hormones and showed that receptors of the 5-HT and GABA neurotransmitters were tightly associated with ovarian maturation. Furthermore, to the best of our knowledge, this is the first study to report the maternal effect gene Zar1 in bivalve mollusks, likewise the maternal immunity genes displayed coordinated and cooperative expression during reproductive periods, which strengthened the environmental adaptation mechanisms of bivalves. Taken together, this study provides the first dynamic transcriptomic analysis of C. farreri at four key reproductive stages, which will assist in revealing the molecular mechanisms underlying bivalves on reproductive regulation in ovarian development and spawn.
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Affiliation(s)
- Ruiyi Xu
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Luqing Pan
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China.
| | - Yingying Yang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Yueyao Zhou
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
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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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Zhang X, Zhou J, Li L, Huang W, Ahmad HI, Li H, Jiang H, Chen J. Full-length transcriptome sequencing and comparative transcriptomic analysis to uncover genes involved in early gametogenesis in the gonads of Amur sturgeon ( Acipenser schrenckii). Front Zool 2020; 17:11. [PMID: 32308726 PMCID: PMC7147073 DOI: 10.1186/s12983-020-00355-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 03/12/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Sturgeons (Acipenseriformes) are polyploid chondrostean fish that constitute an important model species for studying development and evolution in vertebrates. To better understand the mechanisms of reproduction regulation in sturgeon, this study combined PacBio isoform sequencing (Iso-Seq) with Illumina short-read RNA-seq methods to discover full-length genes involved in early gametogenesis of the Amur sturgeon, Acipenser schrenckii. RESULTS A total of 50.04 G subread bases were generated from two SMRT cells, and herein 164,618 nonredundant full-length transcripts (unigenes) were produced with an average length of 2782 bp from gonad tissues (three testes and four ovaries) from seven 3-year-old A. schrenckii individuals. The number of ovary-specific expressed unigenes was greater than those of testis (19,716 vs. 3028), and completely different KEGG pathways were significantly enriched between the ovary-biased and testis-biased DEUs. Importantly, 60 early gametogenesis-related genes (involving 755 unigenes) were successfully identified, and exactly 50% (30/60) genes of those showed significantly differential expression in testes and ovaries. Among these, the Amh and Gsdf with testis-biased expression, and the Foxl2 and Cyp19a with ovary-biased expression strongly suggested the important regulatory roles in spermatogenesis and oogenesis of A. schrenckii, respectively. We also found the four novel Sox9 transcript variants, which increase the numbers of regulatory genes and imply function complexity in early gametogenesis. Finally, a total of 236,672 AS events (involving 36,522 unigenes) were detected, and 10,556 putative long noncoding RNAs (lncRNAs) and 4339 predicted transcript factors (TFs) were also respectively identified, which were all significantly associated with the early gametogenesis of A. schrenckii. CONCLUSIONS Overall, our results provide new genetic resources of full-length transcription data and information as a genomic-level reference for sturgeon. Crucially, we explored the comprehensive genetic characteristics that differ between the testes and ovaries of A. schrenckii in the early gametogenesis stage, which could provide candidate genes and theoretical basis for further the mechanisms of reproduction regulation of sturgeon.
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Affiliation(s)
- Xiujuan Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260 Guangdong China
| | - Jiabin Zhou
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260 Guangdong China
| | - Linmiao Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260 Guangdong China
| | - Wenzhong Huang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260 Guangdong China
| | - Hafiz Ishfaq Ahmad
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260 Guangdong China
| | - Huiming Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260 Guangdong China
| | - Haiying Jiang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260 Guangdong China
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260 Guangdong China
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De novo transcriptome assembly of four organs of Collichthys lucidus and identification of genes involved in sex determination and reproduction. PLoS One 2020; 15:e0230580. [PMID: 32218589 PMCID: PMC7100973 DOI: 10.1371/journal.pone.0230580] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/03/2020] [Indexed: 01/04/2023] Open
Abstract
The spinyhead croaker (Collichthys lucidus) is a commercially important fish species, which is mainly distributed in the coastal regions of China. However, little is known about the molecular regulatory mechanism underlying reproduction in C. lucidus. A de novo transcriptome assembly in brain, liver, ovary and testis tissues of C. lucidus was performed. Illumina sequencing generated 60,322,004, 57,044,284, 60,867,978 and 57,087,688 clean reads from brain, liver, ovary and testis tissues of C. lucidus, respectively. Totally, 131,168 unigenes with an average length of 644 bp and an N50 value of 1033 bp were assembled. In addition, 1288 genes were differentially expressed between ovary and testis, including 442 up-regulated and 846 down-regulated in ovary. Functional analysis revealed that the differentially expressed genes between ovary and testis were mainly involved in the function of sexual reproduction, sex differentiation, development of primary male sexual characteristics, female gamete generation, and male sex differentiation. A number of genes which might be involved in the regulation of reproduction and sex determination were found, including HYAL and SYCP3 and BMP15. Furthermore, 35,476 simple sequence repeats (SSRs) were identified in this transcriptome dataset, which would contribute to further genetic and mechanism researches. De novo transcriptome sequencing analysis of four organs of C. lucidus provides rich resources for understanding the mechanism of reproductive development of C. lucidus and further investigation of the molecular regulation of sex determination and reproduction of C. lucidus.
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Qiu B, Fang S, Ikhwanuddin M, Wong L, Ma H. Genome survey and development of polymorphic microsatellite loci for Sillago sihama based on Illumina sequencing technology. Mol Biol Rep 2020; 47:3011-3017. [PMID: 32124169 DOI: 10.1007/s11033-020-05348-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 02/25/2020] [Indexed: 10/24/2022]
Abstract
In this study, we first conducted a genome survey assay for Sillago sihama by Illumina sequencing platform, and then developed 15 polymorphic microsatellite loci in a wild population. A total of 129.46 Gb raw data were obtained, of which 115.07 Gb were clean data, with a sequencing depth of 179.3-folds. This genome was estimated to be 522.6 Mb in size, with the heterozygosity, repeat content and GC content being 0.63%, 21% and 44%. A total of 630,028 microsatellites were identified from the genome, of which, dinucleotide repeat was the most abundant (56.80%), followed by mononucleotide repeat (30.23%). Furthermore, 60 pairs of primers were designed and synthesized based on microsatellite sequences, of which 15 were polymorphic in a wild population. A total of 91 alleles were found, with an average of 6.07 per locus. Number of alleles, observed and expected heterozygosity per locus ranged from two to 13, from 0.250 to 0.862, and from 0.396 to 0.901, respectively. Twelve loci were highly informative (PIC > 0.5), and the others were medium informative (0.25 < PIC < 0.5). Seven loci deviated from Hardy-Weinberg equilibrium after Bonferroni correction (P < 0.0033). No significant linkage disequilibrium was detected between loci pairs. This study provided a large number of genomic resources and 15 polymorphic microsatellite loci that should be helpful for the further genetic studies in S. sihama.
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Affiliation(s)
- Bixun Qiu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, 243 Daxue Road, Shantou, 515063, China.,STU‑UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Shaobin Fang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, 243 Daxue Road, Shantou, 515063, China.,STU‑UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Mhd Ikhwanuddin
- STU‑UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China.,Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Malaysia
| | - Lilian Wong
- STU‑UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China.,Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Malaysia
| | - Hongyu Ma
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, 243 Daxue Road, Shantou, 515063, China. .,STU‑UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, 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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Lu X, Wen H, Li Q, Wang G, Li P, Chen J, Sun Y, Yang C, Wu F. Comparative analysis of growth performance and liver transcriptome response of juvenile Ancherythroculter nigrocauda fed diets with different protein levels. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 31:100592. [PMID: 31200228 DOI: 10.1016/j.cbd.2019.05.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 04/27/2019] [Accepted: 05/01/2019] [Indexed: 01/16/2023]
Abstract
This study aimed at investigating the effects of dietary protein levels on the growth and liver transcriptome in juvenile Ancherythroculter nigrocauda. Six semi-purified diets were formulated containing 25 (control), 30, 35, 40, 45, and 50% protein. Each diet was fed to three groups of 35 fish (mean initial weight: 5.86 ± 0.10 g) for 56 days. The rate of weight gain and specific growth rate increased with dietary protein levels from 25% to 40%, but remained unchanged when fed with 45 or 50% dietary protein. The feed conversion ratio was significantly influenced by the dietary protein levels, being the lowest in fish fed 40% protein. Illumina RNA-seq analysis was performed to investigate liver gene expression changes under different dietary protein treatments. A total of 367.78 million clean reads were obtained from the six libraries. Compared with 25% protein treatment library, there were 734, 1946, 1755, 2726, and 1523 upregulated genes, and 407, 1882, 1865, 2216 and 1624 downregulated genes in the 30, 35, 40, 45, and 50% protein treatment libraries, respectively. Trend analysis of these differentially expressed genes (DEGs) identified six statistically significant trends. A series of DEGs that related to protein metabolism, growth and development, lipid metabolism and immune and stress response were identified. Moreover, gene ontology enrichment analysis of the DEGs demonstrated that cellular process, single-organism process, metabolic process and biological regulation were the most highly overrepresented biological processes. Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that protein processing in endoplasmic reticulum, PPAR signaling pathway, complement and coagulation cascades, and cytochrome P450 (CYP450s) were significantly enriched in the dietary protein treatment groups. Furthermore, qPCR results showed excellent agreement on those of RNA-seq for both up- and down-regulated genes (including fasn, accα, SCD, CPT-I, igf1, ST, AST, trdmt1, hsp70, cyp450, MHC-II, C4, tgfβ, ube4b, apoE and abcb7). Thus, our results provide the baseline information for the feed formulation and nutritional research for A. nigrocauda.
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Affiliation(s)
- Xing Lu
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan 430207, Hubei, China; Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, Hubei, China
| | - Hua Wen
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, Hubei, China
| | - Qing Li
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan 430207, Hubei, China; Wuhan Xianfeng Aquaculture Technology Co. Ltd, Wuhan 430207, China.
| | - Guiying Wang
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan 430207, Hubei, China; Wuhan Xianfeng Aquaculture Technology Co. Ltd, Wuhan 430207, China
| | - Pei Li
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan 430207, Hubei, China; Wuhan Xianfeng Aquaculture Technology Co. Ltd, Wuhan 430207, China
| | - Jian Chen
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan 430207, Hubei, China; Wuhan Xianfeng Aquaculture Technology Co. Ltd, Wuhan 430207, China
| | - Yanhong Sun
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan 430207, Hubei, China; Wuhan Xianfeng Aquaculture Technology Co. Ltd, Wuhan 430207, China
| | - Changgeng Yang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, Hubei, China
| | - Fan Wu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, Hubei, China
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31
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Sun A, Zhu H, Dong Y, Wang W, Hu HX. Establishment of a novel testicular cell line from sterlet Acipenser ruthenus and evaluation of its applications. JOURNAL OF FISH BIOLOGY 2019; 94:804-809. [PMID: 30484862 DOI: 10.1111/jfb.13855] [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: 06/08/2018] [Accepted: 10/24/2018] [Indexed: 06/09/2023]
Abstract
In this study, a cell line, designated as Acipenser ruthenus testis (ART), was successfully established from testis tissues of the sterlet Acipenser ruthenus and characterized by studying and comparing the expression of specific genes between the cell line and the parent gonad tissues. The results suggested that the developed ART cell line was composed of a mixture of germ cells and somatic cells. Ploidy analysis indicated that the cell line exhibited a high degree of genetic stability and that the cells remained in a good proliferating state after being subcultured to passage 80.
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Affiliation(s)
- Ai Sun
- Beijing Fisheries Research Institute & National Freshwater Fisheries Engineering Technology Research Center, Ministry of Science and Technology of China, Lab of Biological Technology and Breeding, Beijing Key Laboratory of Fishery Biotechnology, Beijing, China
| | - Hua Zhu
- Beijing Fisheries Research Institute & National Freshwater Fisheries Engineering Technology Research Center, Ministry of Science and Technology of China, Lab of Biological Technology and Breeding, Beijing Key Laboratory of Fishery Biotechnology, Beijing, China
| | - Ying Dong
- Beijing Fisheries Research Institute & National Freshwater Fisheries Engineering Technology Research Center, Ministry of Science and Technology of China, Lab of Biological Technology and Breeding, Beijing Key Laboratory of Fishery Biotechnology, Beijing, China
| | - Wei Wang
- Beijing Fisheries Research Institute & National Freshwater Fisheries Engineering Technology Research Center, Ministry of Science and Technology of China, Lab of Biological Technology and Breeding, Beijing Key Laboratory of Fishery Biotechnology, Beijing, China
| | - Hong Xia Hu
- Beijing Fisheries Research Institute & National Freshwater Fisheries Engineering Technology Research Center, Ministry of Science and Technology of China, Lab of Biological Technology and Breeding, Beijing Key Laboratory of Fishery Biotechnology, Beijing, China
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32
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Yebra-Pimentel ES, Gebert M, Jansen HJ, Jong-Raadsen SA, Dirks RPH. Deep transcriptome analysis of the heat shock response in an Atlantic sturgeon (Acipenser oxyrinchus) cell line. FISH & SHELLFISH IMMUNOLOGY 2019; 88:508-517. [PMID: 30862517 DOI: 10.1016/j.fsi.2019.03.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/28/2019] [Accepted: 03/08/2019] [Indexed: 06/09/2023]
Abstract
Despite efforts to restore Atlantic sturgeon in European rivers, aquaculture techniques result in animals with high post-release mortality due to, among other reasons, their low tolerance to increasing water temperature. Marker genes to monitor heat stress are needed in order to identify heat-resistant fish. Therefore, an Atlantic sturgeon cell line was exposed to different heat shock protocols (30 °C and 35 °C) and differences in gene expression were investigated. In total 3020 contigs (∼1.5%) were differentially expressed. As the core of the upregulated contigs corresponded to heat shock proteins (HSP), the heat shock factor (HSF) and the HSP gene families were annotated in Atlantic sturgeon and mapped via Illumina RNA sequencing to identify heat-inducible family members. Up to 6 hsf and 76 hsp genes were identified in the Atlantic sturgeon transcriptome resources, 16 of which were significantly responsive to the applied heat shock. The previously studied hspa1 (hsp70) gene was only significantly upregulated at the highest heat shock (35 °C), while a set of 5 genes (hspc1, hsph3a, hspb1b, hspb11a, and hspb11b) was upregulated at all conditions. Although the hspc1 (hsp90a) gene was previously used as heat shock-marker in sturgeons, we found that hspb11a is the most heat-inducible gene, with up to 3296-fold higher expression in the treated cells, constituting the candidate gene markers for in vivo trials.
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Affiliation(s)
- Elena Santidrián Yebra-Pimentel
- ZF-screens B.V., 2333CH, Leiden, the Netherlands; Department of Basic Sciences and Aquatic Medicine, Norwegian University of Life Sciences, 0454, Oslo, Norway.
| | - Marina Gebert
- Working Group Aquatic Cell Technology and Aquaculture, Fraunhofer Research Institution for Marine Biotechnology and Cell Technology, 23562, Lübeck, Germany
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Luo D, Li Y, Zhao Q, Zhao L, Ludwig A, Peng Z. Highly Resolved Phylogenetic Relationships within Order Acipenseriformes According to Novel Nuclear Markers. Genes (Basel) 2019; 10:E38. [PMID: 30634684 PMCID: PMC6356338 DOI: 10.3390/genes10010038] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 12/28/2018] [Accepted: 01/02/2019] [Indexed: 11/16/2022] Open
Abstract
Order Acipenseriformes contains 27 extant species distributed across the northern hemisphere, including so-called "living fossil" species of garfish and sturgeons. Previous studies have focused on their mitochondrial genetics and have rarely used nuclear genetic data, leaving questions as to their phylogenetic relationships. This study aimed to utilize a bioinformatics approach to screen for candidate single-copy nuclear genes, using transcriptomic data from sturgeon species and genomic data from the spotted gar, Lepisosteus oculatus. We utilized nested polymerase chain reaction (PCR) and degenerate primers to identify nuclear protein-coding (NPC) gene markers to determine phylogenetic relationships among the Acipenseriformes. We identified 193 nuclear single-copy genes, selected from 1850 candidate genes with at least one exon larger than 700 bp. Forty-three of these genes were used for primer design and development of 30 NPC markers, which were sequenced for at least 14 Acipenseriformes species. Twenty-seven NPC markers were found completely in 16 species. Gene trees according to Bayesian inference (BI) and maximum likelihood (ML) were calculated based on the 30 NPC markers (20,946 bp total). Both gene and species trees produced very similar topologies. A molecular clock model estimated the divergence time between sturgeon and paddlefish at 204.1 Mya, approximately 10% later than previous estimates based on cytochrome b data (184.4 Mya). The successful development and application of NPC markers provides a new perspective and insight for the phylogenetic relationships of Acipenseriformes. Furthermore, the newly developed nuclear markers may be useful in further studies on the conservation, evolution, and genomic biology of this group.
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Affiliation(s)
- Dehuai Luo
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China.
| | - Yanping Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China.
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Qingyuan Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China.
| | - Lianpeng Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China.
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, 10315 Berlin, Germany.
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China.
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Zhang C, Su S, Li X, Li B, Yang B, Zhu J, Wang W. Comparative transcriptomics identifies genes differentially expressed in the intestine of a new fast-growing strain of common carp with higher unsaturated fatty acid content in muscle. PLoS One 2018; 13:e0206615. [PMID: 30395585 PMCID: PMC6218049 DOI: 10.1371/journal.pone.0206615] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 10/16/2018] [Indexed: 01/01/2023] Open
Abstract
We have created a new, fast-growing strain of common carp with higher unsaturated fatty acid content in muscle. To better understand the impacts of gene regulation in intestinal tissue on growth and unsaturated fatty acid content, we conducted a comparative RNA-Seq transcriptome analysis between intestine samples of Selected and Control groups (and corroborated selected results by PCR). After eight weeks of cage culture, weight gain of the Selected group was 20.84% higher. In muscles of the control group, monounsaturated fatty acids (FAs) were more abundant, whereas polyunsaturated FAs were more abundant in muscles of the Selected group. In total, we found 106 differentially expressed genes (DEGs) between the two groups. Only the endocytosis pathway was significantly enriched in DEGs, with two upregulated genes: il2rb and ehd1. The latter is involved in the growth hormone/insulin-like growth factor (Gh/Igf) axis, which plays a key role in the regulation of growth in animals. tll2, which is known to be associated with intestinal regeneration, was extremely highly upregulated in both transcriptomic (infinite) and qPCR (610.70) analyses. Two of the upregulated genes are associated with the fatty acid metabolism, several genes are likely to be indicators of heightened transcription levels, several are associated with metabolic and developmental roles, several with neuronal functions (including two with vision), several with the immune system, and two downregulated genes with the development of vasculature. The higher growth rate of the Selected group is likely to be at least partially attributed to increased endocytosis efficiency and genetically-driven behavioural differences (higher aggression levels). There are some indications that this new strain might have slightly impaired immune responses, and a higher propensity for inherited diseases leading to sight impairment, as well for neurodegenerative diseases in general, but these indications still need to be confirmed.
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Affiliation(s)
- Chengfeng Zhang
- College of Fisheries, Huazhong Agricultural University, Wuhan, PR China
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, PR China
| | - Shengyan Su
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, PR China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, PR China
| | - Xinyuan Li
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, PR China
| | - Bing Li
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, PR China
| | - Baojuan Yang
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, PR China
| | - Jian Zhu
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, PR China
- * E-mail: (JZ); (WW)
| | - Weimin Wang
- College of Fisheries, Huazhong Agricultural University, Wuhan, PR China
- * E-mail: (JZ); (WW)
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Vizziano-Cantonnet D, Lasalle A, Di Landro S, Klopp C, Genthon C. De novo transcriptome analysis to search for sex-differentiation genes in the Siberian sturgeon. Gen Comp Endocrinol 2018; 268:96-109. [PMID: 30081002 DOI: 10.1016/j.ygcen.2018.08.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 07/08/2018] [Accepted: 08/02/2018] [Indexed: 01/09/2023]
Abstract
The sturgeon family includes many species that are lucrative for commercial caviar production, some of which face critical conservation problems. The purpose of this study was to identify genes involved in gonadal sex differentiation in sturgeons, contributing to our understanding of the biological cycle of this valuable species. A high-quality de novo Siberian sturgeon gonadal transcriptome was built for this study using gonadal samples from undifferentiated fish at 3, 5, and 6 months of age; recently sex-differentiated fish at 9 months of age; and immature males and females at 14-17 months of age. Undifferentiated fish were sexed after validation of forkhead box L2 (foxl2) and cytochrome P450, family 19, subfamily A, and polypeptide 1a (cyp19a1a) as sex markers, and the transcriptomes of the 3-month-old undifferentiated fish, 5-6-month-old future females, and 5-6-month-old putative males were compared. The ovarian program was associated with strong activation of genes involved in estrogen synthesis (cyp19a1, foxl2, and estradiol 17-beta-dehydrogenase 1), stem-cell niche building and regulation, and sex-specific nerve cell development. The genes related to the stem-cell niche were: (1) the family of iroquois-class homeodomain proteins 3, 4, and 5 (irx3, irx4, irx5-1, irx5-2, and irx5-3), which are essential for somatic-germ cell interaction; (2) extracellular matrix remodeling genes, such as collagen type XXVIII alpha 1 chain and collagen type II alpha 1 chain, matrix metalloproteinases 24-1 and 24-2, and NADPH oxidase organizer 1, which, along with the somatic cells, provide architectural support for the stem-cell niche; and (3) mitogenic factors, such as lim homeobox 2, amphiregulin, G2/M phase-specific E3 ubiquitin-protein ligase, and connector enhancer of kinase suppressor of ras 2, which are up regulated in conjunction with the anti-apoptotic gene G2/M phase-specific E3 ubiquitin-protein ligase suggesting a potential involvement in regulating the number of germ cells. Genes related to sex-specific nerve cell developments were: the neurofilament medium polypeptides, the gene coding for serotonin receptor 7, 5-hydroxytryptamine receptor 7; neurotensin, isoform CRA-a, the neuron-specific transmembrane protein Delta/Notch-like epidermal growth factor-related receptor; and insulinoma-associated protein 1. The putative testicular program was poorly characterized by elements of the immune response. The classic markers of maleness were not specifically activated, indicating that testicular differentiation occurs at a later stage. In sum, the ovarian program, but not the testicular program, is in place by 5-6 months of age in the Siberian sturgeon. The female program is characterized by estrogen-related genes with well-established roles in gonadal differentiation, but also by several genes with no previously-described function in the ovarian development of fish. These newly-reported genes are involved in stem-cell niche building and regulation as well as sex-specific nerve development.
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Affiliation(s)
- 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 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 11400, 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 11400, Uruguay
| | - Christophe Klopp
- INRA, SIGENAE, MIAT UR875, Chemin de Borde-Rouge - Auzeville, BP 52627, 31326 Castanet-Tolosan Cedex, France
| | - Clémence Genthon
- Plateforme Génomique, INRA Auzeville, Chemin de Borde Rouge-CS 52627, 31326 Castanet-Tolosan Cédex, France
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Adolfi MC, Nakajima RT, Nóbrega RH, Schartl M. Intersex, Hermaphroditism, and Gonadal Plasticity in Vertebrates: Evolution of the Müllerian Duct and Amh/Amhr2 Signaling. Annu Rev Anim Biosci 2018; 7:149-172. [PMID: 30303691 DOI: 10.1146/annurev-animal-020518-114955] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In vertebrates, sex organs are generally specialized to perform a male or female reproductive role. Acquisition of the Müllerian duct, which gives rise to the oviduct, together with emergence of the Amh/Amhr2 system favored evolution of viviparity in jawed vertebrates. Species with high sex-specific reproductive adaptations have less potential to sex reverse, making intersex a nonfunctional condition. Teleosts, the only vertebrate group in which hermaphroditism evolved as a natural reproductive strategy, lost the Müllerian duct during evolution. They developed for gamete release complete independence from the urinary system, creating optimal anatomic and developmental preconditions for physiological sex change. The common and probably ancestral role of Amh is related to survival and proliferation of germ cells in early and adult gonads of both sexes rather than induction of Müllerian duct regression. The relationship between germ cell maintenance and sex differentiation is most evident in species in which Amh became the master male sex-determining gene.
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Affiliation(s)
- Mateus Contar Adolfi
- Physiological Chemistry, Biocenter, University of Würzburg, D-97074 Würzburg, Germany;
| | - Rafael Takahiro Nakajima
- Integrative Genomics Laboratory, Department of Morphology, Institute of Bioscience of Botucatu, São Paulo State University, Botucatu, São Paulo 01049-010, Brazil;
| | - Rafael Henrique Nóbrega
- Reproductive and Molecular Biology Group, Department of Morphology, Institute of Bioscience of Botucatu, São Paulo State University, Botucatu, São Paulo 01049-010, Brazil;
| | - Manfred Schartl
- Physiological Chemistry, Biocenter, University of Würzburg, D-97074 Würzburg, Germany; .,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, 97074 Würzburg, Germany.,Hagler Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, Texas 77843, USA;
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Yu L, Xu D, Ye H, Yue H, Ooka S, Kondo H, Yazawa R, Takeuchi Y. Gonadal Transcriptome Analysis of Pacific Abalone Haliotis discus discus: Identification of Genes Involved in Germ Cell Development. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:467-480. [PMID: 29616430 DOI: 10.1007/s10126-018-9809-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 03/08/2018] [Indexed: 06/08/2023]
Abstract
Little is known about the molecular mechanisms governing gonadal developmental processes in abalones. Here, we conducted transcriptome analysis of Pacific abalone Haliotis discus discus for gene discovery in the brain, ovary, testis, and unfertilized eggs. Among the annotated unigenes, 48.6% of unigenes were identified by Venn diagram analysis as having universal or tissue-specific expression. Twenty-three genes with gonad-biased gene ontology (GO) terms were first obtained. Secondly, 36 genes were found by screening known gene names related to germ cell development. Finally, 17 genes were obtained by querying the annotated unigene database for zygotically expressed gonadal genes (ovary and testis) and maternally expressed gonadal genes (ovary, testis, and unfertilized eggs) using keywords related to reproduction. To further verify tissue distribution pattern and subcellular localization of these genes, RT-PCR and in situ hybridization were performed using a unigene encoding a germ cell marker, vasa, as control. The results showed that vasa was expressed mainly in the early developmental stages of germ cells in both sexes. One of the candidate genes, vitelline envelope zona pellucida domain protein 12 (ZP12), was expressed in the primordial germ cells of immature gonad and early developmental stages of germ cells of the adult female. The results obtained from the present study suggest that vasa and ZP12 are involved in germ cell development of Pacific abalone and that ZP12 is an especially useful germ cell-specific marker in immature adults. The current gonadal transcriptome profile is an extensive resource for future reproductive molecular biology studies of this species.
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Affiliation(s)
- Lingyun Yu
- Research Center for Advanced Science and Technology, Tokyo University of Marine Science and Technology, 670 Banda, Tateyama, Chiba, 294-0308, Japan
| | - Dongdong Xu
- Research Center for Advanced Science and Technology, Tokyo University of Marine Science and Technology, 670 Banda, Tateyama, Chiba, 294-0308, Japan
- Marine Fishery Institute of Zhejiang Province, Key Lab of Mariculture and Enhancement of Zhejiang Province, Zhoushan, Zhejiang Province, 316100, China
| | - Huan Ye
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China
| | - Huamei Yue
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China
| | - Shioh Ooka
- Japan Ocean Resources Development and Engineering Co., Ltd., 7-1 Jizohamacho, Kishiwada, Osaka, 596-0015, Japan
| | - Hidehiro Kondo
- Department of Marine Bioscience, Tokyo University of Marine Science and Technology, Minato, Konan 4-5-7, Tokyo, 108-8477, Japan
| | - Ryosuke Yazawa
- Department of Marine Bioscience, Tokyo University of Marine Science and Technology, Minato, Konan 4-5-7, Tokyo, 108-8477, Japan
| | - Yutaka Takeuchi
- Faculty of Fisheries, Kagoshima University, 4-50-20 Shimoarata, Kagoshima, 890-0056, Japan.
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Chen Y, Liu Y, Gong Q, Lai J, Song M, Du J, Deng X. Gonadal transcriptome sequencing of the critically endangered Acipenser dabryanus to discover candidate sex-related genes. PeerJ 2018; 6:e5389. [PMID: 30065900 PMCID: PMC6065465 DOI: 10.7717/peerj.5389] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 07/17/2018] [Indexed: 01/14/2023] Open
Abstract
Background Acipenser dabryanus, an endemic Chinese species, has been listed as a first-class protected animal in China. Sturgeons are among the oldest and most primitive group of existing fish in the world and occupy a special place in the evolutionary history of fish. Thus, a study of the reproduction and sex differentiation of sturgeon will be of great value for fish as well as the whole vertebrate group. Methods In this study, we conducted comparative analysis of the testes and ovaries transcriptomes of A. dabryanus to screen for sex-differentiation and sexual development-related genes. Results The transcriptome sequencing of six cDNA libraries generated 265 million clean reads, encompassing 79 Gb of sequences. The N50 and mean length of the identified 91,375 unigenes were 1,718 and 989 bp, respectively. A total of 6,306, 9,961, 13,170, 15,484, and 23,588 unigenes were annotated in the clusters of orthologous groups, gene ontology categories, Kyoto Encyclopedia of Genes and Genomes Pathway, euKaryotic orthologous groups, and NCBI non-redundant protein databases, respectively. A total of 5,396 differentially expressed genes were found between the two sexes, with 1,938 predicted to be up-regulated in ovaries and 3,458 in testes. A total of 73 candidate genes known to be involved in sex differentiation and sexual development were searched in the transcriptome of A. dabryanus of which 52 showed significant similarity. We highlighted six genes that are differentially expressed between the two sexes and may play important roles in sex differentiation and gonad maintenance. In addition, 24,271 simple sequence repeats (SSRs) and 550,519 single-nucleotide polymorphisms (SNPs) were detected. Discussion This work represents the first transcriptome study comparing the ovary and testis in A. dabryanus. The putative differentially expressed genes between the gonads provide an important source of information for further study of the sex-differentiation related genes and the sex-differentiation mechanism in sturgeons. The SSRs or SNPs identified in this study will be helpful in the discovery of sex-related markers in A. dabryanus.
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Affiliation(s)
- Yeyu Chen
- The Sichuan Academy of Agricultural Sciences, The Fishery Institute, Chengdu, China
| | - Ya Liu
- The Sichuan Academy of Agricultural Sciences, The Fishery Institute, Chengdu, China
| | - Quan Gong
- The Sichuan Academy of Agricultural Sciences, The Fishery Institute, Chengdu, China
| | - Jiansheng Lai
- The Sichuan Academy of Agricultural Sciences, The Fishery Institute, Chengdu, China
| | - Mingjiang Song
- The Sichuan Academy of Agricultural Sciences, The Fishery Institute, Chengdu, China
| | - Jun Du
- The Sichuan Academy of Agricultural Sciences, The Fishery Institute, Chengdu, China
| | - Xiaochuan Deng
- The Sichuan Academy of Agricultural Sciences, The Fishery Institute, Chengdu, China
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Expression Characterization of Six Genes Possibly Involved in Gonad Development for Stellate Sturgeon Individuals ( Acipenser stellatus, Pallas 1771). Int J Genomics 2018; 2018:7835637. [PMID: 29785396 PMCID: PMC5896241 DOI: 10.1155/2018/7835637] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 12/12/2017] [Accepted: 03/11/2018] [Indexed: 02/04/2023] Open
Abstract
Nowadays, in sturgeon's aquaculture, there is a necessity for sex identification at early stages in order to increase the efficiency of this commercial activity. The basis for a correct identification is studying the different factors that influence the gonad development. The research has been directed towards molecular methods that have been employed with various degrees of success in identifying genes with different expression patterns between male and female sturgeons during their development stages. For the purpose of understanding the sexual development of 4-year-old stellate sturgeon (Acipenser stellatus) individuals, we have selected six genes (foxl2, cyp17a1, ar, dmrt1, sox9, and star). We analysed the gene expression of the selected genes for gonads, anal fin, liver, body kidney, and white muscle. The cyp17a1, ar, dmrt1, and sox9 genes have a significant higher expression in male gonads than in female gonads, while the data shows no significant differences in the expression of the investigated genes in the other organs. We investigate these genes to shed light on aquaculture sturgeon sexual development.
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Transcriptome profiling reveals candidate cleft palate-related genes in cultured Chinese sturgeons (Acipenser sinensis). Gene 2018; 666:1-8. [PMID: 29733966 DOI: 10.1016/j.gene.2018.05.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/26/2018] [Accepted: 05/03/2018] [Indexed: 11/20/2022]
Abstract
The Chinese sturgeon (Acipenser sinensis) is an anadromous fish distributed in the Yangtze River and the East China Sea. In this study, we report the novel finding of cleft palates in Chinese sturgeons derived from artificial fertilization. To explore the genetic basis of palate malformation in A. sinensis, Illumina RNA-seq technology was used to analyze the transcriptome data of farmed Chinese sturgeons with normal palates and cleft-palates. Raw reads were obtained and assembled into 808,612 unigenes, with an average length of 509.33 bp and an N50 of 574 bp. Sequence similarity analyses against four public databases (Nr, UniProt, KEGG, and COGs) found 158,642 unigenes that could be annotated. GABAergic synapses and TGF-β signal pathways were the two most enriched pathways with high Rich Factors in the analyses of differentially expressed genes. In these two signal pathways, six genes (GABRA4, GS, GNS, S6K, PITX2, and BMP8) were found as candidate cleft-palate genes in Chinese sturgeon. These findings contribute to our understanding of cleft palate genetics in sturgeon, while simultaneously adding to our knowledge about craniofacial development.
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Hu F, Xu K, Zhou Y, Wu C, Wang S, Xiao J, Wen M, Zhao R, Luo K, Tao M, Duan W, Liu S. Different expression patterns of sperm motility-related genes in testis of diploid and tetraploid cyprinid fish†. Biol Reprod 2018; 96:907-920. [PMID: 28340181 PMCID: PMC5441299 DOI: 10.1093/biolre/iox010] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 03/01/2017] [Indexed: 11/25/2022] Open
Abstract
Sperm motility is an important standard to measure the fertility of male. In our previous study, we found that the diploid spermatozoa from allotetraploid hybrid (4nAT) had longer durations of rapid and slow progressive motility than haploid spermatozoa from common carp (COC). In this study, to explore sperm motility-related molecular mechanisms, we compared the testis tissues transcriptomes from 2-year-old male COC and 4nAT. The RNA-seq data revealed that 2985 genes were differentially expressed between COC and 4nAT, including 2216 upregulated and 769 downregulated genes in 4nAT. Some differentially expressed genes, such as tubulin genes, dynein, axonemal, heavy chain(dnah) genes, mitogen-activated protein kinase(mapk) genes, tektin 4, FOX transcription factors, proteasome genes, and ubiquitin carboxyl-terminal hydrolase(uchl) genes, are involved in the regulation of cell division, flagellar and ciliary motility, gene transcription, cytoskeleton, energy metabolism, and the ubiquitin–proteasome system, suggesting that these genes were related to sperm motility of the 4nAT. We confirmed the differential expression of 12 such genes in 4nAT by quantitative PCR. By western blotting, we also confirmed increased expression of Uchl3 in 4nAT testis. In addition, we identified 1915 and 2551 predicted long noncoding RNA (lncRNA) transcripts from testis tissue transcriptomes of COC and 4nAT, respectively. Of these, 1575 lncRNAs were specifically expressed in 4nAT and 939 were specifically expressed in COC. This study provides insights into the transcriptome profile of testis tissues from diploid and tetraploid, which are useful for research on regulatory mechanisms behind sperm motility in male polyploidy.
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Affiliation(s)
- Fangzhou Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan, P. R. of China.,College of Life Sciences, Hunan Normal University, Changsha, Hunan, P. R. of China
| | - Kang Xu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan, P. R. of China.,College of Life Sciences, Hunan Normal University, Changsha, Hunan, P. R. of China
| | - Yunfan Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan, P. R. of China.,College of Life Sciences, Hunan Normal University, Changsha, Hunan, P. R. of China
| | - Chang Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan, P. R. of China.,College of Life Sciences, Hunan Normal University, Changsha, Hunan, P. R. of China
| | - Shi Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan, P. R. of China.,College of Life Sciences, Hunan Normal University, Changsha, Hunan, P. R. of China
| | - Jun Xiao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan, P. R. of China.,College of Life Sciences, Hunan Normal University, Changsha, Hunan, P. R. of China
| | - Min Wen
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan, P. R. of China.,College of Life Sciences, Hunan Normal University, Changsha, Hunan, P. R. of China
| | - Rurong Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan, P. R. of China.,College of Life Sciences, Hunan Normal University, Changsha, Hunan, P. R. of China
| | - Kaikun Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan, P. R. of China.,College of Life Sciences, Hunan Normal University, Changsha, Hunan, P. R. of China
| | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan, P. R. of China.,College of Life Sciences, Hunan Normal University, Changsha, Hunan, P. R. of China
| | - Wei Duan
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan, P. R. of China.,College of Life Sciences, Hunan Normal University, Changsha, Hunan, P. R. of China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan, P. R. of China.,College of Life Sciences, Hunan Normal University, Changsha, Hunan, P. R. of China
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Zhang X, Li L, Jiang H, Ma JE, Li J, Chen J. Identification and differential expression of microRNAs in testis and ovary of Amur sturgeon (Acipenser schrenckii). Gene 2018. [PMID: 29524574 DOI: 10.1016/j.gene.2018.03.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND MicroRNAs (miRNAs) cooperate with sex-related genes in post-transcriptional regulation and play extremely important roles in the establishment of sexually dimorphic traits in animals. However, the gonad miRNAs and expression patterns of miRNAs in sturgeon have not been investigated. METHODS In the present study, we used high-throughput small RNA sequencing (RNA-Seq) to discover gonad miRNAs from the ovaries and testes of Amur sturgeons (Acipenser schrenckii). Further, microarray and real-time PCR assays were performed to identify the expression patterns of gonad miRNAs. RESULTS As a result, a total of 679 conserved and 51 novel miRNAs were successfully discovered in the gonads of A. schrenckii. Moreover, we found wide sequence variations (isomiRs) in gonad miRNAs, including 5' and 3' isomiRs. Our microarray analysis further characterized the 730 miRNAs expression profiles, which indicated that 117 differentially expressed miRNAs were detected with sex-biased patterns: 71 testis-biased and 46 ovary-biased miRNAs. Based on bioinformatics prediction, we found that there were functional differences between the testis-biased and ovary-biased miRNA targets involved in reproductive-related GO and KEGG pathways. Further, the association of the differentially expressed miRNAs and sex-related target mRNAs was uncovered. Finally, the expression patterns of 11 sex-biased miRNAs and 7 sex-related targets were validated in testes and ovaries using real-time PCR. Putative, negatively expressed miRNA-mRNA relationships were confirmed, such as Dmrt1 and asc-miR-2779, AR and asc-miR-203b-3p, foxl2 and asc-miR-30d. CONCLUSION This study provides information regarding the gonad miRNAs in sturgeon. The differential expression miRNAs in the gonads will help us to further understand the role of miRNA-mediated post-transcriptional regulation in the ovary and testis of sturgeon.
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Affiliation(s)
- Xiujuan Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Linmiao Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Haiying Jiang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Jing E Ma
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Juan Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China..
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Molecular characterization, tissue distribution, localization and mRNA expression of the bucky ball gene in the Dabry's sturgeon (Acipenser dabryanus) during oogenesis. Gene Expr Patterns 2018; 28:62-71. [PMID: 29481878 DOI: 10.1016/j.gep.2018.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 01/24/2018] [Accepted: 02/22/2018] [Indexed: 01/08/2023]
Abstract
In many organisms, germ cells are specified during embryogenesis by the inheritance of maternally deposited RNAs and proteins termed germ plasm. In vertebrates, the bucky ball (buc) gene plays an essential role in the germ plasm aggregation. In this study, the full-length cDNA of buc homologue in Dabry's sturgeon, Adbuc, was isolated and characterized. Multiple sequence alignments showed that the BUVE domain of Buc was highly conserved in vertebrates, despite exhibiting low identities with each other across the whole protein. By quantitative real-time PCR analysis, we found that Adbuc RNAs were only detected in the gonad with a high level in the ovary and a very low level in the testis. During embryogenesis, these RNAs were highly expressed from the unfertilized eggs to blastula, declined dramatically from the gastrula stage, and hardly found after the neurula stage. Moreover, with the development of ovary, the expression level of Adbuc was increasing. By in situ hybridization, the signal of Adbuc was not found in the oogonia, increased slightly in the stage I oocytes, and extremely strong in the stage II oocytes, suggesting that the signal became much stronger with increasing size of oocytes. Additionally, Adbuc co-localized with the mitochondrial cloud. Thus, we conclude that Dabry's sturgeon buc gene might also function in germplasm formation.
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Schedina IM, Groth D, Schlupp I, Tiedemann R. The gonadal transcriptome of the unisexual Amazon molly Poecilia formosa in comparison to its sexual ancestors, Poecilia mexicana and Poecilia latipinna. BMC Genomics 2018; 19:12. [PMID: 29298680 PMCID: PMC5753479 DOI: 10.1186/s12864-017-4382-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 12/14/2017] [Indexed: 12/15/2022] Open
Abstract
Background The unisexual Amazon molly (Poecilia formosa) originated from a hybridization between two sexual species, the sailfin molly (Poecilia latipinna) and the Atlantic molly (Poecilia mexicana). The Amazon molly reproduces clonally via sperm-dependent parthenogenesis (gynogenesis), in which the sperm of closely related species triggers embryogenesis of the apomictic oocytes, but typically does not contribute genetic material to the next generation. We compare for the first time the gonadal transcriptome of the Amazon molly to those of both ancestral species, P. mexicana and P. latipinna. Results We sequenced the gonadal transcriptomes of the P. formosa and its parental species P. mexicana and P. latipinna using Illumina RNA-sequencing techniques (paired-end, 100 bp). De novo assembly of about 50 million raw read pairs for each species was performed using Trinity, yielding 106,922 transcripts for P. formosa, 115,175 for P. latipinna, and 133,025 for P. mexicana after eliminating contaminations. On the basis of sequence similarity comparisons to other teleost species and the UniProt databases, functional annotation, and differential expression analysis, we demonstrate the similarity of the transcriptomes among the three species. More than 40% of the transcripts for each species were functionally annotated and about 70% were assigned to orthologous genes of a closely related species. Differential expression analysis between the sexual and unisexual species uncovered 2035 up-regulated and 564 down-regulated genes in P. formosa. This was exemplary validated for six genes by qRT-PCR. Conclusions We identified more than 130 genes related to meiosis and reproduction within the apomictically reproducing P. formosa. Overall expression of these genes seems to be down-regulated in the P. formosa transcriptome compared to both ancestral species (i.e., 106 genes down-regulated, 29 up-regulated). A further 35 meiosis and reproduction related genes were not found in the P. formosa transcriptome, but were only expressed in the sexual species. Our data support the hypothesis of general down-regulation of meiosis-related genes in the apomictic Amazon molly. Furthermore, the obtained dataset and identified gene catalog will serve as a resource for future research on the molecular mechanisms behind the reproductive mode of this unisexual species. Electronic supplementary material The online version of this article (10.1186/s12864-017-4382-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ina Maria Schedina
- Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 26, 14476, Potsdam, Germany
| | - Detlef Groth
- Department of Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 14, 14476, Potsdam, Germany
| | - Ingo Schlupp
- Department of Biology, University of Oklahoma, 730 Van Vleet Oval, Norman, OK, 73019, USA
| | - Ralph Tiedemann
- Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 26, 14476, Potsdam, Germany.
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Wang W, Zhu H, Dong Y, Tian Z, Dong T, Hu H, Niu C. Dimorphic expression of sex-related genes in different gonadal development stages of sterlet, Acipenser ruthenus, a primitive fish species. FISH PHYSIOLOGY AND BIOCHEMISTRY 2017; 43:1557-1569. [PMID: 28963671 DOI: 10.1007/s10695-017-0392-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 05/30/2017] [Indexed: 06/07/2023]
Abstract
Molecular mechanism of sex determination and differentiation of sturgeon, a primitive fish species, is extraordinarily important due to the valuable caviar; however, it is still poorly known. The present work aimed to identify the major genes involved in regulating gonadal development of sterlet, a small species of sturgeon, from 13 candidate genes which have been shown to relate to gonadal differentiation and development in other teleost fish. The sex and gonadal development of sterlets were determined by histological observation and levels of sex steroids testosterone (T), 11-ketotestosterone (11-KT), and 17β-estradiol (E2) in serum. Sexually dimorphic gene expressions were investigated. The results revealed that gonadal development were asynchronous in 2-year-old male and female sterlets with the testes in early or mid-spermatogenesis and the ovaries in chromatin nucleolus stage or perinucleolus stage, respectively. The levels of T and E2 were not significantly different between sexes or different gonadal development stages while 11-KT had the higher level in mid-spermatogenesis testis stage. In all the investigated gonadal development stages, gene dmrt1 and hsd11b2 were expressed higher in male whereas foxl2 and cyp19a1 were expressed higher in female. Thus, these genes provided the promising markers for sex identification of sterlet. It was unexpected that dkk1 and dax1 had significantly higher expression in ovarian perinucleolus stage than in ovarian chromatin nucleolus stage and in the testis, suggesting that these two genes had more correlation with ovarian development than with the testis, contrary to the previous reports in other vertebrates. Testicular development-related genes (gsdf and amh) and estrogen receptor genes (era and erb) differentially expressed at different testis or ovary development stages, but their expressions were not absolutely significantly different in male and female, depending on the gonadal development stage. Expression of androgen receptor gene ar or rspo, which was supposed to be related to ovarian development, presented no difference between gonadal development stages investigated in this study whenever in male or female.
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Affiliation(s)
- Wei Wang
- Beijing Normal University, No. 19 Xin Jie Kou Wai Avenue, Haidian District, Beijing, 100875, China
- National Freshwater Fisheries Engineering Technology Research Center, Ministry of Science and Technology of China, Beijing Key Laboratory of Fishery Biotechnology (No. BZ0301), Beijing Fisheries Research Institute, No.18 Ma Jia Pu Road, Fengtai District, Beijing, 100068, China
| | - Hua Zhu
- National Freshwater Fisheries Engineering Technology Research Center, Ministry of Science and Technology of China, Beijing Key Laboratory of Fishery Biotechnology (No. BZ0301), Beijing Fisheries Research Institute, No.18 Ma Jia Pu Road, Fengtai District, Beijing, 100068, China
| | - Ying Dong
- National Freshwater Fisheries Engineering Technology Research Center, Ministry of Science and Technology of China, Beijing Key Laboratory of Fishery Biotechnology (No. BZ0301), Beijing Fisheries Research Institute, No.18 Ma Jia Pu Road, Fengtai District, Beijing, 100068, China
| | - ZhaoHui Tian
- National Freshwater Fisheries Engineering Technology Research Center, Ministry of Science and Technology of China, Beijing Key Laboratory of Fishery Biotechnology (No. BZ0301), Beijing Fisheries Research Institute, No.18 Ma Jia Pu Road, Fengtai District, Beijing, 100068, China
| | - Tian Dong
- National Freshwater Fisheries Engineering Technology Research Center, Ministry of Science and Technology of China, Beijing Key Laboratory of Fishery Biotechnology (No. BZ0301), Beijing Fisheries Research Institute, No.18 Ma Jia Pu Road, Fengtai District, Beijing, 100068, China
| | - HongXia Hu
- National Freshwater Fisheries Engineering Technology Research Center, Ministry of Science and Technology of China, Beijing Key Laboratory of Fishery Biotechnology (No. BZ0301), Beijing Fisheries Research Institute, No.18 Ma Jia Pu Road, Fengtai District, Beijing, 100068, China.
| | - CuiJuan Niu
- Beijing Normal University, No. 19 Xin Jie Kou Wai Avenue, Haidian District, Beijing, 100875, China.
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Liu Y, Chen Y, Gong Q, Lai J, Du J, Deng X. Paternity assignment in the polyploid Acipenser dabryanus based on a novel microsatellite marker system. PLoS One 2017; 12:e0185280. [PMID: 28953941 PMCID: PMC5617196 DOI: 10.1371/journal.pone.0185280] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 09/08/2017] [Indexed: 11/25/2022] Open
Abstract
Acipenser dabryanus is listed as a Critical Endangered species in the IUCN Red List and the first class protected animals in China. Fortunately, A. dabryanus specimens are being successfully bred in captivity for conservation. However, for effective ex situ conservation, we should be aware of the genetic diversity and the degree of relatedness of the individuals selected for breeding. In this study, we aimed at the development of novel and reliable microsatellites used for the genetic study of A. dabryanus. A total of 14,321 simple sequence repeats (SSRs) were detected by transcriptome sequencing and screening. We selected 20 novel and polymorphic microsatellites (non-dinucleotide) with good repeatability from the 100 tested loci for a subsequent genetic and paternity study. A set of captive broodstock (F1 stock, n = 43) and their offspring (F2 stock, n = 96) were used to examine the efficiency of the 20 SSRs for assigning parentage to offspring, with an allocation success of 91.7%. We also found that only a few families predominantly contributed to the progeny produced by the 43 breeders. In addition, mitochondrial DNA data showed that the captive broodstock (F1 individuals) had an excellent probability of the same lineage, implying that a high level of inbreeding may have occurred in these individuals. Our research provides useful information on genetic diversity and reproductive pattern of A. dabryanus, and the 20 SSRs developed in this study can be applied to the future breeding program to avoid inbreeding for this stock or other related species of Acipenseriformes.
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Affiliation(s)
- Ya Liu
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Yeyu Chen
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Quan Gong
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Jiansheng Lai
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Jun Du
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, China
- * E-mail: (XCD); (JD)
| | - Xiaochuan Deng
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, China
- * E-mail: (XCD); (JD)
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Oomen RA, Hutchings JA. Transcriptomic responses to environmental change in fishes: Insights from RNA sequencing. Facets (Ott) 2017. [DOI: 10.1139/facets-2017-0015] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The need to better understand how plasticity and evolution affect organismal responses to environmental variability is paramount in the face of global climate change. The potential for using RNA sequencing (RNA-seq) to study complex responses by non-model organisms to the environment is evident in a rapidly growing body of literature. This is particularly true of fishes for which research has been motivated by their ecological importance, socioeconomic value, and increased use as model species for medical and genetic research. Here, we review studies that have used RNA-seq to study transcriptomic responses to continuous abiotic variables to which fishes have likely evolved a response and that are predicted to be affected by climate change (e.g., salinity, temperature, dissolved oxygen concentration, and pH). Field and laboratory experiments demonstrate the potential for individuals to respond plastically to short- and long-term environmental stress and reveal molecular mechanisms underlying developmental and transgenerational plasticity, as well as adaptation to different environmental regimes. We discuss experimental, analytical, and conceptual issues that have arisen from this work and suggest avenues for future study.
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Affiliation(s)
- Rebekah A. Oomen
- Department of Biology, Dalhousie University, Halifax, NS B3H 4J1, Canada
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0371 Oslo, Norway
- Institute of Marine Research, Flødevigen Research Station, 4817 His, Norway
| | - Jeffrey A. Hutchings
- Department of Biology, Dalhousie University, Halifax, NS B3H 4J1, Canada
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0371 Oslo, Norway
- Institute of Marine Research, Flødevigen Research Station, 4817 His, Norway
- Department of Natural Sciences, University of Agder, 4604 Kristiansand, Norway
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De novo sequencing and comparative analysis of testicular transcriptome from different reproductive phases in freshwater spotted snakehead Channa punctatus. PLoS One 2017; 12:e0173178. [PMID: 28253373 PMCID: PMC5333912 DOI: 10.1371/journal.pone.0173178] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 02/16/2017] [Indexed: 12/14/2022] Open
Abstract
The spotted snakehead Channa punctatus is a seasonally breeding teleost widely distributed in the Indian subcontinent and economically important due to high nutritional value. The declining population of C. punctatus prompted us to focus on genetic regulation of its reproduction. The present study carried out de novo testicular transcriptome sequencing during the four reproductive phases and correlated differential expression of transcripts with various testicular events in C. punctatus. The Illumina paired-end sequencing of testicular transcriptome from resting, preparatory, spawning and postspawning phases generated 41.94, 47.51, 61.81 and 44.45 million reads, and 105526, 105169, 122964 and 106544 transcripts, respectively. Transcripts annotated using Rattus norvegicus reference protein sequences and classified under various subcategories of biological process, molecular function and cellular component showed that the majority of the subcategories had highest number of transcripts during spawning phase. In addition, analysis of transcripts exhibiting differential expression during the four phases revealed an appreciable increase in upregulated transcripts of biological processes such as cell proliferation and differentiation, cytoskeleton organization, response to vitamin A, transcription and translation, regulation of angiogenesis and response to hypoxia during spermatogenically active phases. The study also identified significant differential expression of transcripts relevant to spermatogenesis (mgat3, nqo1, hes2, rgs4, cxcl2, alcam, agmat), steroidogenesis (star, tkt, gipc3), cell proliferation (eef1a2, btg3, pif1, myo16, grik3, trim39, plbd1), cytoskeletal organization (espn, wipf3, cd276), sperm development (klhl10, mast1, hspa1a, slc6a1, ros1, foxj1, hipk1), and sperm transport and motility (hint1, muc13). Analysis of functional annotation and differential expression of testicular transcripts depending on reproductive phases of C. punctatus helped in developing a comprehensive understanding on genetic regulation of spermatogenic and steroidogenic events in seasonally breeding teleosts. Our findings provide the basis for future investigation on the precise role of testicular genes in regulation of seasonal reproduction in male teleosts.
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Ye H, Li CJ, Yue HM, Du H, Yang XG, Yoshino T, Hayashida T, Takeuchi Y, Wei QW. Establishment of intraperitoneal germ cell transplantation for critically endangered Chinese sturgeon Acipenser sinensis. Theriogenology 2017; 94:37-47. [PMID: 28407859 DOI: 10.1016/j.theriogenology.2017.02.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/11/2017] [Accepted: 02/11/2017] [Indexed: 01/28/2023]
Abstract
Recent progress in germ cell transplantation techniques in fish has paved the way for the conservation of endangered species. Here, we developed an intraperitoneal germ cell transplantation procedure using Chinese and Dabry's sturgeon as donor and recipient species, respectively. Histological analysis revealed that primordial germ cells migrated on the peritoneal wall at 16 days post-hatch (dph) in Dabry's sturgeon. The genital ridges of Dabry's sturgeon (recipient) first formed at 28 dph, suggesting that for successful colonization of donor germ cells in the recipient gonads, the transplantation should be performed earlier than this age. Sexual dimorphism of gonadal structure was first observed at 78 dph. Gonadal germ cell proliferation was not seen in either sex during this period. Immunohistochemistry using the anti-Vasa antibody found that donor testes from 2-year-old Dabry's sturgeon mainly consisted of single- or paired-type A spermatogonia, while donor ovaries from 11.5-year-old Chinese sturgeon had perinucleolus stage oocytes and clusters of oogonia. Donor cells isolated from Dabry's sturgeon testes or Chinese sturgeon ovary labeled with PKH26 fluorescent dye were transplanted into the peritoneal cavity of the 7- or 8-dph Dabry's sturgeon larvae. More than 90% and 70% of transplanted larvae survived after 2 days post-transplantation (dpt) and 51 dpt, respectively. At 51 dpt, PKH26-labeled cells exhibiting germ cell-specific nuclear morphology and diameter were observed in excised recipient gonads by fluorescent and confocal microscopy. The colonization rate of allogeneic testicular germ cell transplantation (Group 1) was 70%, while that of two batches of xenogeneic ovarian germ cell transplantation (Group 2 and Group 3) were 6.7% and 40%, respectively. The ratio of colonized germ cells to endogenous germ cells was 11.96%, 5.35% and 3.56% for Group 1, Group 2 and Group 3, respectively. Thus, we established a germ cell transplantation technique for the critically endangered Chinese sturgeon using the most closely related species as a recipient and demonstrated the successful preparation of transplantable female germ cells from aged adult Chinese sturgeon.
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Affiliation(s)
- Huan Ye
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China; Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan, 430072, China; Research Center for Advanced Science and Technology, Tokyo University of Marine Science and Technology, 670 Banda, Tateyama-shi, Chiba, 294-0308, Japan
| | - Chuang-Ju Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China; Freshwater Fisheries Research Center, Chinese Academy of Fisheries Science, Wuxi, 214081, China
| | - Hua-Mei Yue
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China; Freshwater Fisheries Research Center, Chinese Academy of Fisheries Science, Wuxi, 214081, China
| | - Hao Du
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China; Freshwater Fisheries Research Center, Chinese Academy of Fisheries Science, Wuxi, 214081, China
| | - Xiao-Ge Yang
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China; Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan, 430072, China
| | - Tasuku Yoshino
- Research Center for Advanced Science and Technology, Tokyo University of Marine Science and Technology, 670 Banda, Tateyama-shi, Chiba, 294-0308, Japan
| | - Takao Hayashida
- Research Center for Advanced Science and Technology, Tokyo University of Marine Science and Technology, 670 Banda, Tateyama-shi, Chiba, 294-0308, Japan
| | - Yutaka Takeuchi
- Research Center for Advanced Science and Technology, Tokyo University of Marine Science and Technology, 670 Banda, Tateyama-shi, Chiba, 294-0308, Japan.
| | - Qi-Wei Wei
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China; Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan, 430072, China; Freshwater Fisheries Research Center, Chinese Academy of Fisheries Science, Wuxi, 214081, China.
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Expression Patterns of Atlantic Sturgeon ( Acipenser oxyrinchus) During Embryonic Development. G3-GENES GENOMES GENETICS 2017; 7:533-542. [PMID: 27974440 PMCID: PMC5295599 DOI: 10.1534/g3.116.036699] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
During teleost ontogeny the larval and embryonic stages are key stages, since failure during this period of tissue differentiation may cause malformations, developmental delays, poor growth, and massive mortalities. Despite the rapid advances in sequencing technologies, the molecular backgrounds of the development of economically important but endangered fish species like the Atlantic sturgeon (Acipenser oxyrinchus) have not yet been thoroughly investigated. The current study examines the differential expression of transcripts involved in embryonic development of the Atlantic sturgeon. Addressing this goal, a reference transcriptome comprising eight stages was generated using an Illumina HiSequation 2500 platform. The constructed de novo assembly counted to 441,092 unfiltered and 179,564 filtered transcripts. Subsequently, the expression profile of four developmental stages ranging from early (gastrula) to late stages of prelarval development [2 d posthatching (dph)] were investigated applying an Illumina MiSeq platform. Differential expression analysis revealed distinct expression patterns among stages, especially between the two early and the two later stages. Transcripts upregulated at the two early stages were mainly enriched in transcripts linked to developmental processes, while transcripts expressed at the last two stages were mainly enriched in transcripts important to muscle contraction. Furthermore, important stage-specific expression has been detected for the hatching stage with transcripts enriched in molecule transport, and for the 2 dph stage with transcripts enriched in visual perception and lipid digestion. Our investigation represents a significant contribution to the understanding of Atlantic sturgeon embryonic development, and transcript characterization along with the differential expression results will significantly contribute to sturgeon research and aquaculture.
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