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Gong D, Wang X, Yang J, Liang J, Tao M, Hu F, Wang S, Liu Z, Tang C, Luo K, Zhang C, Ma M, Wang Y, Liu S. Protection and utilization status of Parabramis and Megalobrama germplasm resources. REPRODUCTION AND BREEDING 2023. [DOI: 10.1016/j.repbre.2023.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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Ağdamar S, Baysal Ö, Yıldız A, Tarkan AS. Genetic differentiation of non-native populations of Gibel Carp, Carassius gibelio in Western Turkey by ISSR and SRAP markers. ZOOLOGY IN THE MIDDLE EAST 2020. [DOI: 10.1080/09397140.2020.1835215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Sevan Ağdamar
- Gökçeada School of Applied Sciences, Çanakkale Onsekiz Mart University, Çanakkale, Turkey
| | - Ömür Baysal
- Department of Molecular Biology and Genetics, Faculty of Science, Muğla Sıtkı Koçman University, Muğla, Turkey
| | - Ayşegül Yıldız
- Department of Molecular Biology and Genetics, Faculty of Science, Muğla Sıtkı Koçman University, Muğla, Turkey
| | - Ali Serhan Tarkan
- Faculty of Fisheries, Muğla Sıtkı Koçman University, Muğla, Turkey
- Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
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Genetic diversity in tilapia populations in a freshwater reservoir assayed by randomly amplified polymorphic DNA markers. Saudi J Biol Sci 2019; 26:363-367. [PMID: 31485178 PMCID: PMC6717130 DOI: 10.1016/j.sjbs.2018.11.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 11/06/2018] [Accepted: 11/20/2018] [Indexed: 11/22/2022] Open
Abstract
Genetic variation in fish stocks decreasing due to water pollution in the freshwater rivers, streams and canals. The objective of this study was to determine the genetic diversity and polymorphism in Oreochromis niloticus collected from the Wadi Hanefah Riyadh, Saudi Arabia by using RAPD-PCR. Total thirty fish specimens were harvested from each of four pre-determined locations of the reservoir which were designated as H1, H2, H3, and H4. Five random decamer primers were used to assess the diversity in the stock of O. niloticus. In this fish stock 48 bands were polymorphic and 12 were monomorphic. The maximum polymorphism (100%) was recorded in the fish samples procured from H4, followed by 88.75, 87.33 and 76.12% of the tilapia collected from H3, H2, and H4, respectively. Nei's genetic distance value was ranged as 0.0005 to 0.1006. Maximum and minimum genetic distance was recorded as 0.1006 and 0.005 in tilapia harvested from H1 and H2 locations. Average heterozygosity was ranged from 0.3009 to 0.3744. This information about the genetic polymorphism of O. niloticus may be used by the concerned authorities to evolve strategies to conserve the diversity of tilapia in the country.
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Xie P, Zhao G, Niu J, Wang J, Zhou Q, Guo Y, Ma X. Comprehensive analysis of population genetics of Phoxinus phoxinus ujmonensis in the Irtysh River: Abiotic and biotic factors. Ecol Evol 2019; 9:7997-8012. [PMID: 31380067 PMCID: PMC6662318 DOI: 10.1002/ece3.5320] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 05/14/2019] [Accepted: 05/15/2019] [Indexed: 12/25/2022] Open
Abstract
As a widely distributed species along the Irtysh River, Phoxinus phoxinus ujmonensis (Kaschtschenko, 1899) was used as a model to investigate genetic diversity and population structure as well as the influence of environmental factors on population genetics. In this study, we specifically developed 12 polymorphic microsatellite loci. The analysis of microsatellite and mtDNA markers revealed a high and a moderate genetic diversity across seven populations, respectively. Moderate differentiation was also detected among several populations, indicating the impact of habitat fragmentation and divergence. The absence of isolation by distance implied an extensive gene flow, while the presence of isolation by adaptation implied that these populations might be in the process of adapting to divergent habitats. Correlation analysis showed that abiotic factors like dissolved oxygen, pH, total dissolved solids, and conductivity in water as well as biotic factors like plankton diversity and fish species diversity had impact on genetic diversity and divergence in P. phoxinus ujmonensis populations. The results of this study will provide an insight into the effect of environmental factors on genetic diversity and contribute to the study of population genetics of sympatric species.
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Affiliation(s)
- Peng Xie
- College of FisheriesHuazhong Agricultural UniversityWuhanChina
| | - Guang Zhao
- College of FisheriesHuazhong Agricultural UniversityWuhanChina
| | - Jian‐Gong Niu
- Fisheries Research Institute of Xinjiang Uygur Autonomous RegionUrumqiChina
| | - Jun Wang
- Institute of International Rivers and Eco‐securityYunnan UniversityKunmingChina
| | - Qiong Zhou
- College of FisheriesHuazhong Agricultural UniversityWuhanChina
| | - Yan Guo
- Fisheries Research Institute of Xinjiang Uygur Autonomous RegionUrumqiChina
| | - Xu‐Fa Ma
- College of FisheriesHuazhong Agricultural UniversityWuhanChina
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Huang Y, Gong W, Xiong J, Gao XC, Ren HT. Discovery and characterization of conserved and novel microRNAs from blunt snout bream (Megalobrama amblycephala) by deep sequencing. Gene 2018; 654:57-63. [PMID: 29466763 DOI: 10.1016/j.gene.2018.02.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/27/2018] [Accepted: 02/15/2018] [Indexed: 10/18/2022]
Abstract
MicroRNAs (miRNAs) are short, single stranded RNA molecules with approximately 22 nts in length, which regulate the stability and translation of messenger RNAs in several organisms. To increase the repertoire of miRNAs characterized in M. amblycephala, we used the deep sequencing technology to sequence a small RNA library using pooled RNA sample isolated from the 4 different tissues of M. amblycephala. A total of 309 conserved miRNAs that originated from 131 miRNA families were detected. 15 novel candidates miRNA were identified. Randomly selected 6 miRNAs were analyzed by stem-loop qRT-PCR and differential expression patterns were observed in 6 different tissues of M. amblycephala. Furthermore, the potential targets were predicted. GO analysis showed that most of the targets were involved in a broad range of physiological functions including fish growth, development, metabolism, stress responses and so on. Overall, our results significantly increased the number of novel miRNAs in M. amblycephala, which should be useful for further investigation into the role of miRNAs in regulating diverse biological processes.
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Affiliation(s)
- Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China.
| | - Wangbao Gong
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jianli Xiong
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Xiao Chan Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Hong Tao Ren
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
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Genetic diversity and population structure of the northern snakehead (Channa argus Channidae: Teleostei) in central China: implications for conservation and management. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1023-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Tran NT, Jakovlić I, Wang WM. The first report of diablo in Megalobrama amblycephala: characterization, phylogenetic analysis, functional annotation and expression. J Genet 2017; 96:613-623. [PMID: 28947709 DOI: 10.1007/s12041-017-0816-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Smac/DIABLO gene is essential for the apoptosis mechanism in mammals. This study is the first report of the Megalobrama amblycephala (ma) diablo gene, and the first report of the tertiary structure of a Diablo polypeptide in fish. Madiablo is 1540-bp long with an open reading frame of 792 bp, encoding a putative protein of 263 amino acids with a molecular weight of 29.2 kDa. Phylogenetic analysis indicates that it is closely related to the zebrafish Diablo-a homologue. It also indicates the existence of two diablo copies (a and b) in teleosts; apart fromthe Percomorpha group,where diablo-b has been lost, but diablo-a had undergone an independent duplication. Madiablo protein contains a long Smac_DIABLO super family domain (Leu32-Asp263) and alpha helices were prevalent in the secondary structure. Homology model of madiablo protein was constructed using the comparative modelling method. Expression of madiablo mRNA transcript was investigated using qPCR: (i) in five tissues from a healthy blunt snout bream, indicating the highest constitutive expression level in liver. (ii) During the embryo and juvenile development, indicating a spike in expression during hatching and in later phases of the juvenile development. (iii) In response to Aeromonas hydrophila infection, indicating the downregulation in liver, spleen and kidney during the first 12 h postinfection and upregulation in spleen and kidney after 24 h postinfection (hpi). The results imply that madiablo is homologous to Diablo orthologues in other species, both structurally and functionally, and that, it probably plays a role in the immune system of M. amblycephala.
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Affiliation(s)
- Ngoc Tuan Tran
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, Hubei, People's Republic of China.
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Yuhong J, Leilei T, Fuyun Z, Hongyang J, Xiaowen L, Liying Y, Lei Z, Jingrong M, Jinpeng Y. Identification and characterization of immune-related microRNAs in blunt snout bream, Megalobrama amblycephala. FISH & SHELLFISH IMMUNOLOGY 2016; 49:470-492. [PMID: 26773859 DOI: 10.1016/j.fsi.2015.12.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 12/03/2015] [Accepted: 12/11/2015] [Indexed: 06/05/2023]
Abstract
MicroRNAs (miRNAs) play vital roles in diverse biological processes, including in immune response. Blunt snout bream (Megalobrama amblycephala) is a prevalent and important commercial endemic freshwater fish species in China's intensive polyculture systems. To identify immune-related miRNAs of M. amblycephala, two small RNA (sRNA) libraries from immune tissues with or without lipopolysaccharide (LPS) stimulation were constructed and sequenced using the high-throughput sequencing technology. Totally, 16,425,543 and 15,076,813 raw reads, corresponding to 14,156,755 and 13,445,869 clean reads, were obtained in the normal and infected libraries, respectively. A total of 324 miRNAs, including 218 known miRNAs and 106 putative novel miRNAs were identified by bioinformatic analysis. We analyzed differentially expressed miRNAs between two libraries using pairwise comparison. 113 (34.88%) miRNAs were found to be significantly differentially expressed between two libraries, with 63 (55.75%) exhibiting elevated expression in LPS stimulation sample. Thereinto, a number of known miRNAs were identified immune-related. Real-time quantitative PCR (RT-qPCR) were implemented for 12 miRNAs of two samples, and agreement was confirmed between the sequencing and RT-qPCR data. Target genes likely regulated by these differentially expressed miRNAs were predicted using computational prediction. The functional annotation of target genes by Gene Ontology enrichment (GO) and Kyoto Encyclopedia of Genes and Genomes pathway analysis (KEGG) indicated that a majority of differential miRNAs might involved in immune response. To our knowledge, this is the first comprehensive study of miRNAs in response to LPS stimulation in M. amblycephala, even in fish. These results deepened our understanding of the role of miRNAs in the intricate host's immune system, and should be useful to develop new control strategies for host immune defense against various bacterial invasions in M. amblycephala.
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Affiliation(s)
- Jiang Yuhong
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410017, China
| | - Tang Leilei
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410017, China
| | - Zhang Fuyun
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410017, China
| | - Jiang Hongyang
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410017, China
| | - Liu Xiaowen
- Xiangya School of Medcine, Central South University, Changsha 410017, China
| | - Yang Liying
- Xiangya School of Medcine, Central South University, Changsha 410017, China
| | - Zhang Lei
- Xiangya School of Medcine, Central South University, Changsha 410017, China
| | - Mao Jingrong
- Xiangya School of Medcine, Central South University, Changsha 410017, China
| | - Yan Jinpeng
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410017, China.
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