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Abstract
Transposable elements (TEs) are genomic parasites that are found in all genomes, some of which display sequence similarity to certain viruses. In insects, TEs are controlled by the Piwi-interacting small interfering RNA (piRNA) pathway in gonads, while the small interfering RNA (siRNA) pathway is dedicated to TE somatic control and defense against viruses. So far, these two small interfering RNA pathways are considered to involve distinct molecular effectors and are described as independent. Using Sindbis virus (SINV) in Drosophila, here we show that viral infections affect TE transcript amounts via modulations of the piRNA and siRNA repertoires, with the clearest effects in somatic tissues. These results suggest that viral acute or chronic infections may impact TE activity and, thus, the tempo of genetic diversification. In addition, these results deserve further evolutionary considerations regarding potential benefits to the host, the virus, or the TEs.
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2
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Jiang X, Tang H, Mohammed Ismail W, Lynch M. A Maximum-Likelihood Approach to Estimating the Insertion Frequencies of Transposable Elements from Population Sequencing Data. Mol Biol Evol 2018; 35:2560-2571. [PMID: 30099533 PMCID: PMC6188571 DOI: 10.1093/molbev/msy152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Transposable elements (TEs) contribute to a large fraction of the expansion of many eukaryotic genomes due to the capability of TEs duplicating themselves through transposition. A first step to understanding the roles of TEs in a eukaryotic genome is to characterize the population-wide variation of TE insertions in the species. Here, we present a maximum-likelihood (ML) method for estimating allele frequencies and detecting selection on TE insertions in a diploid population, based on the genotypes at TE insertion sites detected in multiple individuals sampled from the population using paired-end (PE) sequencing reads. Tests of the method on simulated data show that it can accurately estimate the allele frequencies of TE insertions even when the PE sequencing is conducted at a relatively low coverage (=5X). The method can also detect TE insertions under strong selection, and the detection ability increases with sample size in a population, although a substantial fraction of actual TE insertions under selection may be undetected. Application of the ML method to genomic sequencing data collected from a natural Daphnia pulex population shows that, on the one hand, most (>90%) TE insertions present in the reference D. pulex genome are either fixed or nearly fixed (with allele frequencies >0.95); on the other hand, among the nonreference TE insertions (i.e., those detected in some individuals in the population but absent from the reference genome), the majority (>70%) are still at low frequencies (<0.1). Finally, we detected a substantial fraction (∼9%) of nonreference TE insertions under selection.
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Affiliation(s)
- Xiaoqian Jiang
- Department of Biology, Indiana University, Bloomington, IN
| | - Haixu Tang
- School of Informatics and Computing, Indiana University, Bloomington, IN
| | | | - Michael Lynch
- Center for Mechanisms of Evolution, Arizona State University, Temple, AZ
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Barrón MG, Fiston-Lavier AS, Petrov DA, González J. Population genomics of transposable elements in Drosophila. Annu Rev Genet 2014; 48:561-81. [PMID: 25292358 DOI: 10.1146/annurev-genet-120213-092359] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Studies of the population dynamics of transposable elements (TEs) in Drosophila melanogaster indicate that consistent forces are affecting TEs independently of their modes of transposition and regulation. New sequencing technologies enable biologists to sample genomes at an unprecedented scale in order to quantify genome-wide polymorphism for annotated and novel TE insertions. In this review, we first present new insights gleaned from high-throughput data for population genomics studies of D. melanogaster. We then consider the latest population genomics models for TE evolution and present examples of functional evidence revealed by genome-wide studies of TE population dynamics in D. melanogaster. Although most of the TE insertions are deleterious or neutral, some TE insertions increase the fitness of the individual that carries them and play a role in genome adaptation.
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Affiliation(s)
- Maite G Barrón
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain 08003; ,
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Vergilino R, Elliott TA, Desjardins-Proulx P, Crease TJ, Dufresne F. Evolution of a transposon in Daphnia hybrid genomes. Mob DNA 2013; 4:7. [PMID: 23384095 PMCID: PMC3575242 DOI: 10.1186/1759-8753-4-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 11/06/2012] [Indexed: 11/17/2022] Open
Abstract
Background Transposable elements play a major role in genome evolution. Their capacity to move and/or multiply in the genome of their host may have profound impacts on phenotypes, and may have dramatic consequences on genome structure. Hybrid and polyploid clones have arisen multiple times in the Daphnia pulex complex and are thought to reproduce by obligate parthenogenesis. Our study examines the evolution of a DNA transposable element named Pokey in the D. pulex complex. Results Portions of Pokey elements inserted in the 28S rRNA genes from various Daphnia hybrids (diploids and polyploids) were sequenced and compared to sequences from a previous study to understand the evolutionary history of the elements. Pokey sequences show a complex phylogenetic pattern. We found evidence of recombination events in numerous Pokey alleles from diploid and polyploid hybrids and also from non-hybrid diploids. The recombination rate in Pokey elements is comparable to recombination rates previously estimated for 28S rRNA genes in the congener, Daphnia obtusa. Some recombinant Pokey alleles were encountered in Daphnia isolates from multiple locations and habitats. Conclusions Phylogenetic and recombination analyses showed that recombination is a major force that shapes Pokey evolution. Based on Pokey phylogenies, reticulation has played and still plays an important role in shaping the diversity of the D. pulex complex. Horizontal transfer of Pokey seems to be rare and hybrids often possess Pokey elements derived from recombination among alleles encountered in the putative parental species. The insertion of Pokey in hotspots of recombination may have important impacts on the diversity and fitness of this transposable element.
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Affiliation(s)
- Roland Vergilino
- Department of Integrative Biology, University of Guelph, Science complex, N1G 2 W1, Guelph, ON, Canada.
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Kofler R, Betancourt AJ, Schlötterer C. Sequencing of pooled DNA samples (Pool-Seq) uncovers complex dynamics of transposable element insertions in Drosophila melanogaster. PLoS Genet 2012; 8:e1002487. [PMID: 22291611 PMCID: PMC3266889 DOI: 10.1371/journal.pgen.1002487] [Citation(s) in RCA: 187] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 12/01/2011] [Indexed: 12/16/2022] Open
Abstract
Transposable elements (TEs) are mobile genetic elements that parasitize genomes by semi-autonomously increasing their own copy number within the host genome. While TEs are important for genome evolution, appropriate methods for performing unbiased genome-wide surveys of TE variation in natural populations have been lacking. Here, we describe a novel and cost-effective approach for estimating population frequencies of TE insertions using paired-end Illumina reads from a pooled population sample. Importantly, the method treats insertions present in and absent from the reference genome identically, allowing unbiased TE population frequency estimates. We apply this method to data from a natural Drosophila melanogaster population from Portugal. Consistent with previous reports, we show that low recombining genomic regions harbor more TE insertions and maintain insertions at higher frequencies than do high recombining regions. We conservatively estimate that there are almost twice as many “novel” TE insertion sites as sites known from the reference sequence in our population sample (6,824 novel versus 3,639 reference sites, with on average a 31-fold coverage per insertion site). Different families of transposable elements show large differences in their insertion densities and population frequencies. Our analyses suggest that the history of TE activity significantly contributes to this pattern, with recently active families segregating at lower frequencies than those active in the more distant past. Finally, using our high-resolution TE abundance measurements, we identified 13 candidate positively selected TE insertions based on their high population frequencies and on low Tajima's D values in their neighborhoods. Transposable elements (TE's) are parasitic genetic elements that spread by replicating themselves within a host genome. Most organisms are burdened with transposable elements; in fact, up to 80% of some genomes can consist of TE–derived DNA. Here, we use new sequencing technology to examine variation in genomic TE composition within a population at a finer scale and in a more unbiased fashion than has been possible before. We study a Portuguese population of D. melanogaster and find a large number of TE insertions, most of which occur in few individuals. Our analysis confirms that TE insertions are subject to purifying selection that counteracts their spread, and it suggests that the genome records waves of past TE invasions, with recently active elements occurring at low population frequency. We also find indications that TE insertions may sometimes have beneficial effects.
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Affiliation(s)
- Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria
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6
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Vasil’eva LA, Antonenko OV, Zakharov IK. Role of transposable elements in the genome of Drosophila melanogaster. ACTA ACUST UNITED AC 2011. [DOI: 10.1134/s2079059711060128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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STRUCHINER CLAUDIOJ, KIDWELL MARGARETG, RIBEIRO JOSÉMC. POPULATION DYNAMICS OF TRANSPOSABLE ELEMENTS: COPY NUMBER REGULATION AND SPECIES INVASION REQUIREMENTS. J BIOL SYST 2011. [DOI: 10.1142/s021833900500163x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A deterministic population dynamics model of the spread of transposable elements (TE) in sexually reproducing populations is presented. The population is modeled by a three-parameter equation describing host reproductive capacity, population size and the strength of the density dependence, while TE dynamics were modeled based also on three parameters, the maximum ability of the element to copy itself in the absence of regulation (T0), the regulatory effect of copy number decreasing transposition (C0.5), and the deleterious effect of each new transposition on host fitness (d). The mechanism of transposition control is therefore a function of the number of new TE copies. Our results indicate that non-regulated elements cannot fix in host populations, and that prediction of stable copy number following successful invasion is mainly a function of the combination of T0and C0.5values. Fitness reduction does not affect the final copy number after successful invasion of the element. Fitness reduction, however, will affect the surface of the {T0× C0.5} parameter space leading to successful invasion of the TE. Invasion of host populations by eight or more individuals containing elements with appropriate parameters will lead to successful element fixation at any size of the host population. Host population extinction due to the invasion of TE's is observed in a small area of the {T0× C0.5} parameter space. These results are qualitatively preserved under alternative choices for the shape of the functions defining regulation of transposition and distinct sets of parameters determining host population dynamics.
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Affiliation(s)
- CLAUDIO J. STRUCHINER
- ENSP/FIOCRUZ and IMS/UERJ, Av. Brasil 4365, Rio de Janeiro-RJ, Brazil 21040 360, Brazil
| | - MARGARET G. KIDWELL
- Department of Ecology and Evolutionary Biology, The University of Arizona, Bio-Sciences West Building Room 310, Tucson, AZ 85721, USA
| | - JOSÉ M. C. RIBEIRO
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, 12735 Twinbrook Parkway, Room 2E-32, Twinbrook III Building NIAID, NIH, MSC 8132, Bethesda, MD 20892-8132, USA
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Lu J, Clark AG. Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila. Genome Res 2009; 20:212-27. [PMID: 19948818 DOI: 10.1101/gr.095406.109] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Transposable elements (TEs) are mobile DNA sequences that make up a large fraction of eukaryotic genomes. Recently it was discovered that PIWI-interacting RNAs (piRNAs), a class of small RNA molecules that are mainly generated from transposable elements, are crucial repressors of active TEs in the germline of fruit flies. By quantifying expression levels of 32 TE families in piRNA pathway mutants relative to wild-type fruit flies, we provide evidence that piRNAs can severely silence the activities of retrotransposons. We incorporate piRNAs into a population genetic framework for retrotransposons and perform forward simulations to model the population dynamics of piRNA loci and their targets. Using parameters optimized for Drosophila melanogaster, our simulation results indicate that (1) piRNAs can significantly reduce the fitness cost of retrotransposons; (2) retrotransposons that generate piRNAs (piRTs) are selectively more advantageous, and such retrotransposon insertions more easily attain high frequency or fixation; (3) retrotransposons that are repressed by piRNAs (targetRTs), however, also have an elevated probability of reaching high frequency or fixation in the population because their deleterious effects are attenuated. By surveying the polymorphisms of piRT and targetRT insertions across nine strains of D. melanogaster, we verified these theoretical predictions with population genomic data. Our theoretical and empirical analysis suggests that piRNAs can significantly increase the fitness of individuals that bear them; however, piRNAs may provide a shelter or Trojan horse for retrotransposons, allowing them to increase in frequency in a population by shielding the host from the deleterious consequences of retrotransposition.
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Affiliation(s)
- Jian Lu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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9
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Venner S, Feschotte C, Biémont C. Dynamics of transposable elements: towards a community ecology of the genome. Trends Genet 2009; 25:317-23. [PMID: 19540613 PMCID: PMC2945704 DOI: 10.1016/j.tig.2009.05.003] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Revised: 05/27/2009] [Accepted: 05/28/2009] [Indexed: 12/13/2022]
Abstract
Like ecological communities, which vary in species composition, eukaryote genomes differ in the amount and diversity of transposable elements (TEs) that they harbor. Given that TEs have a considerable impact on the biology of their host species, we need to better understand whether their dynamics reflects some form of organization or is primarily driven by stochastic processes. Here, we borrow ecological concepts on species diversity to explore how interactions between TEs can contribute to structure TE communities within their genomic ecosystem. Whereas the niche theory predicts a stable diversity of TEs because of their divergent characteristics, the neutral theory of biodiversity predicts the assembly of TE communities from stochastic processes acting at the level of the individual TE. Contrary to ecological communities, however, TE communities are shaped by selection at the level of their ecosystem (i.e. the host individual). Developing ecological models specific to the genome will thus be a prerequisite for modeling the dynamics of TEs.
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Venner S, Feschotte C, Biémont C. Dynamics of transposable elements: towards a community ecology of the genome. Trends Genet 2009. [PMID: 19540613 DOI: 10.1016/j.tig.2009.05.003.epub] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Like ecological communities, which vary in species composition, eukaryote genomes differ in the amount and diversity of transposable elements (TEs) that they harbor. Given that TEs have a considerable impact on the biology of their host species, we need to better understand whether their dynamics reflects some form of organization or is primarily driven by stochastic processes. Here, we borrow ecological concepts on species diversity to explore how interactions between TEs can contribute to structure TE communities within their genomic ecosystem. Whereas the niche theory predicts a stable diversity of TEs because of their divergent characteristics, the neutral theory of biodiversity predicts the assembly of TE communities from stochastic processes acting at the level of the individual TE. Contrary to ecological communities, however, TE communities are shaped by selection at the level of their ecosystem (i.e. the host individual). Developing ecological models specific to the genome will thus be a prerequisite for modeling the dynamics of TEs.
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11
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García Guerreiro MP, Chávez-Sandoval BE, Balanyà J, Serra L, Fontdevila A. Distribution of the transposable elements bilbo and gypsy in original and colonizing populations of Drosophila subobscura. BMC Evol Biol 2008; 8:234. [PMID: 18702820 PMCID: PMC2533020 DOI: 10.1186/1471-2148-8-234] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2008] [Accepted: 08/14/2008] [Indexed: 01/23/2023] Open
Abstract
Background Transposable elements (TEs) constitute a substantial amount of all eukaryotic genomes. They induce an important proportion of deleterious mutations by insertion into genes or gene regulatory regions. However, their mutational capabilities are not always adverse but can contribute to the genetic diversity and evolution of organisms. Knowledge of their distribution and activity in the genomes of populations under different environmental and demographic regimes, is important to understand their role in species evolution. In this work we study the chromosomal distribution of two TEs, gypsy and bilbo, in original and colonizing populations of Drosophila subobscura to reveal the putative effect of colonization on their insertion profile. Results Chromosomal frequency distribution of two TEs in one original and three colonizing populations of D. subobscura, is different. Whereas the original population shows a low insertion frequency in most TE sites, colonizing populations have a mixture of high (frequency ≥ 10%) and low insertion sites for both TEs. Most highly occupied sites are coincident among colonizing populations and some of them are correlated to chromosomal arrangements. Comparisons of TE copy number between the X chromosome and autosomes show that gypsy occupancy seems to be controlled by negative selection, but bilbo one does not. Conclusion These results are in accordance that TEs in Drosophila subobscura colonizing populations are submitted to a founder effect followed by genetic drift as a consequence of colonization. This would explain the high insertion frequencies of bilbo and gypsy in coincident sites of colonizing populations. High occupancy sites would represent insertion events prior to colonization. Sites of low frequency would be insertions that occurred after colonization and/or copies from the original population whose frequency is decreasing in colonizing populations. This work is a pioneer attempt to explain the chromosomal distribution of TEs in a colonizing species with high inversion polymorphism to reveal the putative effect of arrangements in TE insertion profiles. In general no associations between arrangements and TE have been found, except in a few cases where the association is very strong. Alternatively, founder drift effects, seem to play a leading role in TE genome distribution in colonizing populations.
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Affiliation(s)
- María Pilar García Guerreiro
- Grup de Biología Evolutiva, Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain.
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12
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García Guerreiro MP, Fontdevila A. The evolutionary history of Drosophila buzzatii. XXXVI. Molecular structural analysis of Osvaldo retrotransposon insertions in colonizing populations unveils drift effects in founder events. Genetics 2006; 175:301-10. [PMID: 17151248 PMCID: PMC1775019 DOI: 10.1534/genetics.106.064378] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Previous work on transposable element distribution in colonizing populations of Drosophila buzzatii revealed a high frequency of occupancy in several chromosomal sites. Two explanatory hypotheses were advanced: the founder hypothesis, by which founder genetic drift was responsible, and the unstable hypothesis that assigns this unusual distribution to bursts of transposition toward some chromosomal sites. Here, we study the molecular structure of three euchromatic Osvaldo clones isolated from sites occupied at high (A4 and B9) and low frequency (B4) in colonizing populations, to test these hypotheses. Large insertions, duplications, and indels in the Osvaldo coding region and LTR were detected in the A4 clone and a truncated Osvaldo with many substitutions was found in the B9 clone. These altered sequences indicate that the two copies of this retroelement are precolonization insertions. Interestingly, the LTR of the A4 clone and the reverse transcriptase region of B9 show identical sequences in all colonizing populations indicating, most probably, that they are identical by descent. Moreover, Osvaldo is inserted at the same nucleotide site in all colonizing populations. On the other hand an almost identical LTR sequence, except by 1 base deletion, was found in the B4 clone compared to the canonical active Osvaldo element. These results suggest that Osvaldo copies in highly occupied sites are, most probably, identical by descent and strongly favor the founder hypothesis. On the other hand, low-insertion-frequency sites could represent recent transposition events. This work emphasizes the importance of molecular population studies to disentangle the effects of genetic drift and transposition in colonization.
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Affiliation(s)
- María Pilar García Guerreiro
- Grup de Biología Evolutiva, Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
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13
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Abstract
The genomes of virtually all sexually reproducing species contain transposable elements. Although active elements generally transpose more rapidly than they are inactivated by mutation or excision, their number can be kept in check by purifying selection if its effectiveness becomes disproportionately greater as their copy number increases. In sexually reproducing species, such synergistic selection can result from ectopic crossing-over or from homologous recombination under negative epistasis. In addition, there may be controls on transposon activity that are associated with meiosis. Because a sexual lineage that abandons sex must lack such mechanisms, it may be driven to extinction by the unchecked proliferation of deleterious transposons inherited from its sexual progenitor. An important component of the evolutionary advantage of sex over asex may therefore lie in the ability of sex, despite facilitating the spread of deleterious elements within interbreeding populations, also to restrain their intragenomic proliferation.
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Affiliation(s)
- Irina Arkhipova
- Department of Molecular and Cellular Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA.
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Yannopoulos G, Zabalou S, Alahiotis SN. Distribution of P and hobo mobile elements in environmentally manipulated long-term Drosophila melanogaster cage populations. Hereditas 2004; 121:87-102. [PMID: 7995732 DOI: 10.1111/j.1601-5223.1994.t01-1-00087.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The copy number and the chromosome positions of the P and hobo insertions were determined by means of in situ hybridization to polytene chromosomes, in five long-term Drosophila melanogaster cage populations kept for 18 years under different culture conditions (temperature and relative humidity). The analysis revealed that the copy number of both P and hobo elements were similar between the populations kept under the same culture conditions and significantly different among the populations maintained under different culture conditions. A tendency for similar distribution of these elements along the major chromosome arms was also observed in the populations of the same environmental manipulation. The distribution of the insertions along the chromosomes was not random for both the P and hobo elements; sites with high insertion frequencies were found (hot spots of occupation). Some of them were common in all cage populations while others were characteristic of the populations kept under the same conditions. Finally, fixed sites of occupation were also observed in all populations and refer mostly to hobo distribution. The data are discussed on the basis of the possible involvement of the P and hobo elements, in some way, to the adaptation process and speciation.
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15
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Zabalou S, Alahiotis SN, Yannopoulos G. A three-season comparative analysis of the chromosomal distribution of P and hobo mobile elements in a natural population of Drosophila melanogaster. Hereditas 2004; 120:127-40. [PMID: 8083059 DOI: 10.1111/j.1601-5223.1994.00127.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
An analysis on the chromosomal distribution of P and hobo elements in a Greek natural population extending over three seasons showed that the P elements were more abundant in the population than hobos. The copy number distribution per chromosome arm was in general random. The X chromosome had more P copies and the 3R arm more hobos in all three collections. Significant seasonal differences were not observed for these two elements in relation to the total number of insertions per haploid genome. There were, however, certain seasonal differences. They involved the copy number variability, the intra-arm distribution, the distribution along the chromosomes, and the spread and occupancy frequencies. There were no significant differences between the copy numbers of the two elements carried by the standard and the corresponding inverted regions for a number of inversions found in the population. Finally, three out of the five cosmopolitan inversions were found to have hobo insertions at or very near the one of the two breakpoints. Three out of the total had P insertions at or very near the one of the two breakpoints in some squashes and two of the three endemic inversions had a hobo insertion at or very near the one breakpoint, while the third had a P insertion.
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Affiliation(s)
- S Zabalou
- Department of Biology, University of Patras, Greece
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16
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Rizzon C, Martin E, Marais G, Duret L, Ségalat L, Biémont C. Patterns of Selection Against Transposons Inferred From the Distribution of Tc1, Tc3 and Tc5 Insertions in the mut-7 Line of the Nematode Caenorhabditis elegans. Genetics 2003; 165:1127-35. [PMID: 14668370 PMCID: PMC1462815 DOI: 10.1093/genetics/165.3.1127] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
To identify the factors (selective or mutational) that affect the distribution of transposable elements (TEs) within a genome, it is necessary to compare the pattern of newly arising element insertions to the pattern of element insertions that have been fixed in a population. To do this, we analyzed the distribution of recent mutant insertions of the Tc1, Tc3, and Tc5 elements in a mut-7 background of the nematode Caenorhabditis elegans and compared it to the distribution of element insertions (presumably fixed) within the sequenced genome. Tc1 elements preferentially insert in regions with high recombination rates, whereas Tc3 and Tc5 do not. Although Tc1 and Tc3 both insert in TA dinucleotides, there is no clear relationship between the frequency of insertions and the TA dinucleotide density. There is a strong selection against TE insertions within coding regions: the probability that a TE will be fixed is at least 31 times lower in coding regions than in noncoding regions. Contrary to the prediction of theoretical models, we found that the selective pressure against TE insertions does not increase with the recombination rate. These findings indicate that the distribution of these three transposon families in the genome of C. elegans is determined essentially by just two factors: the pattern of insertions, which is a characteristic of each family, and the selection against insertions within coding regions.
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Affiliation(s)
- Carène Rizzon
- Biométrie, Biologie Evolutive, UMR 5558, Université Lyon 1, 69622 Villeurbanne, France
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Borie N, Maisonhaute C, Sarrazin S, Loevenbruck C, Biémont C. Tissue-specificity of 412 retrotransposon expression in Drosophila simulans and D. melanogaster. Heredity (Edinb) 2002; 89:247-52. [PMID: 12242639 DOI: 10.1038/sj.hdy.6800135] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2002] [Accepted: 06/20/2002] [Indexed: 11/09/2022] Open
Abstract
We analyse the expression of the retrotransposon 412 in the soma, testes, and ovaries in populations of Drosophila simulans and D. melanogaster, using RT-PCR and in situ hybridization. We find that expression of 412 is highly variable in the soma, confirming previous findings based on Northern blots. No 412RNA is detected in the ovaries by either in situ hybridization or RT-PCR, in any population of either species. Transcripts are, however, detected in the male germline, which show a very characteristic spatial pattern of 412 expression in primary spermatocytes. There is no relationship between expression of the 412 element in the soma and in the testes in the populations. These findings show that the expression of 412 is independently regulated in the soma and the testes, and this raises the question of the real influence of the somatic transcripts on the organism and on the transposition rate.
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Affiliation(s)
- N Borie
- UMR CNRS 5558 Biométrie et Biologie Evolutive, Université Lyon1 69622 Villeurbanne, France
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18
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Rizzon C, Marais G, Gouy M, Biémont C. Recombination rate and the distribution of transposable elements in the Drosophila melanogaster genome. Genome Res 2002; 12:400-7. [PMID: 11875027 PMCID: PMC155295 DOI: 10.1101/gr.210802] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We analyzed the distribution of 54 families of transposable elements (TEs; transposons, LTR retrotransposons, and non-LTR retrotransposons) in the chromosomes of Drosophila melanogaster, using data from the sequenced genome. The density of LTR and non-LTR retrotransposons (RNA-based elements) was high in regions with low recombination rates, but there was no clear tendency to parallel the recombination rate. However, the density of transposons (DNA-based elements) was significantly negatively correlated with recombination rate. The accumulation of TEs in regions of reduced recombination rate is compatible with selection acting against TEs, as selection is expected to be weaker in regions with lower recombination. The differences in the relationship between recombination rate and TE density that exist between chromosome arms suggest that TE distribution depends on specific characteristics of the chromosomes (chromatin structure, distribution of other sequences), the TEs themselves (transposition mechanism), and the species (reproductive system, effective population size, etc.), that have differing influences on the effect of natural selection acting against the TE insertions.
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Affiliation(s)
- Carène Rizzon
- Laboratoire de Biométrie et Biologie Evolutive, Unité Mixte de Recherche Centre National de la Recherche Scientifique 5558, Université Lyon 1, Cedex, France
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Duret L, Marais G, Biémont C. Transposons but not retrotransposons are located preferentially in regions of high recombination rate in Caenorhabditis elegans. Genetics 2000; 156:1661-9. [PMID: 11102365 PMCID: PMC1461346 DOI: 10.1093/genetics/156.4.1661] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We analyzed the distribution of transposable elements (TEs: transposons, LTR retrotransposons, and non-LTR retrotransposons) in the chromosomes of the nematode Caenorhabditis elegans. The density of transposons (DNA-based elements) along the chromosomes was found to be positively correlated with recombination rate, but this relationship was not observed for LTR or non-LTR retrotransposons (RNA-based elements). Gene (coding region) density is higher in regions of low recombination rate. However, the lower TE density in these regions is not due to the counterselection of TE insertions within exons since the same positive correlation between TE density and recombination rate was found in noncoding regions (both in introns and intergenic DNA). These data are not compatible with a global model of selection acting against TE insertions, for which an accumulation of elements in regions of reduced recombination is expected. We also found no evidence for a stronger selection against TE insertions on the X chromosome compared to the autosomes. The difference in distribution of the DNA and RNA-based elements along the chromosomes in relation to recombination rate can be explained by differences in the transposition processes.
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Affiliation(s)
- L Duret
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, 69622 Villeurbanne Cedex, France.
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Cizeron G, Biémont C. Polymorphism in structure of the retrotransposable element 412 in Drosophila simulans and D. melanogaster populations. Gene 1999; 232:183-90. [PMID: 10352229 DOI: 10.1016/s0378-1119(99)00126-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The structure of the 412 retrotransposable element was investigated in various natural populations of D. melanogaster and D. simulans by a restriction enzyme analysis. We show that although the canonical structure of the 412 element was the same in both species, a high structural polymorphism existed with various rearranged elements. A 412 family was thus composed of heterogeneous copies of different sizes, with a large proportion of full-size copies. D. simulans had more rearranged copies than D. melanogaster, with some specific copies, such as a 5.6-kb BsrBI fragment, present in all populations of D. simulans. Full-size and rearranged copies were detected in both the euchromatin and the heterochromatin, with many rearranged copies in D. simulans, suggesting a recent mobilization of the 412 element in this species.
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Affiliation(s)
- G Cizeron
- Laboratoire de Biométrie, Génétique, Biologie des populations, UMR C.N.R.S. 5558, Université Lyon 1, 69622, Villeurbanne, France
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Hoogland C, Vieira C, Biémont C. Chromosomal distribution of the 412 retrotransposon in natural populations of Drosophila simulans. Heredity (Edinb) 1997; 79 ( Pt 2):128-34. [PMID: 9279009 DOI: 10.1038/hdy.1997.135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The insertion site localization of the 412 retrotransposable element was analysed by in situ hybridization to the polytene chromosomes of 57 individual genomes from 25 natural populations of Drosophila simulans. The 412 insertion sites along the chromosomes show a tendency to aggregate in the distal and proximal ends of the 2R arm, and in several local regions along the 3R arm. The distribution of the 412 insertion sites, weighted by DNA content, along the chromosome arms reveals an overall tendency for the site number to increase from the middle of the arm to the base and tip, with a decrease at the tips, especially pronounced for the X chromosome. Such a distribution differs slightly from that of D. melanogaster, which globally shows an increase of the 412 site number from base to tip of the chromosome arms, indicating differing behaviour of the 412 element in the two species. These results are discussed in connection with the recombination rate along the chromosome arms.
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Affiliation(s)
- C Hoogland
- Laboratoire de Biométrie, Génétique, Biologie des populations, UMR C.N.R.S. 5558, Université Lyon 1, Villeurbanne, France
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22
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Maintenance of transposable element copy number in natural populations of Drosophila melanogaster and D. simulans. ACTA ACUST UNITED AC 1997. [DOI: 10.1007/978-94-011-4898-6_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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23
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Charlesworth B. Background selection and patterns of genetic diversity in Drosophila melanogaster. Genet Res (Camb) 1996; 68:131-49. [PMID: 8940902 DOI: 10.1017/s0016672300034029] [Citation(s) in RCA: 211] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Theoretical models of the effects of selection against deleterious mutations on variation at linked neutral sites (background selection) are used to predict the relations between chromosomal location and genetic variability at the DNA level, in Drosophila melanogaster. The sensitivity of the predictions to variation in the mutation, selection and recombination parameters on which they are based is examined. It is shown that many features of the observed relations between chromosomal location and level of genetic diversity in D. melanogaster can be explained by background selection, especially if the weak selective forces acting on transposable elements are taken into account. In particular, the gradient in diversity in the distal portion of the X chromosome, and the lack of diversity on chromosome 4 and at the bases of the major chromosomes, can be fully accounted for. There are, however, discrepancies between predicted and observed values for some loci in D. melanogaster, which may reflect the effects of forces other than background selection.
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Mukabayire O, Besansky NJ. Distribution of T1, Q, Pegasus and mariner transposable elements on the polytene chromosomes of PEST, a standard strain of Anopheles gambiae. Chromosoma 1996; 104:585-95. [PMID: 8662251 DOI: 10.1007/bf00352298] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The chromosomal locations of four families of transposable elements, T1, Q, Pegasus and mariner, have been determined by in situ hybridization to polytene chromosomes of ovarian nurse cells of the mosquito Anopheles gambiae. As part of this effort, we have developed a vigorous pink-eyed laboratory strain of A. gambiae (PEST), rendered homozygous standard for chromosomal inversions on all autosomes. Ten different individuals of this strain were studied with each transposable element probe. The average number of hybridization sites per genome was 83.9 for T1, 63.4 for Q, 31.5 for Pegasus and 64.7 for mariner, excluding pericentric and centromeric regions. However, some degree of polymorphism was observed within each family such that, considering all ten individuals, 94 different sites were detected for T1, 82 sites for Q, 45 sites for Pegasus and 71 sites for mariner. The mean occupancy per site varied from 0.70 (Pegasus) to 0.91 (mariner), which, while significantly higher than that seen for transposable elements in natural populations of Drosophila melanogaster, is comparable to that seen in established laboratory stocks. In addition, these element families were not randomly distributed. All but Pegasus were concentrated in centromeric heterochromatin and centromere-proximal euchromatin, most showed a deficit of hybridization sites in the distal section of chromosomes, and a significant proportion of sites were coincident between families. These results provide the first detailed examination of the cytogenetic location of transposable elements in a nondrosophilid insect, and, through comparison with the behavior of transposable elements in Drosophila, may provide insight into the interaction between elements and host. The mapped elements are also expected to serve as landmarks useful in integrating the developing physical map of the PEST strain with the chromosomal banding pattern.
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Affiliation(s)
- O Mukabayire
- Division of Parasitic Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
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25
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Wilanowski TM, Gibson JB, Symonds JE. Retrotransposon insertion induces an isozyme of sn-glycerol-3-phosphate dehydrogenase in Drosophila melanogaster. Proc Natl Acad Sci U S A 1995; 92:12065-9. [PMID: 8618845 PMCID: PMC40297 DOI: 10.1073/pnas.92.26.12065] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The insertion of the blood retrotransposon into the untranslated region of exon 7 of the sn-glycerol-3-phosphate dehydrogenase-encoding gene (Gpdh) in Drosophila melanogaster induces a GPDH isozyme-GPDH-4-and alters the pattern of expression of the three normal isozymes-GPDH-1 to GPDH-3. The process of transcript terminus formation inside the retrotransposon insertion reduces the level of the Gpdh transcript that contains exon 8 and increases the level of the transcript that contains exons 1-7. The induced GPDH-4 isozyme is a translation product of the three transcripts that contain fragments of the blood retrotransposon. The mechanism of mutagenesis by the blood insertion is postulated to involve the pause or termination of transcription within the blood sequence, which in turn is caused by the interference of a DNA-binding protein with the RNA polymerase. Thus, we show the formation of a new functional GPDH protein by the insertion of a transposable element and discuss the evolutionary significance of this phenomenon.
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Affiliation(s)
- T M Wilanowski
- Molecular and Population Genetics Group, Research School of Biological Sciences, Australian National University, Canberra, Australia
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26
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Aulard S, Lemeunier F, Hoogland C, Chaminade N, Brookfield JF, Biémont C. Chromosomal distribution and population dynamics of the 412 retrotransposon in a natural population of Drosophila melanogaster. Chromosoma 1995; 103:693-9. [PMID: 7664616 DOI: 10.1007/bf00344230] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The localization of the insertion sites of the 412 retrotransposable element was analysed by in situ hybridization to the polytene chromosomes of the genomes of males from a natural population of Drosophila melanogaster. Non-parametric statistical tests do not reveal any particular distribution of the insertion sites over the chromosomes, suggesting an apparently random distribution of the 412 element. Aggregation and dispersion tests were highly significant with data of copy number (when all genomes are pooled, many copies may be at a given site), suggesting the existence of sites with high insertion frequency. Comparison with other data from the literature confirms the tendency for a low proportion of insertions on the X chromosome in comparison with the autosomes, a result in agreement with selection acting against the detrimental effect of the 412 element insertions.
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Affiliation(s)
- S Aulard
- Laboratoire Populations, Génétique et Evolution, C.N.R.S., F-91198 Gif-sur-Yvette Cedex, France
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Garcia Guerreiro MP, Biémont C. Changes in the chromosomal insertion pattern of the copia element during the process of making chromosomes homozygous in Drosophila melanogaster. MOLECULAR & GENERAL GENETICS : MGG 1995; 246:206-11. [PMID: 7862091 DOI: 10.1007/bf00294683] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
In situ hybridization on polytene chromosomes of Drosophila melanogaster was used to compare the insertion patterns of copia and mdg1 transposable elements on chromosome 2 in male gametes sampled by two different methods: (i) by crossing the males tested with females from a highly inbred line with known copia and mdg1 insertion profiles; (ii) by crossing the same males with females from a marked strain, and analysing the resulting homozygous chromosomes. Crossing of the males with the inbred line led to homogeneous insertion profiles for both the copia and mdg1 elements in larvae, thus giving an accurate estimation of the patterns in the two gamete classes of each male. Crossing with the marked strain led, however, to heterogeneity in insertion patterns of the copia transposable element, while no significant polymorphism was observed for mdg1. The use of balancer chromosomes is thus not an adequate way of inferring transposable element insertion patterns of Drosophila males, at least for the copia element. This technique could, however, be powerful for investigating the control of movements of this element.
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Affiliation(s)
- M P Garcia Guerreiro
- Laboratoire de Biométrie, Génétique et Biologie des Populations, URA 243, Université Claude Bernard, Villeurbanne, France
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Biémont C. Dynamic equilibrium between insertion and excision of P elements in highly inbred lines from an M' strain of Drosophila melanogaster. J Mol Evol 1994; 39:466-72. [PMID: 7807536 DOI: 10.1007/bf00173415] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Six highly inbred lines of Drosophila melanogaster extracted from an M' strain (in the P/M system of hybrid dysgenesis) were studied for the evolution of the number and chromosomal location of complete and defective P elements through generations 52-200. These lines possessed full-sized P elements but differed in their cytotype (M or P). Three lines with P cytotype and full-sized P elements at site 1A had a constant P copy number over generations with low rates of insertion and excision. Three lines with M cytotype and at least one full-sized P element accumulated P copies over the generations and reached a plateau near generation 196, at which rates of transposition and excision were equal to 1.2 x 10(-3) to 3 x 10(-3) events per element per generation. At that time these three lines still presented an M cytotype, produced transposase, and were able to regulate P copy number. The similarity at equilibrium between insertion and excision rates was exactly what was expected from theoretical models for a self-regulated element. The large number of generations necessary to attain the equilibrium in copy number indicates, however, that caution may be de rigueur when testing theoretical models of copy-number containment based on transposition and excision-rate comparison.
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Affiliation(s)
- C Biémont
- Laboratoire de Biométrie, Génétique, Biologie des populations, URA C.N.R.S. 243, Université Lyon 1, Villeurbanne, France
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29
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Charlesworth B, Sniegowski P, Stephan W. The evolutionary dynamics of repetitive DNA in eukaryotes. Nature 1994; 371:215-20. [PMID: 8078581 DOI: 10.1038/371215a0] [Citation(s) in RCA: 986] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Repetitive DNA sequences form a large portion of the genomes of eukaryotes. The 'selfish DNA' hypothesis proposes that they are maintained by their ability to replicate within the genome. The behaviour of repetitive sequences can result in mutations that cause genetic diseases, and confer significant fitness losses on the organism. Features of the organization of repetitive sequences in eukaryotic genomes, and their distribution in natural populations, reflect the evolutionary forces acting on selfish DNA.
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Affiliation(s)
- B Charlesworth
- Department of Ecology and Evolution, University of Chicago, Illinois 60637
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30
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Biémont C, Lemeunier F, Garcia Guerreiro MP, Brookfield JF, Gautier C, Aulard S, Pasyukova EG. Population dynamics of the copia, mdg1, mdg3, gypsy, and P transposable elements in a natural population of Drosophila melanogaster. Genet Res (Camb) 1994; 63:197-212. [PMID: 8082837 DOI: 10.1017/s0016672300032353] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The insertion site polymorphism of the copia, mdg1, mdg3, gypsy, and P transposable elements was analysed by in situ hybridization to the polytene chromosomes in genomes of males from a natural population of Drosophila melanogaster. Parameters of various theoretical models of the population biology of transposable elements were estimated from our data, and different hypotheses explaining TE copy number containment were tested. The copia, mdg1 and gypsy elements show evidence for a deficiency of insertions on the X chromosomes, a result consistent with selection against the mutational effects of insertions. On the contrary, mdg3 and P copy numbers fit a neutral model with a balance between regulated transposition and excisions. There is no strong evidence of a systematic accumulation of elements in the distal and proximal regions of the chromosomes where crossing over and ectopic exchanges are reduced. For all chromosome arms but 3L, however, the TE site density increases from the proximal to the distal parts of the chromosomes (the centromeric regions were excluded in this analysis) with sometimes a sharp decrease in density at the extreme tip, following in part the exchange coefficient. The way the copy number of TEs is contained in genomes depends thus on the element considered, and on various forces acting simultaneously, indicating that models of TE dynamics should include details of each element.
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Affiliation(s)
- C Biémont
- Laboratoire de Biométrie, Génétique, Biologie des populations, URA C.N.R.S. 243, Université Lyon, Villeurbanne, France
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31
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Dufournel I, Garcia Guerreiro MP, Arnault C, Biémont C. Transposable element insertion patterns as test of contamination of a Drosophila melanogaster inbred line. EXPERIENTIA 1994; 50:164-6. [PMID: 8125175 DOI: 10.1007/bf01984957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A highly inbred line of Drosophila melanogaster, stable for the insertion pattern of the transposable elements copia and mdg1, was experimentally contaminated by flies from another line. We show that the alien genome income is clearly detectable by the changes induced in the insertion profiles of transposable elements, even twenty generations later.
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Affiliation(s)
- I Dufournel
- Laboratoire de Biométrie, Génétique, Biologie des populations, URA C.N.R.S. 243, Université Lyon, Villeurbanne, France
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Abstract
Most of the transposons so far characterized from mosquito genomes are retroelements which seem to be distributed worldwide. The Juan transposons constitute a family of non-LTR retroelements, or LINE-retroposons, which are dispersed in the genomes of several mosquito species. Three different Juan subfamilies have been characterized, each being amplified in the genomes of many strains, if not all, of a given mosquito species. These subfamilies have been designated respectively Juan-C in Culex pipiens, Juan-Ct in Culex tarsalis and Juan-A in Aedes aegypti. A large number of the Juan retroposons which are amplified in the mosquito genomes are apparently full-length copies and potentially encode the enzymes necessary for their transposition, a nucleic acid binding protein and a reverse transcriptase. However, these complete Juan copies seem to be most frequently transcriptionally silent in insects reared under laboratory conditions. A few of them are transcribed in C. pipiens cells grown in vitro, but from an external promoter, the Juan-C specific RNA being fused to an upstream RNA sequence. Therefore, the transcription of Juan retroposons seems to depend on external promoters which are most frequently inactive. The occurrence and distribution of Juan retroposon subfamilies among mosquito species do not reflect the phylogeny of these species. Furthermore, complete Juan-C and Juan-A copies which are reiterated in strains collected from regions covering different continents are nearly identical. Juan-C copies belonging to geographically different C. pipiens strains display low levels of divergence between their nucleotide sequences and many of the mutations which have occurred among these copies do not alter their coding potential. These results indicate that the Juan retroposons occur as homogeneous subfamilies distributed worldwide and that selective constraints against amino acid change have been acting recently on these elements, despite the fact that they are now highly repeated through mosquito genomes. Therefore, Juan transposons have most probably been recently amplified in mosquito genomes. Each subfamily may have been amplified from one master element present in a unique population which has since spread worldwide. Alternatively, this amplification may have arisen in many mosquito populations, but from highly conserved master elements submitted to selection pressures. Horizontal transfers between species may also have contributed to the spread of these transposons.
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Affiliation(s)
- N Bensaadi-Merchermek
- Laboratoire d'Ecologie Moléculaire, Université de Pau et des Pays de l'Adour, France
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Arnault C, Dufournel I. Genome and stresses: reactions against aggressions, behavior of transposable elements. Genetica 1994; 93:149-60. [PMID: 7813912 DOI: 10.1007/bf01435247] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The action of stresses on the genome can be considered as responses of cells or organisms to external aggressions. Stress factors are of environmental origin (climatic or trophic) or of genomic nature (introduction of foreign genetic material, for example). In both cases, important perturbations can occur and modify hereditary potentialities, creating new combinations compatible with survival; such a situation may increase the variability of the genome, and allow evolutive processes to take place. The behavior of transposable elements under stress conditions is thus of particular interest, since these sequences are sources of mutations and therefore of genetic variability; they may play an important role in population adaptation. The survey of the available experimental results suggest that, although some examples of mutations and transposable elements movements induced by external factors are clearly described, environmental injuries or introduction of foreign material into a genome are not systematically followed by drastic genomic changes.
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Affiliation(s)
- C Arnault
- Laboratoire de Biométrie, Génétique et Biologie des Populations, URA CNRS 243, Université Claude Bernard Lyon I, Villeurbanne, France
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34
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Ladevèze V, Galindo MI, Pascual L, Periquet G, Lemeunier F. Invasion of the hobo transposable element studied by in situ hybridization on polytene chromosomes of Drosophila melanogaster. Genetica 1994; 93:91-100. [PMID: 7813920 DOI: 10.1007/bf01435242] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The invasion kinetics of hobo transposable element in the Drosophila melanogaster genome was studied by in situ hybridization on the polytene chromosomes. Six independent lines of Drosophila melanogaster flies that had been previously transformed by microinjection of the pHFL1 plasmid containing a complete hobo element were followed over 50 generations. We observed that hobo elements were scattered on each of the chromosome arms, with more insertion sites on the 3R arm. The total number of insertion sites remains quite small, between four and six, at generation 52. On the 2R arm, a short inversion appeared once at generation 52. Most of the integration sites reported here were already described for several transposons but some of them appear to be hotspots for hobo elements.
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Affiliation(s)
- V Ladevèze
- I.B.E.A.S, Université François Rabelais, Tours, France
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Abstract
Recombinant inbred strains have been used in a number of organisms for segregation and linkage analysis of quantitative traits. One major advantage of the recombinant inbred (RI) methodology is that the genetic identity of individuals within a strain permits replicate measures of the same recombinant genotype. Such replicability is important for traits such as aging in Drosophila, where phenotypic expression is highly influenced by different environmental conditions. RI strain methodology has an added advantage for DNA marker-based linkage analysis of traits measured over the lifespan of the organism. The DNA can be extracted from individuals of the same genotype as those measured in a longevity study. In this paper an argument is presented for the use of a set of recombinant inbred strains to map the quantitative trait loci involved in the aging process in Drosophila. A unique use of a set of stable, transposable molecular markers to trace the quantitative trait loci involved is suggested.
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Affiliation(s)
- L K Dixon
- Center for Developmental and Health Genetics, Pennsylvania State University, University Park 16804
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36
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