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Do Ty3/Gypsy Transposable Elements Play Preferential Roles in Sex Chromosome Differentiation? Life (Basel) 2022; 12:life12040522. [PMID: 35455013 PMCID: PMC9025612 DOI: 10.3390/life12040522] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/13/2022] [Accepted: 03/30/2022] [Indexed: 12/16/2022] Open
Abstract
Transposable elements (TEs) comprise a substantial portion of eukaryotic genomes. They have the unique ability to integrate into new locations and serve as the main source of genomic novelties by mediating chromosomal rearrangements and regulating portions of functional genes. Recent studies have revealed that TEs are abundant in sex chromosomes. In this review, we propose evolutionary relationships between specific TEs, such as Ty3/Gypsy, and sex chromosomes in different lineages based on the hypothesis that these elements contributed to sex chromosome differentiation processes. We highlight how TEs can drive the dynamics of sex-determining regions via suppression recombination under a selective force to affect the organization and structural evolution of sex chromosomes. The abundance of TEs in the sex-determining regions originates from TE-poor genomic regions, suggesting a link between TE accumulation and the emergence of the sex-determining regions. TEs are generally considered to be a hallmark of chromosome degeneration. Finally, we outline recent approaches to identify TEs and study their sex-related roles and effects in the differentiation and evolution of sex chromosomes.
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2
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Shiel BP, Hall NE, Cooke IR, Robinson NA, Strugnell JM. Epipodial Tentacle Gene Expression and Predetermined Resilience to Summer Mortality in the Commercially Important Greenlip Abalone, Haliotis laevigata. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2017; 19:191-205. [PMID: 28349286 PMCID: PMC5405107 DOI: 10.1007/s10126-017-9742-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 02/06/2017] [Indexed: 05/05/2023]
Abstract
"Summer mortality" is a phenomenon that occurs during warm water temperature spikes that results in the mass mortality of many ecologically and economically important mollusks such as abalone. This study aimed to determine whether the baseline gene expression of abalone before a laboratory-induced summer mortality event was associated with resilience to summer mortality. Tentacle transcriptomes of 35 greenlip abalone (Haliotis laevigata) were sequenced prior to the animals being exposed to an increase in water temperature-simulating conditions which have previously resulted in summer mortality. Abalone derived from three source locations with different environmental conditions were categorized as susceptible or resistant to summer mortality depending on whether they died or survived after the water temperature was increased. We detected two genes showing significantly higher expression in resilient abalone relative to susceptible abalone prior to the laboratory-induced summer mortality event. One of these genes was annotated through the NCBI non-redundant protein database using BLASTX to an anemone (Exaiptasia pallida) Transposon Ty3-G Gag Pol polyprotein. Distinct gene expression signatures were also found between resilient and susceptible abalone depending on the population origin, which may suggest divergence in local adaptation mechanisms for resilience. Many of these genes have been suggested to be involved in antioxidant and immune-related functions. The identification of these genes and their functional roles have enhanced our understanding of processes that may contribute to summer mortality in abalone. Our study supports the hypothesis that prestress gene expression signatures are indicative of the likelihood of summer mortality.
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Affiliation(s)
- Brett P Shiel
- Department of Ecology, Environment and Evolution, School of Life Sciences, La Trobe University, Kingsbury Drive, Melbourne, VIC, 3086, Australia.
| | - Nathan E Hall
- Department of Ecology, Environment and Evolution, School of Life Sciences, La Trobe University, Kingsbury Drive, Melbourne, VIC, 3086, Australia
- Life Sciences Computation Centre, VLSCI, Parkville, VIC, Australia
- Department of Molecular and Cell Biology, James Cook University, Townsville, Australia
| | - Ira R Cooke
- Life Sciences Computation Centre, VLSCI, Parkville, VIC, Australia
- Department of Molecular and Cell Biology, James Cook University, Townsville, Australia
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Kingsbury Drive, Melbourne, VIC, 3086, Australia
| | - Nicholas A Robinson
- Nofima, P.O. Box 210, 1431, Ås, Norway
- Sustainable Aquaculture Laboratory-Temperate and Tropical (SALTT), School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jan M Strugnell
- Department of Ecology, Environment and Evolution, School of Life Sciences, La Trobe University, Kingsbury Drive, Melbourne, VIC, 3086, Australia
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
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3
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Cho PY, Na BK, Choi KM, Kim JS, Cho SH, Lee WJ, Lim SB, Cha SH, Park YK, Pak JH, Lee HW, Hong SJ, Kim TS. Development of a polymerase chain reaction applicable to rapid and sensitive detection of Clonorchis sinensis eggs in human stool samples. Pathog Glob Health 2014; 107:253-9. [PMID: 23916334 DOI: 10.1179/2047773213y.0000000099] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Microscopic examination of eggs of parasitic helminths in stool samples has been the most widely used classical diagnostic method for infections, but tiny and low numbers of eggs in stool samples often hamper diagnosis of helminthic infections with classical microscopic examination. Moreover, it is also difficult to differentiate parasite eggs by the classical method, if they have similar morphological characteristics. In this study, we developed a rapid and sensitive polymerase chain reaction (PCR)-based molecular diagnostic method for detection of Clonorchis sinensis eggs in stool samples. Nine primers were designed based on the long-terminal repeat (LTR) of C. sinensis retrotransposon1 (CsRn1) gene, and seven PCR primer sets were paired. Polymerase chain reaction with each primer pair produced specific amplicons for C. sinensis, but not for other trematodes including Metagonimus yokogawai and Paragonimus westermani. Particularly, three primer sets were able to detect 10 C. sinensis eggs and were applicable to amplify specific amplicons from DNA samples purified from stool of C. sinensis-infected patients. This PCR method could be useful for diagnosis of C. sinensis infections in human stool samples with a high level of specificity and sensitivity.
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Affiliation(s)
- Pyo Yun Cho
- Department of Parasitology and Inha Research Institute for Medical Sciences, Inha University School of Medicine, Incheon 400-712, Korea
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4
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Abstract
All life must survive their corresponding viruses. Thus antiviral systems are essential in all living organisms. Remnants of virus derived information are also found in all life forms but have historically been considered mostly as junk DNA. However, such virus derived information can strongly affect host susceptibility to viruses. In this review, I evaluate the role viruses have had in the origin and evolution of host antiviral systems. From Archaea through bacteria and from simple to complex eukaryotes I trace the viral components that became essential elements of antiviral immunity. I conclude with a reexamination of the 'Big Bang' theory for the emergence of the adaptive immune system in vertebrates by horizontal transfer and note how viruses could have and did provide crucial and coordinated features.
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5
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Villarreal LP. Viral ancestors of antiviral systems. Viruses 2011; 3:1933-58. [PMID: 22069523 PMCID: PMC3205389 DOI: 10.3390/v3101933] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 10/01/2011] [Accepted: 10/10/2011] [Indexed: 02/06/2023] Open
Abstract
All life must survive their corresponding viruses. Thus antiviral systems are essential in all living organisms. Remnants of virus derived information are also found in all life forms but have historically been considered mostly as junk DNA. However, such virus derived information can strongly affect host susceptibility to viruses. In this review, I evaluate the role viruses have had in the origin and evolution of host antiviral systems. From Archaea through bacteria and from simple to complex eukaryotes I trace the viral components that became essential elements of antiviral immunity. I conclude with a reexamination of the 'Big Bang' theory for the emergence of the adaptive immune system in vertebrates by horizontal transfer and note how viruses could have and did provide crucial and coordinated features.
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Affiliation(s)
- Luis P Villarreal
- Center for Virus Research, University of California, Irvine, CA 92697, USA.
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6
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Shirak A, Grabherr M, Di Palma F, Lindblad-Toh K, Hulata G, Ron M, Kocher TD, Seroussi E. Identification of repetitive elements in the genome of Oreochromis niloticus: tilapia repeat masker. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2010; 12:121-125. [PMID: 19936833 PMCID: PMC3178446 DOI: 10.1007/s10126-009-9236-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Accepted: 10/30/2009] [Indexed: 05/28/2023]
Abstract
The large-scale bacterial artificial chromosome-end sequencing project of Nile tilapia (Oreochromis niloticus) has generated extensive sequence data that allowed the examination of the repeat content in this fish genome and building of a repeat library specific for this species. This library was established based on Tilapiini repeat sequences from GenBank, sequences orthologous to the repeat library of zebrafish in Repbase, and novel repeats detected by genome analysis using MIRA assembler. We estimate that repeats constitute about 14% of the tilapia genome and also give estimates for the occurrence of the different repeats based on the Basic Local Alignment Search Tool searches within the database of known tilapia sequences. The frequent occurrence of novel repeats in the tilapia genome indicates the importance of using the species-specific repeat masker prior to sequence analyses. A web tool based on the RepeatMasker software was designed to assist tilapia genomics.
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Affiliation(s)
- A. Shirak
- Agricultural Research Organization, Institute of Animal Science, Bet-Dagan 50250, Israel
| | - M. Grabherr
- Broad Institute of Harvard and MIT, 320 Charles Street, Cambridge, Massachusetts 02141, USA
| | - F. Di Palma
- Broad Institute of Harvard and MIT, 320 Charles Street, Cambridge, Massachusetts 02141, USA
| | - K. Lindblad-Toh
- Broad Institute of Harvard and MIT, 320 Charles Street, Cambridge, Massachusetts 02141, USA
| | - G. Hulata
- Agricultural Research Organization, Institute of Animal Science, Bet-Dagan 50250, Israel
| | - M. Ron
- Agricultural Research Organization, Institute of Animal Science, Bet-Dagan 50250, Israel
| | - TD. Kocher
- Department of Biology, University of Maryland, College Park, MD, 20742 USA
| | - E. Seroussi
- Agricultural Research Organization, Institute of Animal Science, Bet-Dagan 50250, Israel
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7
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Villarreal LP. The source of self: genetic parasites and the origin of adaptive immunity. Ann N Y Acad Sci 2009; 1178:194-232. [PMID: 19845639 DOI: 10.1111/j.1749-6632.2009.05020.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Stable colonization of the host by viruses (genetic parasites) can alter the systems of host identity and provide immunity against related viruses. To attain the needed stability, some viruses of prokaryotes (P1 phage) use a strategy called an addiction module. The linked protective and destructive gene functions of an addiction module insures both virus persistence but will also destroy cells that interrupt this module and thereby prevent infection by competitors. Previously, I have generalized this concept to also include persistent and lytic states of virus infection, which can be considered as a virus addiction module. Such states often involve defective viruses. In this report, I examine the origin of the adaptive immune system from the perspective of a virus addiction module. The likely role of both endogenous and exogenous retroviruses, DNA viruses, and their defective elements is considered in the origin of all the basal components of adaptive immunity (T-cell receptor, RAG-mediated gene rearrangement, clonal lymphocyte proliferation, antigen surface presentation, apoptosis, and education of immune cells). It is concluded that colonization by viruses and their defectives provides a more coherent explanation for the origin of adaptive immunity.
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Affiliation(s)
- Luis P Villarreal
- Center for Virus Research, Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA.
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8
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Terrat Y, Bonnivard E, Higuet D. GalEa retrotransposons from galatheid squat lobsters (Decapoda, Anomura) define a new clade of Ty1/copia-like elements restricted to aquatic species. Mol Genet Genomics 2007; 279:63-73. [PMID: 17929059 DOI: 10.1007/s00438-007-0295-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2007] [Accepted: 09/19/2007] [Indexed: 11/25/2022]
Abstract
Crustacean species have not been examined in great detail for their transposable elements content. Here we focus on galatheid crabs, which are one of the most diverse and widespread taxonomic groups of Decapoda. Ty1/copia retrotransposons are a diverse and taxonomically dispersed group. Using degenerate primers, we isolated several DNA fragments that show homology with Ty1/copia retroelements reverse transcriptase gene. We named the corresponding elements from which they originated GalEa1 to GalEa3 and analyzed one of them further by isolating various clones containing segments of GalEa1. This is the first LTR retrotransposon described in crustacean genome. Nucleotide sequencing of the clones revealed that GalEa1 has LTRs (124 bp) and that the internal sequence (4,421 bp) includes a single large ORF containing gag and pol regions. Further screening identified highly related elements in six of the nine galatheid species studied. By performing BLAST searches on genome databases, we could also identify GalEa-like elements in some fishes and Urochordata genomes. These elements define a new clade of Ty1/copia retrotransposons that differs from all other Ty1/copia elements and that seems to be restricted to aquatic species.
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Affiliation(s)
- Yves Terrat
- UMR 7138 Systématique Adaptation Evolution, Equipe Génétique et Evolution, Université Pierre and Marie Curie Paris 6, Case 5, Bât A, porte 427, 7 quai St-Bernard, 75252, Paris Cedex 05, France
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9
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Krieger MJB, Ross KG. Molecular evolutionary analyses of mariners and other transposable elements in fire ants (Hymenoptera: Formicidae). INSECT MOLECULAR BIOLOGY 2003; 12:155-165. [PMID: 12653937 DOI: 10.1046/j.1365-2583.2003.00397.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Screens of a library of genomic DNA made during a recent study of the fire ant Solenopsis invicta revealed the presence of three distinct types of transposable elements (TEs). Two of the recovered sequences showed a high similarity to long-terminal repeat (LTR) retrotransposons, while the third showed a high homology to mariner elements. To investigate the distribution and relationships of mariners in related ants, we PCR-amplified these elements from additional Solenopsis species. Phylogenetic analyses showed that they form a single group within the mauritiana subfamily that is part of a larger clade derived from hymenopteran species. We also present partial sequence data for the two LTR-retrotransposons and describe their phylogenetic affinities.
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Affiliation(s)
- M J B Krieger
- Department of Entomology, University of Georgia, Athens GA 30602, USA.
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10
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Bae YA, Moon SY, Kong Y, Cho SY, Rhyu MG. CsRn1, a novel active retrotransposon in a parasitic trematode, Clonorchis sinensis, discloses a new phylogenetic clade of Ty3/gypsy-like LTR retrotransposons. Mol Biol Evol 2001; 18:1474-83. [PMID: 11470838 DOI: 10.1093/oxfordjournals.molbev.a003933] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We screened the genome of a trematode, Clonorchis sinensis, in order to identify novel retrotransposons and thereby provide additional information on retrotransposons for comprehensive phylogenetic study. Considering the vast potential of retrotransposons to generate genetically variable regions among individual genomes, randomly amplified polymorphic DNAs (RAPDs) detected by arbitrarily primed polymerase chain reactions were selected as candidates for retrotransposon-related sequences. From RAPD analysis, we isolated and characterized a novel retrotransposon in C. sinensis as the first member of uncorrupted long-terminal-repeat (LTR) retrotransposons in phylum Platyhelminthes. The retrotransposon, which was named Clonorchis sinensis Retrotransposon 1 (CsRn1), showed a genomewide distribution and had a copy number of more than 100 per haploid genome. CsRn1 encoded an uninterrupted open reading frame (ORF) of 1,304 amino acids, and the deduced ORF exhibited similarities to the pol proteins of Ty3/gypsy-like LTR retrotransposons. The mobile activity of master copies was predicted by sequence analysis and confirmed by the presence of mRNA transcripts. Phylogenetic analysis of Ty3/gypsy-like LTR retrotransposons detected a new clade comprising CsRn1, Kabuki of Bombyx mori, and an uncharacterized element of Drosophila melanogaster. With its high repetitiveness and preserved mobile activity, it is proposed that CsRn1 may play a significant role in the genomic evolution of C. sinensis.
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Affiliation(s)
- Y A Bae
- Department of Microbiology, College of Medicine, Catholic University of Korea, Seoul, Korea
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11
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Butler M, Goodwin T, Poulter R. An unusual vertebrate LTR retrotransposon from the cod Gadus morhua. Mol Biol Evol 2001; 18:443-7. [PMID: 11230547 DOI: 10.1093/oxfordjournals.molbev.a003822] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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12
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Volff JN, Körting C, Altschmied J, Duschl J, Sweeney K, Wichert K, Froschauer A, Schartl M. Jule from the fish Xiphophorus is the first complete vertebrate Ty3/Gypsy retrotransposon from the Mag family. Mol Biol Evol 2001; 18:101-11. [PMID: 11158369 DOI: 10.1093/oxfordjournals.molbev.a003784] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Jule is the second complete long-terminal-repeat (LTR) Ty3/Gypsy retrotransposon identified to date in vertebrates. Jule, first isolated from the poeciliid fish Xiphophorus maculatus, is 4.8 kb in length, is flanked by two 202-bp LTRs, and encodes Gag (structural core protein) and Pol (protease, reverse transcriptase, RNase H, and integrase, in that order) but no envelope. There are three to four copies of Jule per haploid genome in X. maculatus. Two of them are located in a subtelomeric region of the sex chromosomes, where they are associated with the Xmrk receptor tyrosine kinase genes, of which oncogenic versions are responsible for the formation of hereditary melanoma in Xiphophorus. One almost intact copy of Jule was found in the first intron of the X-chromosomal allele of the Xmrk proto-oncogene, and a second, more corrupted copy is present only 56 nt downstream of the polyadenylation signal of the Xmrk oncogene. Jule-related elements were detected by Southern blot hybridization with less than 10 copies per haploid genome in numerous other poeciliids, as well as in more divergent fishes, including the medakafish Oryzias latipes and the tilapia Oreochromis niloticus. Database searches also identified Jule-related sequences in the zebrafish Danio rerio and in both genome project pufferfishes, Fugu rubripes and Tetraodon nigroviridis. Phylogenetic analysis revealed that Jule is the first member of the Mag family of Ty3/Gypsy retrotransposons described to date in vertebrates. This family includes the silkworm Mag and sea urchin SURL retrotransposons, as well as sequences from the nematode Caenorhabditis elegans. Additional related elements were identified in the genomes of the malaria mosquito Anopheles gambiae and the nematode Ascaris lumbricoides. Phylogeny of Mag-related elements suggested that the Mag family of retrotransposons is polyphyletic and is constituted of several ancient lineages that diverged before their host genomes more than 600 MYA.
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Affiliation(s)
- J N Volff
- Physiological Chemistry I, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany.
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13
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Volff JN, Körting C, Schartl M. Multiple lineages of the non-LTR retrotransposon Rex1 with varying success in invading fish genomes. Mol Biol Evol 2000; 17:1673-84. [PMID: 11070055 DOI: 10.1093/oxfordjournals.molbev.a026266] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Rex1, together with the related BABAR: elements, represents a new family of non-long-terminal-repeat (non-LTR) retrotransposons from fish, which might be related to the CR1 clade of LINE elements. Rex1/BABAR: retrotransposons encode a reverse transcriptase and an apurinic/apyrimidinic endonuclease, which is very frequently removed by incomplete reverse transcription. Different Rex1 elements show a conserved terminal 3' untranslated region followed by oligonucleotide tandem repeats of variable size and sequence. Phylogenetic analysis revealed that Rex1 retrotransposons were frequently active during fish evolution. They formed multiple ancient lineages, which underwent several independent and recent bursts of retrotransposition and invaded fish genomes with varying success (from <5 to 500 copies per haploid genome). At least three of these ancient Rex1 lineages were detected within the genome of poeciliids. One lineage is absent from some poeciliids but underwent successive rounds of retrotransposition in others, thereby increasing its copy number from <10 to about 200. At least three ancient Rex1 lineages were also detected in the genome project fish Fugu rubripes. Rex1 distribution within one of its major lineages is discontinuous: Rex1 was found in all Acanthopterygii (common ancestor in the main teleost lineage approximately 90 MYA) and in both European and Japanese eels (divergence from the main teleost lineage about 180 MYA) but not in trout, pike, carp, and zebrafish (divergence 100-120 MYA). This might either result from frequent loss or rapid divergence of Rex1 elements specifically in some fish lineages or represent one of the very rare examples of horizontal transfer of non-LTR retrotransposons. This analysis highlights the dynamics and complexity of retrotransposon evolution and the variability of the impact of retrotransposons on vertebrate genomes.
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Affiliation(s)
- J N Volff
- Physiological Chemistry I, Biocenter, University of Würzburg, Würzburg, Germany.
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14
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Abstract
A systematic search of 1 Mb of genomic sequences from the sea squirt, Ciona intestinalis, revealed the presence of six families of transposable elements. The Cigr-1 retrotransposon contains identical 245-bp long terminal repeats (LTRs) and a 3,630-bp open reading frame (ORF) encoding translation products in the same order as the domains characteristic of gypsy/Ty3-type LTR retrotransposons. The closest homologs of the reverse transcriptase domain were in gypsy elements from Drosophila and the sushi element from the pufferfish. However, the capsid-nucleocapsid region shows the clearest homology to an echinoderm element, Tgr1. Database searches also indicated two classes of non-LTR retrotransposon, named Cili-1 and Cili-2. The Cili-1 sequences show matches to regions of the ORF2 product of mammalian L1 elements. The Cili-2 sequences possess similarity to the RNaseH domain of Lian-Aa1, a mosquito non-LTR retrotransposon. The most abundant element was a short interspersed nucleotide element named Cics-1 with a copy number estimated at 40,000. Cics-1 consists of two conserved domains separated by an A-rich stretch. The 172-bp 5' domain is related to tRNA sequences, whereas the 110-bp 3' domain is unique. Cics-1 is unusual, not just in its modular structure, but also in its lack of a 3' poly(A) tail or direct flanking repeats. A second abundant element, Cimi-1, has an A+T-rich 193-bp consensus sequence and 30-bp terminal inverted repeats (TIRs) and is usually flanked by A+T-rich 2-4-bp putative target site duplications-characteristics of miniature inverted-repeat transposable elements found in plants and insects. A single 2,444-bp foldback element was found, possessing long TIRs containing an A+T-rich internal domain, an array of subrepeats, and a flanking domain at the TIR ends; this is the first example of a chordate foldback element. This study provides the first systematic characterization of the families of transposable elements in a lower chordate.
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Affiliation(s)
- M W Simmen
- Institute of Cell and Molecular Biology, University of Edinburgh, Edinburgh, Scotland.
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15
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Roest Crollius H, Jaillon O, Dasilva C, Ozouf-Costaz C, Fizames C, Fischer C, Bouneau L, Billault A, Quetier F, Saurin W, Bernot A, Weissenbach J. Characterization and repeat analysis of the compact genome of the freshwater pufferfish Tetraodon nigroviridis. Genome Res 2000; 10:939-49. [PMID: 10899143 PMCID: PMC310905 DOI: 10.1101/gr.10.7.939] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Tetraodon nigroviridis is a freshwater pufferfish 20-30 million years distant from Fugu rubripes. The genome of both tetraodontiforms is compact, mostly because intergenic and intronic sequences are reduced in size compared to other vertebrate genomes. The previously uncharacterized Tetraodon genome is described here together with a detailed analysis of its repeat content and organization. We report the sequencing of 46 megabases of bacterial artificial chromosome (BAC) end sequences, which represents a random DNA sample equivalent to 13% of the genome. The sequence and location of rRNA gene clusters, centromeric and subtelocentric satellite sequences have been determined. Minisatellites and microsatellites have been cataloged and notable differences were observed in comparison with microsatellites from Fugu. The genome contains homologies to all known families of transposable elements, including Ty3-gypsy, Ty1-copia, Line retrotransposons, DNA transposons, and retroviruses, although their overall abundance is <1%. This structural analysis is an important prerequisite to sequencing the Tetraodon genome.
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16
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Ivics Z, Izsvák Z, Hackett PB. Genetic applications of transposons and other repetitive elements in zebrafish. Methods Cell Biol 1999; 60:99-131. [PMID: 9891333 DOI: 10.1016/s0091-679x(08)61896-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Z Ivics
- Division of Molecular Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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17
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Ashburner M, Hoy MA, Peloquin JJ. Prospects for the genetic transformation of arthropods. INSECT MOLECULAR BIOLOGY 1998; 7:201-213. [PMID: 9662469 DOI: 10.1046/j.1365-2583.1998.00084.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Affiliation(s)
- M Ashburner
- Department of Genetics, University of Cambridge, UK.
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18
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Abstract
In this study we describe the isolation and characterisation of the first full-length vertebrate retrotransposon. Knowledge of vertebrate gypsy LTR-retrotransposons has been limited to short internal sequences from three fish and a corrupt sequence from a salamander. This paper describes the sequence of a full-length (5.645 kb) retrotransposon from the fugu fish Fugu rubripes. The retrotransposon, termed sushi-ichi (032H04), is a representative of a retrotransposon family (sushi) found as multiple copies within the fish genome. Two long open reading frames (ORFs) are predicted from the sequence. The first has homology to retroviral gag genes. The second includes sequences homologous to protease, reverse transcriptase/RNase H and integrase domains, in that order. Sequence comparisons of the predicted ORFs indicate that this element is related to the gypsy class of LTR-retrotransposons. Specifically, the sushi retrotransposons are most closely related to the retrotransposon group which includes the MAGGY retroelement from the rice blast fungus Magnaporthe grisea and the CfT-1 element from the fungal tomato pathogen Cladosporium fulvum.
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Affiliation(s)
- R Poulter
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, New Zealand.
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Laten HM, Majumdar A, Gaucher EA. SIRE-1, a copia/Ty1-like retroelement from soybean, encodes a retroviral envelope-like protein. Proc Natl Acad Sci U S A 1998; 95:6897-902. [PMID: 9618510 PMCID: PMC22677 DOI: 10.1073/pnas.95.12.6897] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/1997] [Indexed: 02/07/2023] Open
Abstract
The soybean genome hosts a family of several hundred, relatively homogeneous copies of a large, copia/Ty1-like retroelement designated SIRE-1. A copy of this element has been recovered from a Glycine max genomic library. DNA sequence analysis of two SIRE-1 subclones revealed that SIRE-1 contains a long, uninterrupted, ORF between the 3' end of the pol ORF and the 3' long terminal repeat (LTR), a region that harbors the env gene in retroviral genomes. Conceptual translation of this second ORF produces a 70-kDa protein. Computer analyses of the amino acid sequence predicted patterns of transmembrane domains, alpha-helices, and coiled coils strikingly similar to those found in mammalian retroviral envelope proteins. In addition, a 65-residue, proline-rich domain is characterized by a strong amino acid compositional bias virtually identical to that of the 60-amino acid, proline-rich neutralization domain of the feline leukemia virus surface protein. The assignment of SIRE-1 to the copia/Ty1 family was confirmed by comparison of the conceptual translation of its reverse transcriptase-like domain with those of other retroelements. This finding suggests the presence of a proretrovirus in a plant genome and is the strongest evidence to date for the existence of a retrovirus-like genome closely related to copia/Ty1 retrotransposons.
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Affiliation(s)
- H M Laten
- Biology Department, Loyola University Chicago, 6525 North Sheridan Road, Chicago, IL 60626, USA.
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20
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Izsvák Z, Ivics Z, Hackett PB. Repetitive elements and their genetic applications in zebrafish. Biochem Cell Biol 1997. [DOI: 10.1139/o97-045] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Repetitive elements provide important clues about chromosome dynamics, evolutionary forces, and mechanisms for exchange of genetic information between organisms. Repetitive sequences, especially the mobile elements, have many potential applications in genetic research. DNA transposons and retroposons are routinely used for insertional mutagenesis, gene mapping, gene tagging, and gene transfer in several model systems. Once they are developed for the zebrafish, they will greatly facilitate the identification, mapping, and isolation of genes involved in development as well as the investigation of the evolutionary processes that have been shaping eukaryotic genomes. In this review repetitive elements are characterized in terms of their lengths and other physical properties, copy numbers, modes of amplification, and mobilities within a single genome and between genomes. Examples of how they can be used to screen genomes for species and individual strain differences are presented. This review does not cover repetitive gene families that encode well-studied products such as rRNAs, tRNAs, and the like.
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Marracci S, Batistoni R, Pesole G, Citti L, Nardi I. Gypsy/Ty3-like elements in the genome of the terrestrial Salamander hydromantes (Amphibia, Urodela). J Mol Evol 1996; 43:584-93. [PMID: 8995055 DOI: 10.1007/bf02202106] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We have studied a family of long repetitive DNA sequences (Hsr1) interspersed in the large genome of the European plethodontid salamander Hydromantes. The sequence analysis of a 5-kb fragment (Hsr1A) of one member has revealed significant similarities with amino acidic domains of retroviruses and retrotransposons. The similarity of the reverse transcriptase domain and the gene organization identifies Hsr1A as a member of the gypsy/Ty3 class of retrotransposons. We hypothesize that Hsr1 sequences are vestiges of an invasion of the Hydromantes genome that occurred early in the evolutionary history of these European plethodontids. About 10(6) Hsr1 sequences are present in the large Hydromantes genome. This is the highest number of copies so far discovered for retrotransposon-like elements in eukaryote organisms.
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Affiliation(s)
- S Marracci
- Laboratori di Biologia Cellulare e dello Sviluppo, Dipartimento di Fisiologia e Biochimica, Pisa, Italy
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22
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Abstract
Over a third of the human genome consists of interspersed repetitive sequences which are primarily degenerate copies of transposable elements. In the past year, the identities of many of these transposable elements were revealed. The emerging concept is that only three mechanisms of amplification are responsible for the vast majority of interspersed repeats and that with each autonomous element a number of dependent non-autonomous sequences have co-amplified.
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Affiliation(s)
- A F Smit
- Department of Molecular Biotechnology, University of Washington, Seattle 98195, USA.
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23
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Neuveglise C, Sarfati J, Latge JP, Paris S. Afut1, a retrotransposon-like element from Aspergillus fumigatus. Nucleic Acids Res 1996; 24:1428-34. [PMID: 8628674 PMCID: PMC145799 DOI: 10.1093/nar/24.8.1428] [Citation(s) in RCA: 77] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
A repeated DNA sequence used for epidemiological studies of the human opportunistic pathogen Aspergillus fumigatus has been characterized. It is a retroelement of 6914 bp in length, bounded by long terminal repeats of 282 bp, with sequence and features characteristic of retroviruses and retrotransposons. A 5 bp duplication site was found at its borders. This element, designated Afut1, encodes amino acid sequences homologous to the reverse transcriptase, RNase H and endonuclease encoded by the pol genes of retroelements. Comparison of the peptidic sequences with other putative polypeptides of fungal LTR retrotransposons showed that Afut1 is a member of the gypsy group. This is the first report of a transposable element in A.fumigatus. Afut1 is a defective element: the putative coding domains contain multiple stop codons due exclusively to transitions from C:G to T:A.
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Affiliation(s)
- C Neuveglise
- Laboratoire des Aspergillus, Institut Pasteur, Paris, France
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24
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Takasaki N, Park L, Kaeriyama M, Gharrett AJ, Okada N. Characterization of species-specifically amplified SINEs in three salmonid species--chum salmon, pink salmon, and kokanee: the local environment of the genome may be important for the generation of a dominant source gene at a newly retroposed locus. J Mol Evol 1996; 42:103-16. [PMID: 8919862 DOI: 10.1007/bf02198835] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Short interspersed repetitive elements (SINEs), known as the HpaI family, are present in the genomes of all salmonid species (Kido et al., Proc. Natl. Acad. Sci. USA 1991, 88: 2326-2330). Recently, we showed that the retropositional efficiency of the SINE family in the lineage of chum salmon is extraordinarily high in comparison with that in other salmonid lineages. (Takasaki et al., Proc. Natl. Acad. Sci. USA 1994, 91: 10153-10157). To investigate the reason for this high efficiency, we searched for members of the HpaI SINE family that have been amplified species-specifically in pink salmon. Since the efficiency of the species-specific amplification in pink salmon is not high and since other members of the same subfamily of SINEs were also amplified species-specifically in pink salmon, the actual sequence of this subfamily might not be the cause of the high retropositional efficiency of SINEs in chum salmon. Rather, it appears that a highly dominant source gene for the subfamily may have been newly created by retroposition, and some aspect of the local environment around the site of retroposition may have been responsible for the creation of this dominant source gene in chum salmon. Furthermore, a total of 11 sequences of HpaI SINEs that have been amplified species-specifically in three salmon lineages was compiled and characterized. Judging from the distribution of members of the same-sequence subfamily of SINEs in different lineages and from the distribution of the different-sequence subfamilies in the same lineage, we have concluded that multiple dispersed loci are responsible for the amplification of SINEs. We also discuss the additional possibility of horizontal transmission of SINEs between species. The availability of the sets of primers used for the detection of the species-specific amplifications of the SINEs provides a convenient and reliable method for identification of these salmonid species.
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Affiliation(s)
- N Takasaki
- Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
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Tristem M, Kabat P, Herniou E, Karpas A, Hill F. Easel, a gypsy LTR-retrotransposon in the Salmonidae. MOLECULAR & GENERAL GENETICS : MGG 1995; 249:229-36. [PMID: 7500945 DOI: 10.1007/bf00290370] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Despite the close similarities between retroviruses and the gypsy/Ty3 group of LTR-retrotransposons their host ranges are largely distinct: the retroviruses are found only in vertebrates, whereas the gypsy LTR-retrotransposons are almost exclusively restricted to invertebrates, plants and fungi. Here we report the amplification by PCR, and characterisation, of one of the first LTR-retrotransposons to be discovered in vertebrates--in several members of the piscine family Salmonidae. Phylogenetic analysis of this retroelement, termed easel, indicates that it is probably a phylogeneticaly basal member of the gypsy group of LTR-retrotransposons and occurs in some of the same species from which retroviruses have previously been isolated. Thus some members of the Salmonidae are the first organisms known to harbour both retroviral branch elements and the gypsy LTR-retrotransposon branch elements. This creates an overlap in the host ranges of the two retroelement families.
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Affiliation(s)
- M Tristem
- Department of Biology, Imperial College, Ascot, Berkshire, UK
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Britten RJ. Active gypsy/Ty3 retrotransposons or retroviruses in Caenorhabditis elegans. Proc Natl Acad Sci U S A 1995; 92:599-601. [PMID: 7530364 PMCID: PMC42789 DOI: 10.1073/pnas.92.2.599] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A gypsy/Ty3-class retrotransposon (Cer1) is integrated in the DNA of Caenorhabditis elegans chromosome III. It is 8865 nt in length and has 492-nt long terminal repeats that are identical in DNA sequence. There is an exceptionally long (6819 nt) open reading frame uninterrupted by frame-shift mutations in the period since the insertion, which must therefore have been rather recent. Alignment with other gypsy-class elements and with retroviruses indicates that an env gene occupies the 3' 1.2 kb of the open reading frame. A search through GenBank has uncovered two additional gypsy-class elements from C. elegans that are very closely related in DNA sequence to this insert and are transcribed. Since gypsy of Drosophila has been shown to be an infectious element, it is possible that retrovirus-like gypsy elements are active in C. elegans.
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Affiliation(s)
- R J Britten
- Division of Biology, California Institute of Technology, Corona del Mar, 92625
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