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Toro-Ascuy D, Cárdenas M, Vásquez-Martínez Y, Cortez-San Martín M. Rescue of Infectious Salmon Anemia Virus (ISAV) from Cloned cDNA. Methods Mol Biol 2024; 2733:87-99. [PMID: 38064028 DOI: 10.1007/978-1-0716-3533-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
The piscine orthomyxovirus called infectious salmon anemia virus (ISAV) is one of the most important emerging pathogens affecting the salmon industry worldwide. The first reverse genetics system for ISAV, which allows the generation of recombinant ISA virus (rISAV), is an important tool for the characterization and study of this virus. The plasmid-based reverse genetics system for ISAV includes the use of a novel fish promoter, the Atlantic salmon internal transcribed spacer region 1 (ITS-1). The salmon, viral, and mammalian genetic elements included in the pSS-URG vectors allow the expression of the eight viral RNA segments. In addition to four cytomegalovirus (CMV)-based vectors that express the four proteins of the ISAV ribonucleoprotein complex, the eight pSS-URG vectors allowed the generation of infectious rISAV in salmon cells.
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Affiliation(s)
- Daniela Toro-Ascuy
- Laboratory of Virology, Department of Biology, Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | - Matías Cárdenas
- Department of Population Health College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Yesseny Vásquez-Martínez
- Escuela de Medicina, Faculty of Health Sciences, University of Santiago de Chile, Santiago, Chile
| | - Marcelo Cortez-San Martín
- Laboratory of Molecular Virology and Pathogens Control, Faculty of Chemistry and Biology, University of Santiago de Chile, Santiago, Chile.
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2
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Symonová R, Howell WM. Vertebrate Genome Evolution in the Light of Fish Cytogenomics and rDNAomics. Genes (Basel) 2018; 9:genes9020096. [PMID: 29443947 PMCID: PMC5852592 DOI: 10.3390/genes9020096] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/25/2018] [Accepted: 01/29/2018] [Indexed: 12/19/2022] Open
Abstract
To understand the cytogenomic evolution of vertebrates, we must first unravel the complex genomes of fishes, which were the first vertebrates to evolve and were ancestors to all other vertebrates. We must not forget the immense time span during which the fish genomes had to evolve. Fish cytogenomics is endowed with unique features which offer irreplaceable insights into the evolution of the vertebrate genome. Due to the general DNA base compositional homogeneity of fish genomes, fish cytogenomics is largely based on mapping DNA repeats that still represent serious obstacles in genome sequencing and assembling, even in model species. Localization of repeats on chromosomes of hundreds of fish species and populations originating from diversified environments have revealed the biological importance of this genomic fraction. Ribosomal genes (rDNA) belong to the most informative repeats and in fish, they are subject to a more relaxed regulation than in higher vertebrates. This can result in formation of a literal 'rDNAome' consisting of more than 20,000 copies with their high proportion employed in extra-coding functions. Because rDNA has high rates of transcription and recombination, it contributes to genome diversification and can form reproductive barrier. Our overall knowledge of fish cytogenomics grows rapidly by a continuously increasing number of fish genomes sequenced and by use of novel sequencing methods improving genome assembly. The recently revealed exceptional compositional heterogeneity in an ancient fish lineage (gars) sheds new light on the compositional genome evolution in vertebrates generally. We highlight the power of synergy of cytogenetics and genomics in fish cytogenomics, its potential to understand the complexity of genome evolution in vertebrates, which is also linked to clinical applications and the chromosomal backgrounds of speciation. We also summarize the current knowledge on fish cytogenomics and outline its main future avenues.
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Affiliation(s)
- Radka Symonová
- Faculty of Science, Department of Biology, University of Hradec Králové, 500 03 Hradec Králové, Czech Republic.
| | - W Mike Howell
- Department of Biological and Environmental Sciences, Samford University, Birmingham, AL 35229, USA.
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Wang C, Zhang T, Wang Y, Katz LA, Gao F, Song W. Disentangling sources of variation in SSU rDNA sequences from single cell analyses of ciliates: impact of copy number variation and experimental error. Proc Biol Sci 2017; 284:20170425. [PMID: 28747472 PMCID: PMC5543213 DOI: 10.1098/rspb.2017.0425] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/19/2017] [Indexed: 12/25/2022] Open
Abstract
Small subunit ribosomal DNA (SSU rDNA) is widely used for phylogenetic inference, barcoding and other taxonomy-based analyses. Recent studies indicate that SSU rDNA of ciliates may have a high level of sequence variation within a single cell, which impacts the interpretation of rDNA-based surveys. However, sequence variation can come from a variety of sources including experimental errors, especially the mutations generated by DNA polymerase in PCR. In the present study, we explore the impact of four DNA polymerases on sequence variation and find that low-fidelity polymerases exaggerate the estimates of single-cell sequence variation. Therefore, using a polymerase with high fidelity is essential for surveys of sequence variation. Another source of variation results from errors during amplification of SSU rDNA within the polyploidy somatic macronuclei of ciliates. To investigate further the impact of SSU rDNA copy number variation, we use a high-fidelity polymerase to examine the intra-individual SSU rDNA polymorphism in ciliates with varying levels of macronuclear amplification: Halteria grandinella, Blepharisma americanum and Strombidium stylifer We estimate the rDNA copy numbers of these three species by single-cell quantitative PCR. The results indicate that: (i) sequence variation of SSU rDNA within a single cell is authentic in ciliates, but the level of intra-individual SSU rDNA polymorphism varies greatly among species; (ii) rDNA copy numbers vary greatly among species, even those within the same class; (iii) the average rDNA copy number of Halteria grandinella is about 567 893 (s.d. = 165 481), which is the highest record of rDNA copy number in ciliates to date; and (iv) based on our data and the records from previous studies, it is not always true in ciliates that rDNA copy numbers are positively correlated with cell or genome size.
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Affiliation(s)
- Chundi Wang
- Insititute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Tengteng Zhang
- Insititute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Yurui Wang
- Insititute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA
| | - Feng Gao
- Insititute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, People's Republic of China
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, People's Republic of China
| | - Weibo Song
- Insititute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
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Abstract
The piscine Orthomyxovirus called Infectious Salmon Anemia Virus (ISAV) is one of the most important emerging pathogens affecting the salmon industry worldwide. The first reverse genetics system for ISAV, which allows the generation of recombinant ISA virus (rISAV), is an important tool for the characterization and study of this fish virus. The plasmid-based reverse genetics system for ISAV includes the use of a novel fish promoter, the Atlantic salmon internal transcribed spacer region 1 (ITS-1). The salmon, viral and mammalian genetic elements included in pSS-URG vectors allow the expression of the eight viral RNA segments. In addition to four cytomegalovirus (CMV)-based vectors that express the four proteins of the ISAV ribonucleoprotein complex, the eight pSS-URG vectors allowed the generation of infectious rISAV in salmon cells.
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Affiliation(s)
- Daniela Toro-Ascuy
- Laboratory of Molecular Virology, Faculty of Chemistry and Biology, University of Santiago of Chile, Santiago, Chile
| | - Marcelo Cortez-San Martín
- Laboratory of Molecular Virology, Faculty of Chemistry and Biology, University of Santiago of Chile, Santiago, Chile.
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Development of a reverse genetic system for infectious salmon anemia virus: rescue of recombinant fluorescent virus by using salmon internal transcribed spacer region 1 as a novel promoter. Appl Environ Microbiol 2016; 81:1210-24. [PMID: 25480750 DOI: 10.1128/aem.03153-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Infectious salmon anemia (ISA) is a serious disease of marine-farmed Atlantic salmon (Salmo salar) caused by ISA virus (ISAV), belonging to the genus Isavirus, family Orthomyxoviridae. There is an urgent need to understand the virulence factors and pathogenic mechanisms of ISAV and to develop new vaccine approaches. Using a recombinant molecular biology approach, we report the development of a plasmid-based reverse genetic system for ISAV, which includes the use of a novel fish promoter, the Atlantic salmon internal transcribed spacer region 1 (ITS-1). Salmon cells cotransfected with pSS-URG-based vectors expressing the eight viral RNA segments and four cytomegalovirus (CMV)-based vectors that express the four proteins of the ISAV ribonucleoprotein complex allowed the generation of infectious recombinant ISAV (rISAV). We generated three recombinant viruses, wild-type rISAV(901_09) and rISAVr(S6-NotI-HPR) containing a NotI restriction site and rISAV(S6/EGFP-HPR) harboring the open reading frame of enhanced green fluorescent protein (EGFP), both within the highly polymorphic region (HPR) of segment 6. All rescued viruses showed replication activity and cytopathic effect in Atlantic salmon kidney-infected cells. The fluorescent recombinant viruses also showed a characteristic cytopathic effect in salmon cells, and the viruses replicated to a titer of 6.5105 PFU/ml,similar to that of the wild-type virus. This novel reverse genetics system offers a powerful tool to study the molecular biology of ISAV and to develop a new generation of ISAV vaccines to prevent and mitigate ISAV infection, which has had a profound effect on the salmon industry.
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Gornung E. Twenty years of physical mapping of major ribosomal RNA genes across the teleosts: A review of research. Cytogenet Genome Res 2013; 141:90-102. [PMID: 24080951 DOI: 10.1159/000354832] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Molecular cytogenetic data on the number and position of 45S ribosomal RNA genes (rDNA; located in nucleolus organizing regions, NORs) detected by FISH in 330 species of 77 families and 22 orders of bony fishes (Teleostei) and, additionally, 11 species of basal ray-finned fishes are compiled and analyzed. The portion of species with single rDNA sites in the sample amounts to 72%. The percentage of species with multiple NORs decreases with increasing numbers of rDNA loci per genome, i.e. scarcely 3% of species carry 4 or more rDNA-bearing chromosome pairs. 43% of all rDNA sites analyzed occur terminally on the short arms of chromosomes or constitute them. In general, terminal rDNA sites account for 87% of all examined cases. Interspecific variation in the location of single rDNA sites among related taxa, polymorphisms of multiple NORs in some groups of teleosts and analytical outcomes on the subject are reviewed.
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Affiliation(s)
- E Gornung
- 'Charles Darwin' Department of Biology and Biotechnologies, University of Rome 'La Sapienza', Rome, Italy
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7
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Intragenomic variability and pseudogenes of ribosomal DNA in Stone flounder Kareius bicoloratus. Mol Phylogenet Evol 2009; 52:157-66. [DOI: 10.1016/j.ympev.2009.03.031] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2008] [Revised: 03/21/2009] [Accepted: 03/25/2009] [Indexed: 11/13/2022]
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Pisano E, Ghigliotti L. Ribosomal genes in notothenioid fishes: Focus on the chromosomal organisation. Mar Genomics 2009; 2:75-80. [DOI: 10.1016/j.margen.2009.03.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Revised: 03/13/2009] [Accepted: 03/25/2009] [Indexed: 11/25/2022]
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Kitano S, Hasegawa K, Maekawa K. Evidence for interspecific hybridization between native white-spotted charr Salvelinus leucomaenis and non-native brown trout Salmo trutta on Hokkaido Island, Japan. JOURNAL OF FISH BIOLOGY 2009; 74:467-473. [PMID: 20735572 DOI: 10.1111/j.1095-8649.2008.02095.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Hybrids between native white-spotted charr Salvelinus leucomaenis and non-native brown trout Salmo trutta were identified in streams of Hokkaido, Japan, using both appearance and genetic characters. The DNA analyses indicated that the specimens were hybrids between female S. leucomaenis and male S. trutta. Occurrence of such hybrids implies increased mating opportunities between these species in wild streams.
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Affiliation(s)
- S Kitano
- Nagano Environmental Conservation Research Institute, Nagano 381-0075, Japan.
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Bauer N, Horvat T, Birus I, Vicić V, Zoldos V. Nucleotide sequence, structural organization and length heterogeneity of ribosomal DNA intergenic spacer in Quercus petraea (Matt.) Liebl. and Q. robur L. Mol Genet Genomics 2008; 281:207-21. [PMID: 19052776 DOI: 10.1007/s00438-008-0404-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2008] [Accepted: 11/08/2008] [Indexed: 11/29/2022]
Abstract
18S-5.8S-26S rDNA family comprises tandemly arranged, repeating units separated by an intergenic spacer (IGS) that contains transcription initiation/termination signals and usually repeating elements. In this study, we performed for the first time thorough sequence analysis of rDNA IGS region in two dominant European oaks, Quercus petraea and Q. robur, in order to investigate (1) if IGS sequence composition allows discrimination between these two species, and (2) if there is an rDNA length heterogeneity arising from IGS sequence. Two spacer length variants (slvs), 2 and 4 kb in length, were found in the genomes of both species. Inter-comparison of both slvs revealed no species-specificity in sequence or structural organization. Both slvs could be divided into four subregions; (1) the subrepeat region containing three repeated elements, (2) the AT-rich region containing matrix attachment sites and putative origin of replication, (3) the promoter region containing putative transcription initiation site and (4) the 5'ETS region. In the 4-kb slvs all four subregions are extended, and the subrepeat, AT-rich and promoter regions are duplicated. This is unique compared to other known IGS sequences where the variation in number of subrepeats is responsible for slvs creation. We also propose a possible evolutionary scenario to explain the formation of the subrepeat region in oak IGS. Results obtained in this work add to the previous picture of low-genetic differentiation of the two oaks and provide important data for further analyses of the function of IGS in control of rRNA gene expression.
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Affiliation(s)
- Natasa Bauer
- Department of Molecular Biology, University of Zagreb, Horvatovac, Zagreb, Croatia
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Chelomina GN, Rozhkovan KV, Kiselev KV, Ivanov SA, Bulgakov VP. Multiplicity of alleles of nuclear 18S rRNA gene of Amur sturgeons: genes and pseudogenes? DOKL BIOCHEM BIOPHYS 2008; 420:115-8. [PMID: 18680905 DOI: 10.1134/s1607672908030058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- G N Chelomina
- Institute of Biology and Soil Sciences, Far East Division, Russian Academy of Sciences, pr. Stoletiya Vladivostoka 159, Vladivostok, 690022 Russia
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Artamonova VS. Genetic markers in population studies of Atlantic salmon Salmo salar L.: Analysis of DNA sequences. RUSS J GENET+ 2007. [DOI: 10.1134/s1022795407040011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ruggiero MV, Procaccini G. The rDNA ITS region in the lessepsian marine angiosperm Halophila stipulacea (Forssk.) Aschers. (Hydrocharitaceae): intragenomic variability and putative pseudogenic sequences. J Mol Evol 2004; 58:115-21. [PMID: 14743319 DOI: 10.1007/s00239-003-2536-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2003] [Accepted: 08/04/2003] [Indexed: 10/26/2022]
Abstract
Halophila stipulacea is a dioecious marine angiosperm, widely distributed along the western coasts of the Indian Ocean and the Red Sea. This species is thought to be a Lessepsian immigrant that entered the Mediterranean Sea from the Red Sea after the opening of the Suez Canal (1869). Previous studies have revealed both high phenotypic and genetic variability in Halophila stipulacea populations from the western Mediterranean basin. In order to test the hypothesis of a Lessepsian introduction, we compare genetic polymorphism between putative native (Red Sea) and introduced (Mediterranean) populations through rDNA ITS region (ITS1-5.8S-ITS2) sequence analysis. A high degree of intraindividual variability of ITS sequences was found. Most of the intragenomic polymorphism was due to pseudogenic sequences, present in almost all individuals. Features of ITS functional sequences and pseudogenes are described. Possible causes for the lack of homogenization of ITS paralogues within individuals are discussed.
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Affiliation(s)
- Maria Valeria Ruggiero
- Stazione Zoologica A. Dohrn,, Laboratorio di Ecologia del Benthos, 80077 Ischia, Naples, Italy
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Lee Y, Song J. Phylogenetic analysis of the genusdendmnephthya(nephtheidae, alcyonacea) based on internal transcribed spacer sequences of nuclear rDNA. ACTA ACUST UNITED AC 2000. [DOI: 10.1080/12265071.2000.9647563] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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