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Wang B, Wu B, Liu X, Hu Y, Ming Y, Bai M, Liu J, Xiao K, Zeng Q, Yang J, Wang H, Guo B, Tan C, Hu Z, Zhao X, Li Y, Yue Z, Mei J, Jiang W, Yang Y, Li Z, Gao Y, Chen L, Jian J, Du H. Whole-genome Sequencing Reveals Autooctoploidy in Chinese Sturgeon and Its Evolutionary Trajectories. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzad002. [PMID: 38862424 DOI: 10.1093/gpbjnl/qzad002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 09/12/2023] [Accepted: 09/20/2023] [Indexed: 06/13/2024]
Abstract
The order Acipenseriformes, which includes sturgeons and paddlefishes, represents "living fossils" with complex genomes that are good models for understanding whole-genome duplication (WGD) and ploidy evolution in fishes. Here, we sequenced and assembled the first high-quality chromosome-level genome for the complex octoploid Acipenser sinensis (Chinese sturgeon), a critically endangered species that also represents a poorly understood ploidy group in Acipenseriformes. Our results show that A. sinensis is a complex autooctoploid species containing four kinds of octovalents (8n), a hexavalent (6n), two tetravalents (4n), and a divalent (2n). An analysis taking into account delayed rediploidization reveals that the octoploid genome composition of Chinese sturgeon results from two rounds of homologous WGDs, and further provides insights into the timing of its ploidy evolution. This study provides the first octoploid genome resource of Acipenseriformes for understanding ploidy compositions and evolutionary trajectories of polyploid fishes.
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Affiliation(s)
- Binzhong Wang
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
- Yangtze River Biodiversity Research Center, China Three Gorges Corporation, Wuhan 430014, China
| | - Bin Wu
- BGI-Shenzhen, Shenzhen 518083, China
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Xueqing Liu
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
- Yangtze River Biodiversity Research Center, China Three Gorges Corporation, Wuhan 430014, China
| | - Yacheng Hu
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
- Yangtze River Biodiversity Research Center, China Three Gorges Corporation, Wuhan 430014, China
| | - Yao Ming
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Mingzhou Bai
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby 2800, Denmark
| | - Juanjuan Liu
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
- Yangtze River Biodiversity Research Center, China Three Gorges Corporation, Wuhan 430014, China
| | - Kan Xiao
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
- Yangtze River Biodiversity Research Center, China Three Gorges Corporation, Wuhan 430014, China
| | - Qingkai Zeng
- River Basin Complex Administration Center, China Three Gorges Corporation, Yichang 443100, China
| | - Jing Yang
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
- Yangtze River Biodiversity Research Center, China Three Gorges Corporation, Wuhan 430014, China
| | - Hongqi Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Baifu Guo
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
- Yangtze River Biodiversity Research Center, China Three Gorges Corporation, Wuhan 430014, China
| | - Chun Tan
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
- Yangtze River Biodiversity Research Center, China Three Gorges Corporation, Wuhan 430014, China
| | - Zixuan Hu
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
- Yangtze River Biodiversity Research Center, China Three Gorges Corporation, Wuhan 430014, China
| | - Xun Zhao
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
- Yangtze River Biodiversity Research Center, China Three Gorges Corporation, Wuhan 430014, China
| | - Yanhong Li
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhen Yue
- BGI-Sanya, BGI-Shenzhen, Sanya 572025, China
| | - Junpu Mei
- BGI-Shenzhen, Shenzhen 518083, China
- BGI-Sanya, BGI-Shenzhen, Sanya 572025, China
| | - Wei Jiang
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
- Yangtze River Biodiversity Research Center, China Three Gorges Corporation, Wuhan 430014, China
| | - Yuanjin Yang
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
- Yangtze River Biodiversity Research Center, China Three Gorges Corporation, Wuhan 430014, China
| | - Zhiyuan Li
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
- Yangtze River Biodiversity Research Center, China Three Gorges Corporation, Wuhan 430014, China
| | - Yong Gao
- Yangtze Eco-Environment Engineering Research Center, China Three Gorges Corporation, Beijing 100038, China
| | - Lei Chen
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
- River Basin Complex Administration Center, China Three Gorges Corporation, Yichang 443100, China
| | - Jianbo Jian
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby 2800, Denmark
| | - Hejun Du
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
- Yangtze River Biodiversity Research Center, China Three Gorges Corporation, Wuhan 430014, China
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2
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Káldy J, Fazekas G, Kovács B, Molnár M, Lázár B, Pálinkás-Bodzsár N, Ljubobratović U, Fazekas G, Kovács G, Várkonyi E. Unidirectional hybridization between American paddlefish Polyodon spathula (Walbaum, 1792) and sterlet Acipenser ruthenus (Linnaeus, 1758). PeerJ 2024; 12:e16717. [PMID: 38259665 PMCID: PMC10802154 DOI: 10.7717/peerj.16717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 12/04/2023] [Indexed: 01/24/2024] Open
Abstract
Interspecific hybridizations among sturgeon species are feasible and often bidirectional. The American paddlefish (Polyodon spathula) from Family Polyodontidae and sturgeon species from Family Acipenseridae were reported capable of hybridization, but viable hybrids have been described only in crosses with the American paddlefish as paternal parents. In the reciprocal cross, the hybrids were not viable however embryos start to develop and reach late gastrula and early neurula stages. The goal of this study was to examine the hybridization between the sterlet sturgeon (Acipenser ruthenus) and the American paddlefish. Hybrid and purebred crosses were produced by artificial fertilization. Viable hybrid offspring were harvested (three month old) and verified in the families produced by female sterlet crossing with male American paddlefish. In the reciprocal hybrid crosses with female American paddlefish and male sterlet, the embryos development did not pass over 120 h post fertilization, indicating the unidirectional hybridization between American paddlefish and sterlet. Chromosome counting showed for the same ploidy level of viable hybrid and parent species. Analysis of three microsatellite markers confirmed the unidirectional hybridization between the American paddlefish and the sterlet species. Overall, the inferred genetic cause suggests that unidirectional hybridization between American paddlefish and sterlet may be the case not only for these two species but likely also between American paddlefish and other sturgeon species.
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Affiliation(s)
- Jenő Káldy
- Research Centre for Fisheries and Aquaculture, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Szarvas, Békés, Hungary
| | - Georgina Fazekas
- Research Centre for Fisheries and Aquaculture, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Szarvas, Békés, Hungary
- PhD School of Animal Biotechnology and Animal Science, Hungarian University of Agriculture and Life Sciences, Gödöllő, Pest, Hungary
| | - Balázs Kovács
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Gödöllő, Pest, Hungary
| | - Mariann Molnár
- PhD School of Animal Biotechnology and Animal Science, Hungarian University of Agriculture and Life Sciences, Gödöllő, Pest, Hungary
- National Centre for Biodiversity and Gene Conservation, Institute for Farm Animal Gene Conservation, Gödöllő, Pest, Hungary
| | - Bence Lázár
- National Centre for Biodiversity and Gene Conservation, Institute for Farm Animal Gene Conservation, Gödöllő, Pest, Hungary
- Animal Biotechnology Department, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, Pest, Hungary
| | - Nóra Pálinkás-Bodzsár
- National Centre for Biodiversity and Gene Conservation, Institute for Farm Animal Gene Conservation, Gödöllő, Pest, Hungary
| | - Uroš Ljubobratović
- Research Centre for Fisheries and Aquaculture, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Szarvas, Békés, Hungary
| | - Gyöngyvér Fazekas
- Research Centre for Fisheries and Aquaculture, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Szarvas, Békés, Hungary
| | - Gyula Kovács
- Research Centre for Fisheries and Aquaculture, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Szarvas, Békés, Hungary
| | - Eszter Várkonyi
- National Centre for Biodiversity and Gene Conservation, Institute for Farm Animal Gene Conservation, Gödöllő, Pest, Hungary
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Ferreira A, Aversa-Marnai M, Villarino A, Silva-Álvarez V. Innate immune and chronic heat stress responses in sturgeons: Advances and insights from studies on Russian sturgeons. FISH AND SHELLFISH IMMUNOLOGY REPORTS 2023; 5:100121. [PMID: 37964807 PMCID: PMC10641160 DOI: 10.1016/j.fsirep.2023.100121] [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: 07/31/2023] [Revised: 09/30/2023] [Accepted: 10/19/2023] [Indexed: 11/16/2023] Open
Abstract
Chronic stress deteriorates the immune function of fish, thereby increasing their vulnerability to infections. However, the molecular and cellular mechanisms underlying stress-mediated immunosuppression and infection susceptibility in fish remain largely unknown. Understanding these mechanisms will contribute to improving fish welfare and their farm production. Herein, we review the challenges of sturgeon aquaculture in subtropical countries, where current climate change has giving rise to significant temperature increments during summer. This leads to the exposure of fish to stressful conditions during these months. Chronic heat stress deserves attention considering the rapid warming rate of the planet. It is already affecting wild fish populations, with disastrous consequences for sturgeons, which are one of the most endangered fish species in the world. In this context, we discuss the most recent advances through the studies on the effects of chronic heat stress on the innate immune components of sturgeons. To this end, we summarise the findings of studies focusing on the aquaculture of Russian sturgeons and observations made on other Acipenser species. Special attention is given to acute-phase proteins, as they might be valuable biomarkers of heat stress and infection, with applicability in monitoring the fish health status in farms.
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Affiliation(s)
- A.M. Ferreira
- Unidad Asociada de Inmunología, Instituto de Química Biológica, Facultad de Ciencias, Instituto de Higiene, Universidad de la República, Montevideo, Uruguay
| | - M. Aversa-Marnai
- Área Inmunología, Departamento de Biociencias, Facultad de Química, Instituto de Higiene, Universidad de la República, Montevideo, Uruguay
| | - A. Villarino
- Sección Bioquímica, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - V. Silva-Álvarez
- Área Inmunología, Departamento de Biociencias, Facultad de Química, Instituto de Higiene, Universidad de la República, Montevideo, Uruguay
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Mezzasalma M, Brunelli E, Odierna G, Guarino FM. Evolutionary and Genomic Diversity of True Polyploidy in Tetrapods. Animals (Basel) 2023; 13:ani13061033. [PMID: 36978574 PMCID: PMC10044425 DOI: 10.3390/ani13061033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/02/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
True polyploid organisms have more than two chromosome sets in their somatic and germline cells. Polyploidy is a major evolutionary force and has played a significant role in the early genomic evolution of plants, different invertebrate taxa, chordates, and teleosts. However, the contribution of polyploidy to the generation of new genomic, ecological, and species diversity in tetrapods has traditionally been underestimated. Indeed, polyploidy represents an important pathway of genomic evolution, occurring in most higher-taxa tetrapods and displaying a variety of different forms, genomic configurations, and biological implications. Herein, we report and discuss the available information on the different origins and evolutionary and ecological significance of true polyploidy in tetrapods. Among the main tetrapod lineages, modern amphibians have an unparalleled diversity of polyploids and, until recently, they were considered to be the only vertebrates with closely related diploid and polyploid bisexual species or populations. In reptiles, polyploidy was thought to be restricted to squamates and associated with parthenogenesis. In birds and mammals, true polyploidy has generally been considered absent (non-tolerated). These views are being changed due to an accumulation of new data, and the impact as well as the different evolutionary and ecological implications of polyploidy in tetrapods, deserve a broader evaluation.
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Affiliation(s)
- Marcello Mezzasalma
- Department of Biology, Ecology and Earth Science, University of Calabria, Via P. Bucci 4/B, 87036 Rende, Italy
- Correspondence: (M.M.); (E.B.)
| | - Elvira Brunelli
- Department of Biology, Ecology and Earth Science, University of Calabria, Via P. Bucci 4/B, 87036 Rende, Italy
- Correspondence: (M.M.); (E.B.)
| | - Gaetano Odierna
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80126 Naples, Italy (F.M.G.)
| | - Fabio Maria Guarino
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80126 Naples, Italy (F.M.G.)
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Flamio R, Swift DG, Portnoy DS, Chojnacki KA, DeLonay AJ, Powell J, Braaten PJ, Heist EJ. Haploid gynogens facilitate disomic marker development in paleotetraploid sturgeons. Mol Ecol Resour 2022. [PMID: 36453984 DOI: 10.1111/1755-0998.13742] [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: 06/01/2022] [Revised: 11/02/2022] [Accepted: 11/22/2022] [Indexed: 12/03/2022]
Abstract
Acipenseriformes (sturgeons and paddlefishes) are of substantial conservation concern, and development of genomic resources for these species is difficult due to past whole genome duplication. Development of disomic markers for polyploid organisms can be challenging due to difficulty in resolving alleles at a single locus from those among duplicated loci. In this study, we detail the development of disomic markers for the endangered pallid sturgeon (Scaphirhynchus albus) found in North America. One of the strategies for pallid sturgeon conservation is to stock U.S. rivers with offspring of pure pallid sturgeon, but introgression with the sympatric shovelnose sturgeon (S. platorynchus) threatens pallid sturgeon genetic integrity. Currently, 19 microsatellite loci are used to differentiate between both species and their hybrids, but the markers are insufficient to robustly identify backcrosses. We performed double digest restriction site-associated DNA sequencing (ddRADseq) on shovelnose sturgeon haploid gynogens to produce a reduced-representation genomic reference. Contiguous sequences that were heterozygous within a haploid individual were flagged as potentially encompassing multiple loci. Approximately 60 individuals of each species from two management units were sequenced, and reads were mapped to the haploid reference to identify single nucleotide polymorphisms (SNPs) at individual loci. The final data set contained 11,082 microhaplotyped loci which offer at least an order of magnitude greater resolution for species discrimination than the current panel of 19 microsatellites. These markers will be used to examine a larger sample of Scaphirhynchus individuals throughout their ranges to determine the extent and trajectory of hybridization.
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Affiliation(s)
- Richard Flamio
- Department of Zoology, Southern Illinois University Carbondale, Carbondale, Illinois, USA
| | - Dominic G Swift
- Marine Genomics Laboratory, Department of Life Sciences, Texas A&M University Corpus Christi, Corpus Christi, Texas, USA
| | - David S Portnoy
- Marine Genomics Laboratory, Department of Life Sciences, Texas A&M University Corpus Christi, Corpus Christi, Texas, USA
| | - Kimberly A Chojnacki
- U.S. Geological Survey, Columbia Environmental Research Center, Columbia, Missouri, USA
| | - Aaron J DeLonay
- U.S. Geological Survey, Columbia Environmental Research Center, Columbia, Missouri, USA
| | - Jeffrey Powell
- U.S. Fish and Wildlife Service, Gavins Point National Fish Hatchery, Yankton, South Dakota, USA
| | - Patrick J Braaten
- U.S. Geological Survey, Columbia Environmental Research Center, Columbia, Missouri, USA
| | - Edward J Heist
- Department of Zoology, Southern Illinois University Carbondale, Carbondale, Illinois, USA
- Center for Fisheries, Aquaculture, and Aquatic Sciences, Southern Illinois University Carbondale, Carbondale, Illinois, USA
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Hubálek M, Kašpar V, Tichopád T, Rodina M, Flajšhans M. How do suboptimal temperatures affect polyploid sterlet Acipenser ruthenus during early development? JOURNAL OF FISH BIOLOGY 2022; 101:77-91. [PMID: 35475498 DOI: 10.1111/jfb.15072] [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: 08/10/2021] [Accepted: 04/25/2022] [Indexed: 06/14/2023]
Abstract
Sturgeons are ancient fish exhibiting unique genome plasticity and a high tendency to produce spontaneously autopolyploid genome states. The temperature profiles of the rivers in which sturgeon live and reproduce have been severely altered by human intervention, and the effect of global warming is expected to cause further temperature shifts, which may be detrimental for early developmental stages with narrow windows of thermal tolerance. The comparison of the performance of diploid and autopolyploid sturgeon kept at unfavourable temperatures contributes to scientific knowledge of the effects of polyploid genome states on organisms and can shed light on the ability of polyploids to cope with human-induced alterations to natural conditions. Using the sterlet Acipenser ruthenus as a model species, we carried out conventional artificial fertilization, as well as the induction of the second polar body retention (SPBR), of the first mitotic division suppression (FMDS) and of the second polar body retention followed by the first mitotic division suppression (SPBR+FMDS). Two experiments were conducted to evaluate the effect of polyploidy on two basic performance parameters, survival and growth. In Experiment 1, fish belonging to untreated, SPBR-, FMDS- and SPBR+FMDS-induced groups were kept at 10, 16 and 20°C from the neurula stage until the end of endogenous feeding. In Experiment 2, larvae from the untreated and SPBR-induced groups were reared at 10, 16 and 20°C after their endogenous feeding transition for 3 weeks. Based on our findings, we report that the embryos, prelarvae and larvae of triploid A. ruthenus do not differ from diploids in their ability to survive, grow and develop under suboptimal temperature conditions, while the survival of tetraploids was significantly reduced even at the optimal temperature and even more so at temperatures far from the optimum. This was also the case in the 2n/4n mosaics observed in FMDS-induced group. Thus, we assume that in tetraploid and 2n/4n individuals, the limits of thermal tolerance are closer to the optimum than in diploids. We also conclude that the hexaploid genome state is probably lethal in A. ruthenus since none of the hexaploids or 3n/6n mosaics arising from the SPBR+FMDS induction survived the prelarval period.
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Affiliation(s)
- Martin Hubálek
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
| | - Vojtěch Kašpar
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
| | - Tomáš Tichopád
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
| | - Marek Rodina
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
| | - Martin Flajšhans
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
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7
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Palatnikov GM. A Comparative Analysis of Morphofunctional Characteristics of Cartilaginous Ganoid Fishes (Order Chondrostei). J EVOL BIOCHEM PHYS+ 2022. [DOI: 10.1134/s002209302202003x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Soto E, Fast MD, Purcell SL, Denver Coleman D, Yazdi Z, Kenelty K, Yun S, Camus A. Expression of immune markers of white sturgeon (Acipenser transmontanus) during Veronaea botryosa infection at different temperatures. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 41:100950. [PMID: 34973489 DOI: 10.1016/j.cbd.2021.100950] [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: 07/22/2021] [Revised: 11/19/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Systemic phaeohyphomycosis caused by Veronaea botryosa is one of the most important emergent diseases to affect sturgeon aquaculture in North America. White sturgeon (Acipenser transmontanus) cultured at temperatures above 15 °C are at higher risk of severe disseminated disease and higher mortalities. Despite this, little is known regarding disease pathogenesis and the immune response to infection. The objective of this study was to investigate the acute (2 days post-challenge [dpc]) and chronic (32 dpc) response of white sturgeon at 13 °C and 18 °C challenged with V. botryosa via intramuscular injection, using gene expression analysis of a diverse array of soluble immune and inflammatory mediators. Significantly greater amounts of irf8 (p < 0.05) and tfg-β (p < 0.05) genes were detected in gills of exposed fish at 18 °C when compared to those at 13 °C 32 dpc. Transcript levels of haptoglobin, serotransferrin, serum amyloid, cathelicidin, tnf-α, and il-17 were significantly increased in splenic tissues of challenged fish maintained at 18 °C late in infection (p < 0.05). However, only haptoglobin and serotransferrin transcript abundance were significantly greater in exposed fish when compared to controls 32dpc. Moreover, haptoglobin transcripts at this time point were significantly greater in exposed fish at 18 °C when compared to those challenged at 13 °C. Fewer differences were detected in fish kept at 13 °C. In agreement with transcript quantification, western blot assessment of haptoglobin showed increased levels in the challenged fish maintained at 18 °C.
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Affiliation(s)
- Esteban Soto
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, 95616 Davis, CA, USA.
| | - Mark D Fast
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Sara L Purcell
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - D Denver Coleman
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, 95616 Davis, CA, USA
| | - Zeinab Yazdi
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, 95616 Davis, CA, USA
| | - Kirsten Kenelty
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, 95616 Davis, CA, USA
| | - Susan Yun
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, 95616 Davis, CA, USA
| | - Alvin Camus
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
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9
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Stundl J, Soukup V, Franěk R, Pospisilova A, Psutkova V, Pšenička M, Cerny R, Bronner ME, Medeiros DM, Jandzik D. Efficient CRISPR Mutagenesis in Sturgeon Demonstrates Its Utility in Large, Slow-Maturing Vertebrates. Front Cell Dev Biol 2022; 10:750833. [PMID: 35223827 PMCID: PMC8867083 DOI: 10.3389/fcell.2022.750833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 01/17/2022] [Indexed: 11/14/2022] Open
Abstract
In the last decade, the CRISPR/Cas9 bacterial virus defense system has been adapted as a user-friendly, efficient, and precise method for targeted mutagenesis in eukaryotes. Though CRISPR/Cas9 has proven effective in a diverse range of organisms, it is still most often used to create mutant lines in lab-reared genetic model systems. However, one major advantage of CRISPR/Cas9 mutagenesis over previous gene targeting approaches is that its high efficiency allows the immediate generation of near-null mosaic mutants. This feature could potentially allow genotype to be linked to phenotype in organisms with life histories that preclude the establishment of purebred genetic lines; a group that includes the vast majority of vertebrate species. Of particular interest to scholars of early vertebrate evolution are several long-lived and slow-maturing fishes that diverged from two dominant modern lineages, teleosts and tetrapods, in the Ordovician, or before. These early-diverging or “basal” vertebrates include the jawless cyclostomes, cartilaginous fishes, and various non-teleost ray-finned fishes. In addition to occupying critical phylogenetic positions, these groups possess combinations of derived and ancestral features not seen in conventional model vertebrates, and thus provide an opportunity for understanding the genetic bases of such traits. Here we report successful use of CRISPR/Cas9 mutagenesis in one such non-teleost fish, sterlet Acipenser ruthenus, a small species of sturgeon. We introduced mutations into the genes Tyrosinase, which is needed for melanin production, and Sonic hedgehog, a pleiotropic developmental regulator with diverse roles in early embryonic patterning and organogenesis. We observed disruption of both loci and the production of consistent phenotypes, including both near-null mutants’ various hypomorphs. Based on these results, and previous work in lamprey and amphibians, we discuss how CRISPR/Cas9 F0 mutagenesis may be successfully adapted to other long-lived, slow-maturing aquatic vertebrates and identify the ease of obtaining and injecting eggs and/or zygotes as the main challenges.
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Affiliation(s)
- Jan Stundl
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, Vodňany, Czechia
| | - Vladimír Soukup
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Roman Franěk
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, Vodňany, Czechia
| | - Anna Pospisilova
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Viktorie Psutkova
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Martin Pšenička
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, Vodňany, Czechia
| | - Robert Cerny
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Marianne E. Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Daniel Meulemans Medeiros
- Department of Ecology and Evolutionary Biology, University of Colorado in Boulder, Boulder, CO, United States
| | - David Jandzik
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
- Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
- *Correspondence: David Jandzik,
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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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11
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Soto E, Coleman D, Yazdi Z, Purcell SL, Camus A, Fast MD. Analysis of the white sturgeon (Acipenser transmontanus) immune response during immunostimulation and Veronaea botryosa infection. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 40:100879. [PMID: 34607242 DOI: 10.1016/j.cbd.2021.100879] [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: 03/11/2021] [Revised: 06/17/2021] [Accepted: 07/03/2021] [Indexed: 10/20/2022]
Abstract
Systemic phaeohyphomycosis caused by Veronaea botryosa is regarded as an important emerging mycotic disease of sturgeon aquaculture. However, no vaccines or treatments are currently available. The effects of dietary β-glucan supplementation on resistance to V. botryosa infection was examined in controlled challenges by exposing immunostimulated and control fish to ~7.25 × 105 fungal spores/fish via intra-muscular injection. Six weeks post-challenge, cumulative mortality was determined and antibodies to acute phase-proteins (APP) were used to quantify the conserved APP peptides in the serum of challenged and control fish using Western blot. Transcript levels for all tested pro-inflammatory cytokines, APP, and regulatory cytokines in the spleen were similar amongst treatments at the end of the three-week feeding period. However, significantly higher survival occurred in fingerlings fed 0.3% β-glucans compared to non-immunostimulated fish groups (p < 0.05) six weeks post-challenge. A strong proinflammatory response was detected in exposed treatment groups, and greater survival at 6 weeks was associated with higher transcript abundance of Il-17 in fish fed β-glucans. Findings support the important role of this cytokine in response to fungal infection.
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Affiliation(s)
- Esteban Soto
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, 95616 Davis, CA, USA.
| | - Denver Coleman
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, 95616 Davis, CA, USA
| | - Zeinab Yazdi
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, 95616 Davis, CA, USA
| | - Sara L Purcell
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Alvin Camus
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Mark D Fast
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
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12
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Isolation and characterization of 34 SNP markers in Acipenser baerii. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01232-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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13
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Genetic Investigation of Four Beluga Sturgeon (Huso huso, L.) Broodstocks for its Reintroduction in the Po River Basin. ENVIRONMENTS 2021. [DOI: 10.3390/environments8040025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The reintroduction of the extinct beluga sturgeon (Huso huso L.), an anadromous species with economic and traditional relevance, is a priority in next conservation strategies in Northern Italy. The EU-LIFE NATURA project aims to reintroduce the beluga sturgeon in the Po River basin through a captive breeding program. Critical requirements for the success of the program are river connectivity and knowledge of genetic diversity of the selected broodstocks to ensure self-sustainability of reintroduced populations. Here, the four broodstocks used for the reintroduction of beluga sturgeon have been genetically screened, genotyping 13 loci and sequencing mitochondrial DNA cytochrome b (Cyt b) gene and the entire mitochondrial DNA control region (D-Loop). The four broodstocks showed a medium-high level of nuclear genetic variability and the presence of two sub-populations, evidencing a total level of inbreeding coefficients able to sustain the good potential as future breeders. Mitochondrial analyses showed a genetic variability comparable to wild populations, further strengthening the positive potential of the investigated broodstock. Therefore, this study, showed how the degree of genetic diversity found within the four broodstocks used for H. huso reintroduction in the Po River basin could be suitable to ensure the success of the program, avoiding the inbreeding depression associated with founder effect and captive breeding.
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14
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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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15
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Atre I, Mizrahi N, Yebra-Pimentel ES, Hausken K, Yom-Din S, Hurvitz A, Dirks R, Degani G, Levavi-Sivan B. Molecular characterization of two Russian sturgeon gonadotropin receptors: Cloning, expression analysis, and functional activity. Gen Comp Endocrinol 2020; 298:113557. [PMID: 32687934 DOI: 10.1016/j.ygcen.2020.113557] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 06/24/2020] [Accepted: 07/14/2020] [Indexed: 10/23/2022]
Abstract
Sturgeons are being used in aquaculture because wild populations are now endangered due to overfishing for caviar. A challenge in working with sturgeon as an aquacultured species is its long and slow reproductive development. Reproduction is a hormonally regulated process that involves hierarchical signaling between the brain, pituitary gland, and gonads. In an effort to better understand the hormonal regulation of sturgeon reproduction, we have cloned the Russian sturgeon (st), Acipenser gueldenstaedtii, luteinizing hormone receptor (stLHR) and follicle stimulating hormone receptor (stFSHR) and measured their expression from previtellogenic to mature ovarian follicles. Sturgeon LHR and FSHR expression was elevated in early-vitellogenic and mature follicles compared with pre-vitellogenic and mid-vitellogenic follicles, and only LHR expression increased during late-vitellogenesis. Recombinant sturgeon FSH and LH both activated sturgeon LHR and FSHR in a cAMP reporter assay. Further molecular characterization of these receptors was accomplished by in silico modeling and cAMP reporter assays using heterologous recombinant gonadotropins from human and piscine species. There was no apparent trend in heterologous LH and/or FSH activation of the sturgeon LHR or FSHR. These data suggest that permissive activation of LHR and FSHR are a consequence of some yet undetermined biological characteristic(s) of different piscine species.
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MESH Headings
- Amino Acid Sequence
- Animals
- Cloning, Molecular
- Female
- Gene Expression Regulation
- Humans
- Models, Molecular
- Phylogeny
- Protein Domains
- Receptors, FSH/chemistry
- Receptors, FSH/genetics
- Receptors, FSH/metabolism
- Receptors, Gonadotropin/chemistry
- Receptors, Gonadotropin/genetics
- Receptors, Gonadotropin/metabolism
- Receptors, LH/chemistry
- Receptors, LH/genetics
- Receptors, LH/metabolism
- Russia
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Affiliation(s)
- Ishwar Atre
- Department of Animal Sciences, The Robert H. Smith Faculty of Agriculture, Food, and Environment, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Naama Mizrahi
- Department of Animal Sciences, The Robert H. Smith Faculty of Agriculture, Food, and Environment, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | | | - Krist Hausken
- Department of Animal Sciences, The Robert H. Smith Faculty of Agriculture, Food, and Environment, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Svetlana Yom-Din
- Department of Animal Sciences, The Robert H. Smith Faculty of Agriculture, Food, and Environment, Hebrew University of Jerusalem, Rehovot 76100, Israel; MIGAL - Galilee Technology Center, P.O. Box 831, Kiryat Shmona 10200, Israel
| | | | - Ron Dirks
- ZF-screens B.V., Leiden, the Netherlands
| | - Gad Degani
- MIGAL - Galilee Technology Center, P.O. Box 831, Kiryat Shmona 10200, Israel
| | - Berta Levavi-Sivan
- Department of Animal Sciences, The Robert H. Smith Faculty of Agriculture, Food, and Environment, Hebrew University of Jerusalem, Rehovot 76100, Israel.
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Hybridization of Russian Sturgeon ( Acipenser gueldenstaedtii, Brandt and Ratzeberg, 1833) and American Paddlefish ( Polyodon spathula, Walbaum 1792) and Evaluation of Their Progeny. Genes (Basel) 2020; 11:genes11070753. [PMID: 32640744 PMCID: PMC7397225 DOI: 10.3390/genes11070753] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/29/2020] [Accepted: 07/03/2020] [Indexed: 01/09/2023] Open
Abstract
Two species from the families Acipenseridae and Polyodontidae, Russian sturgeon (Acipenser gueldenstaedtii, Brandt and Ratzeberg, 1833; functional tetraploid) and American paddlefish (Polyodon spathula, Walbaum 1792, functional diploid) were hybridized. The hybridization was repeated using eggs from three sturgeon and sperm from four paddlefish individuals. Survival in all hybrid family groups ranged from 62% to 74% 30 days after hatching. This was the first successful hybridization between these two species and between members of the family Acipenseridae and Polyodontidae. Flow cytometry and chromosome analysis revealed two ploidy levels in hybrids. The chromosome numbers of the hybrids ranged between 156-184 and 300-310, in "functional" triploids and "functional" pentaploids, respectively. The hybrid origin and the ploidy levels were also confirmed by microsatellite analyses. In hybrids, the size and the number of dorsal and ventral scutes correlated with the ploidy levels as well as with the calculated ratio of the maternal and paternal chromosome sets. An extra haploid cell lineage was found in three hybrid individuals irrespective of the ploidy level, suggesting polyspermy. Although the growth performance showed high variance in hybrids (mean: 1.2 kg, SD: 0.55), many individuals reached a size of approximately 1 kg by the age of one year under intensive rearing conditions.
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17
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The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization. Nat Ecol Evol 2020; 4:841-852. [PMID: 32231327 PMCID: PMC7269910 DOI: 10.1038/s41559-020-1166-x] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 02/27/2020] [Indexed: 12/20/2022]
Abstract
Sturgeons seem to be frozen in time. The archaic characteristics of this ancient fish lineage place it in a key phylogenetic position at the base of the ~30,000 modern teleost fish species. Moreover, sturgeons are notoriously polyploid, providing unique opportunities to investigate the evolution of polyploid genomes. We assembled a high-quality chromosome-level reference genome for the sterlet, Acipenser ruthenus. Our analysis revealed a very low protein evolution rate that is at least as slow as in other deep branches of the vertebrate tree, such as that of the coelacanth. We uncovered a whole-genome duplication that occurred in the Jurassic, early in the evolution of the entire sturgeon lineage. Following this polyploidization, the rediploidization of the genome included the loss of whole chromosomes in a segmental deduplication process. While known adaptive processes helped conserve a high degree of structural and functional tetraploidy over more than 180 million years, the reduction of redundancy of the polyploid genome seems to have been remarkably random. A genome assembly of the sterlet, Acipenser ruthenus, reveals a whole-genome duplication early in the evolution of the entire sturgeon lineage and provides details about the rediploidization of the genome.
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18
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Hu Y, Liu X, Yang J, Xiao K, Wang B, Du H. Development and characterization of a duplex PCR assay in Chinese sturgeon (Acipenser sinensis) for genetic analysis. Sci Rep 2020; 10:3451. [PMID: 32103060 PMCID: PMC7044248 DOI: 10.1038/s41598-020-60401-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 02/06/2020] [Indexed: 11/09/2022] Open
Abstract
Chinese sturgeon (Acipenser sinensis) has been listed as a critically endangered species on the IUCN Red List and is an endemic fish of China. Five sets of duplex polymerase chain reactions (PCR) assays were developed with 10 tetranucleotide microsatellites for Chinese sturgeon. The size of CS57, ZHX43, ZHX69, AS105, ZHX51, AS074, ZHX2, AS078, AS026 and AS073 products in 184 Chinese sturgeon individuals ranged from 257-305, 191-241, 251-285, 172-244, 236-260, 169-209, 194-234, 92-176, 165-257 and 120-164, respectively. The observed allele number of the 10 microsatellites ranged from 7 to 16, and the total number of alleles was 106. The number of alleles per individual in CS57, ZHX43, AS105, AS074, AS078 and AS026 was 1-4. The number of alleles per individual in ZHX69, ZHX51, ZHX2 and AS073 was 2-4. The mean number of alleles per locus per individual ranged from 2.01-3.76. The expected heterozygosity (HE), observed heterozygosity (HO), polymorphic information content (PIC) and Shannon-Weiner diversity index (H') ranged from 0.582 to 0.899, from 0.676 to 1, from 0.518 to 0.886 and from 1.034 to 2.34, respectively. Despite many advantages, the use of microsatellites as genetic analysis tools can be limited by the cost of the associated experiment. To solve this problem, this set of five duplex PCRs will provide tools that are more helpful, less expensive and less time consuming than others used for genetic analyses in Chinese sturgeon.
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Affiliation(s)
- Yacheng Hu
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang Hubei, 443100, China.,Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang Hubei, 443100, China
| | - Xueqing Liu
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang Hubei, 443100, China.,Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang Hubei, 443100, China
| | - Jing Yang
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang Hubei, 443100, China.,Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang Hubei, 443100, China
| | - Kan Xiao
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang Hubei, 443100, China.,Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang Hubei, 443100, China
| | - Binzhong Wang
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang Hubei, 443100, China.,Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang Hubei, 443100, China
| | - Hejun Du
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang Hubei, 443100, China. .,Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang Hubei, 443100, China.
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19
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Abstract
The diversity of fish hemoglobins and the association with oxygen availability and physiological requirements during the life cycle has attracted scientists since the first report on multiple hemoglobin in fishes (Buhler and Shanks 1959). The functional heterogeneity of the fish hemoglobins enables many species to tolerate hypoxic conditions and exhausting swimming, but also to maintain the gas pressure in the swim bladder at large depths. The hemoglobin repertoire has further increased in various species displaying polymorphic hemoglobin variants differing in oxygen binding properties. The multiplicity of fish hemoglobins as particularly found in the tetraploid salmonids strongly contrasts with the complete loss of hemoglobins in Antarctic icefishes and illustrates the adaptive radiation in the oxygen transport of this successful vertebrate group.
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Affiliation(s)
- Øivind Andersen
- Norwegian Institute of Food, Fisheries and Aquaculture Research (NOFIMA), PO BOX 210,1431, Ås, Norway.
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20
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Abstract
The number of fishes exceeds that of all other vertebrates both in terms of species numbers and in their morphological and phylogenetic diversity. They are an ecologically and economically important group and play an essential role as a resource for humans. This makes the genomic exploration of fishes an important area of research, both from an applied and a basic research perspective. Fish genomes can vary greatly in complexity, which is partially due to differences in size and content of repetitive DNA, a history of genome duplication events and because fishes may be polyploid, all of which complicate the assembly and analysis of genome sequences. However, the advent of modern sequencing techniques now facilitates access to genomic data that permit genome-wide exploration of genetic information even for previously unexplored species. The development of genomic resources for fishes is spearheaded by model organisms that have been subject to genetic analysis and genome sequencing projects for a long time. These offer a great potential for the exploration of new species through the transfer of genomic information in comparative analyses. A growing number of genome sequencing projects and the increasing availability of tools to assemble and access genomic information now move boundaries between model and nonmodel species and promises progress in many interesting but unexplored species that remain to be studied.
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Affiliation(s)
- Arne W Nolte
- AG Ökologische Genomik, Institut für Biologie und Umweltwissenschaften, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany.
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21
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Gilannejad N, Paykan Heyrati F, Dorafshan S, Martos-Sitcha JA, Yúfera M, Martínez-Rodríguez G. Molecular basis of the digestive functionality in developing Persian sturgeon (Acipenser persicus) larvae: additional clues for its phylogenetic status. J Comp Physiol B 2019; 189:367-383. [DOI: 10.1007/s00360-019-01215-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 03/10/2019] [Accepted: 03/20/2019] [Indexed: 12/11/2022]
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22
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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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Takahagi K, Inoue K, Mochida K. Gene Co-expression Network Analysis Suggests the Existence of Transcriptional Modules Containing a High Proportion of Transcriptionally Differentiated Homoeologs in Hexaploid Wheat. FRONTIERS IN PLANT SCIENCE 2018; 9:1163. [PMID: 30135697 PMCID: PMC6092485 DOI: 10.3389/fpls.2018.01163] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 07/23/2018] [Indexed: 05/20/2023]
Abstract
Genome duplications aid in the formation of novel molecular networks through regulatory differentiation of the duplicated genes and facilitate adaptation to environmental change. Hexaploid wheat, Triticum aestivum, contains three homoeologous chromosome sets, the A-, B-, and D-subgenomes, which evolved through interspecific hybridization and subsequent whole-genome duplication. The divergent expression patterns of the homoeologs in hexaploid wheat suggest that they have undergone transcriptional and/or functional differentiation during wheat evolution. However, the distribution of transcriptionally differentiated homoeologs in gene regulatory networks and their related biological functions in hexaploid wheat are still largely unexplored. Therefore, we retrieved 727 publicly available wheat RNA-sequencing (RNA-seq) datasets from various tissues, developmental stages, and conditions, and identified 10,415 expressed homoeologous triplets. Examining the co-expression modules in the wheat transcriptome, we found that 66% of the expressed homoeologous triplets possess all three homoeologs grouped in the same co-expression modules. Among these, 15 triplets contain co-expressed homoeologs with differential expression levels between homoeoalleles across ≥ 95% of the 727 RNA-seq datasets, suggesting a consistent trend of homoeolog expression bias. In addition, we identified 2,831 differentiated homoeologs that showed gene expression patterns that deviated from those of the other two homoeologs. We found that seven co-expression modules contained a high proportion of such differentiated homoeologs, which accounted for ≥ 20% of the genes in each module. We also found that five of the co-expression modules are abundantly composed of genes involved in biological processes such as chloroplast biogenesis, RNA metabolism, putative defense response, putative posttranscriptional modification, and lipid metabolism, thereby suggesting that, the differentiated homoeologs might highly contribute to these biological functions in the gene network of hexaploid wheat.
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Affiliation(s)
- Kotaro Takahagi
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Komaki Inoue
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Keiichi Mochida
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
- *Correspondence: Keiichi Mochida,
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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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Panagiotopoulou H, Austin JD, Zalewska K, Gonciarz M, Czarnogórska K, Gawor J, Weglenski P, Popovic D. Microsatellite Mutation Rate in Atlantic Sturgeon (Acipenser oxyrinchus). J Hered 2017; 108:686-692. [PMID: 28821182 DOI: 10.1093/jhered/esx057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/02/2017] [Indexed: 11/14/2022] Open
Abstract
Understanding mutation rates can greatly extend the utility of population and conservation genetic analyses. Herein, we present an estimate of genome-wide microsatellite mutation rate in Atlantic sturgeon (Acipenser oxyrinchus) based on parent-offspring transmission patterns. We screened 307 individuals for parentage and mutation-rate analysis applying 43 variable markers. Out of 13228 allele transfers, 11 mutations were detected, producing a mutation rate of 8.3 × 10-4 per locus per generation (95% confidence interval: 1.48 × 10-3, 4.15 × 10-4). Single-step mutations predominated and there were trends toward mutations in loci with greater polymorphism and allele length. Two of the detected mutations were most probably cluster mutations, being identified in 12 and 28 sibs, respectively. Finally, we observed evidences of polyploidy based on the sporadic presence of 3 or 4 alleles per locus in the genotyped individuals, supporting previous reports of incomplete diploidization in Atlantic sturgeon.
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Affiliation(s)
- Hanna Panagiotopoulou
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611; Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611; Institute of Genetics and Biotechnology, Department of Biology, University of Warsaw, Warsaw, Poland; University of Newcastle, Callaghan, Australia; Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - James D Austin
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611; Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611; Institute of Genetics and Biotechnology, Department of Biology, University of Warsaw, Warsaw, Poland; University of Newcastle, Callaghan, Australia; Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Katarzyna Zalewska
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611; Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611; Institute of Genetics and Biotechnology, Department of Biology, University of Warsaw, Warsaw, Poland; University of Newcastle, Callaghan, Australia; Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Magdalena Gonciarz
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611; Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611; Institute of Genetics and Biotechnology, Department of Biology, University of Warsaw, Warsaw, Poland; University of Newcastle, Callaghan, Australia; Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Kinga Czarnogórska
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611; Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611; Institute of Genetics and Biotechnology, Department of Biology, University of Warsaw, Warsaw, Poland; University of Newcastle, Callaghan, Australia; Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Jan Gawor
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611; Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611; Institute of Genetics and Biotechnology, Department of Biology, University of Warsaw, Warsaw, Poland; University of Newcastle, Callaghan, Australia; Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Piotr Weglenski
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611; Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611; Institute of Genetics and Biotechnology, Department of Biology, University of Warsaw, Warsaw, Poland; University of Newcastle, Callaghan, Australia; Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Danijela Popovic
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611; Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611; Institute of Genetics and Biotechnology, Department of Biology, University of Warsaw, Warsaw, Poland; University of Newcastle, Callaghan, Australia; Centre of New Technologies, University of Warsaw, Warsaw, Poland
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26
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Kohlmann K, Kersten P, Geßner J, Onără D, Taflan E, Suciu R. Isolation and characterization of 18 polymorphic microsatellite markers for the critically endangered stellate sturgeon, Acipenser stellatus. EUR J WILDLIFE RES 2017. [DOI: 10.1007/s10344-017-1132-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Burcea A, Popa GO, Florescu IE, Dudu A, Georgescu SE, Costache M. Genetic profile analysis of aquaculture Russian sturgeon (Acipenser gueldenstaedtii) – implications for restocking measures. ACTA ZOOL ACAD SCI H 2017. [DOI: 10.17109/azh.63.3.361.2017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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28
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Abstract
Polyploidy-the increase in the number of whole chromosome sets-is an important evolutionary force in eukaryotes. Polyploidy is well recognized throughout the evolutionary history of plants and animals, where several ancient events have been hypothesized to be drivers of major evolutionary radiations. However, fungi provide a striking contrast: while numerous recent polyploids have been documented, ancient fungal polyploidy is virtually unknown. We present a survey of known fungal polyploids that confirms the absence of ancient fungal polyploidy events. Three hypotheses may explain this finding. First, ancient fungal polyploids are indeed rare, with unique aspects of fungal biology providing similar benefits without genome duplication. Second, fungal polyploids are not successful in the long term, leading to few extant species derived from ancient polyploidy events. Third, ancient fungal polyploids are difficult to detect, causing the real contribution of polyploidy to fungal evolution to be underappreciated. We consider each of these hypotheses in turn and propose that failure to detect ancient events is the most likely reason for the lack of observed ancient fungal polyploids. We examine whether existing data can provide evidence for previously unrecognized ancient fungal polyploidy events but discover that current resources are too limited. We contend that establishing whether unrecognized ancient fungal polyploidy events exist is important to ascertain whether polyploidy has played a key role in the evolution of the extensive complexity and diversity observed in fungi today and, thus, whether polyploidy is a driver of evolutionary diversifications across eukaryotes. Therefore, we conclude by suggesting ways to test the hypothesis that there are unrecognized polyploidy events in the deep evolutionary history of the fungi.
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Parentage assignment in the critically endangered European sturgeon (Acipenser sturio) based on a novel microsatellite multiplex assay: a valuable resource for restocking, monitoring and conservation programs. CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0538-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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30
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Song W, Jiang K, Zhang F, Lin Y, Ma L. Transcriptome Sequencing, De Novo Assembly and Differential Gene Expression Analysis of the Early Development of Acipenser baeri. PLoS One 2015; 10:e0137450. [PMID: 26359664 PMCID: PMC4567377 DOI: 10.1371/journal.pone.0137450] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 08/17/2015] [Indexed: 11/25/2022] Open
Abstract
The molecular mechanisms that drive the development of the endangered fossil fish species Acipenser baeri are difficult to study due to the lack of genomic data. Recent advances in sequencing technologies and the reducing cost of sequencing offer exclusive opportunities for exploring important molecular mechanisms underlying specific biological processes. This manuscript describes the large scale sequencing and analyses of mRNA from Acipenser baeri collected at five development time points using the Illumina Hiseq2000 platform. The sequencing reads were de novo assembled and clustered into 278167 unigenes, of which 57346 (20.62%) had 45837 known homologues proteins in Uniprot protein databases while 11509 proteins matched with at least one sequence of assembled unigenes. The remaining 79.38% of unigenes could stand for non-coding unigenes or unigenes specific to A. baeri. A number of 43062 unigenes were annotated into functional categories via Gene Ontology (GO) annotation whereas 29526 unigenes were associated with 329 pathways by mapping to KEGG database. Subsequently, 3479 differentially expressed genes were scanned within developmental stages and clustered into 50 gene expression profiles. Genes preferentially expressed at each stage were also identified. Through GO and KEGG pathway enrichment analysis, relevant physiological variations during the early development of A. baeri could be better cognized. Accordingly, the present study gives insights into the transcriptome profile of the early development of A. baeri, and the information contained in this large scale transcriptome will provide substantial references for A. baeri developmental biology and promote its aquaculture research.
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Affiliation(s)
- Wei Song
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, Shanghai, China
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Keji Jiang
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, Shanghai, China
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Fengying Zhang
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, Shanghai, China
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Yu Lin
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, Shanghai, China
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Lingbo Ma
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, Shanghai, China
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- * E-mail:
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