scholarly journals Phenotypic and genomic analysis of P elements in natural populations of Drosophila melanogaster

2016 ◽  
Author(s):  
I.A. Kozeretska ◽  
V. Bondarenko ◽  
V.I. Shulga ◽  
S.V. Serga ◽  
A.I. Rozhok ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Active Form ◽  
Natural Populations ◽  
Genomic Analysis ◽  
Element Composition ◽  
Strongly Correlated ◽  
Mobile Dna ◽  
P Elements ◽  
The Stability ◽  
Genomic Basis

AbstractThe Drosophila melanogaster P transposable element provides one of the best cases of horizontal transfer of a mobile DNA sequence in eukaryotes. Invasion of natural populations by the P element has led to a syndrome of phenotypes known as “P-M hybrid dysgenesis” that emerges when strains differing in their P element composition mate and produce offspring. Despite extensive research on many aspects of P element biology, questions remain about the stability and genomic basis of variation in P-M dysgenesis phenotypes. Here we report the P-M status for a number of populations sampled recently from Ukraine that appear to be undergoing a shift in their P element composition. Gondal dysgenesis assays reveal that Ukrainian populations of D. melanogaster are currently dominated by the P’ cytotype, a cytotype that was previously thought to be rare in nature, suggesting that a new active form of the P element has recently spread in this region. We also compared gondal dysgenesis phenotypes and genomic P element predictions for isofemale strains obtained from three worldwide populations of D. melanogaster in order to guide further work on the molecular basis of differences in cytotype status across populations. We find that the number of euchromatic P elements per strain can vary significantly across populations but that total P element numbers are not strongly correlated with the degree of gondal dysgenesis. Our work shows that rapid changes in cytotype status can occur in natural populations of D. melanogaster, and informs future efforts to decode the genomic basis of geographic and temporal differences in P element induced phenotypes.

scholarly journals Genomic analysis of P elements in natural populations of Drosophila melanogaster

2017 ◽  
Author(s):  
Casey M. Bergman ◽  
Michael G. Nelson ◽  
Vladyslav Bondarenko ◽  
Iryna A. Kozeretska
Keyword(s):  
Drosophila Melanogaster ◽  
Gonadal Dysgenesis ◽  
Natural Populations ◽  
Genomic Analysis ◽  
Read Depth ◽  
North American Population ◽  
Mobile Dna ◽  
Geographic Differences ◽  
Isofemale Strains ◽  
Genomic Basis

AbstractThe Drosophila melanogaster P transposable element provides one of the best cases of horizontal transfer of a mobile DNA sequence in eukaryotes. Invasion of natural populations by the P element has led to a syndrome of phenotypes known as P-M hybrid dysgenesis that emerges when strains differing in their P element composition mate and produce offspring. Despite extensive research on many aspects of P element biology, many questions remain about the genomic basis of variation in P-M dysgenesis phenotypes in natural populations. Here we compare gonadal dysgenesis phenotypes and genomic P element predictions for isofemale strains obtained from three worldwide populations of D. melanogaster to illuminate the molecular basis of natural variation in cytotype status. We show that the number of predicted P element insertions in genome sequences from isofemale strains is highly correlated across different bioinformatics methods, but the absolute number of insertions per strain is sensitive to method and filtering strategies. Regardless of method used, we find that the number of euchromatic P element insertions predicted per strain varies significantly across populations, with strains from a North American population having fewer P element insertions than strains from populations sampled in Europe or Africa. Despite these geographic differences, numbers of euchromatic P element insertions are not strongly correlated with the degree of gonadal dysgenesis exhibited by an isofemale strain. Thus, variation in P element insertion numbers across different populations does not necessarily lead to corresponding geographic differences in gonadal dysgenesis phenotypes. Additionally, we show that pool-seq samples can uncover population differences in the number of P element insertions observed from isofemale lines, but that efforts to rigorously detect differences in the number of P elements across populations using pool-seq data must properly control for read depth per strain. Our work supports the view that euchromatic P element copy number is not sufficient to explain variation in gonadal dysgenesis across strains of D. melanogaster, and informs future efforts to decode the genomic basis of geographic and temporal differences in P element induced phenotypes.

scholarly journals The Regulatory Properties of Autonomous Subtelomeric P Elements Are Sensitive to a Suppressor of variegation in Drosophila melanogaster

Genetics ◽  
1996 ◽  
Vol 143 (4) ◽  
pp. 1663-1674 ◽  
Author(s):  
Stéphane Ronsseray ◽  
Monique Lehmann ◽  
Danielle Nouaud ◽  
Dominique Anxolabéhère
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Recombination ◽  
Natural Populations ◽  
P Element ◽  
Single Element ◽  
Heterochromatin Protein 1 ◽  
X Chromosomes ◽  
P Elements ◽  
Associated Sequences ◽  
Regulatory Properties

Abstract Genetic recombination was used in Drosophila melanogaster to isolate P elements, inserted at the telomeres of X chromosomes (cytological site 1A) from natural populations, in a genetic background devoid of other P elements. We show that complete maternally inherited P repression in the germline (P cytotype) can be elicited by only two autonomous P elements at 1A and that a single element at this site has partial regulatory properties. The analysis of the surrounding chromosomal regions of the P elements at 1A shows that in all cases these elements are flanked by Telomeric Associated Sequences, tandemly repetitive noncoding sequences that have properties of heterochromatin. In addition, we show that the regulatory properties of P elements at 1A can be inhibited by some of the mutant alleles of the Su(var)205 gene and by a deficiency of this gene. However, the regulatory properties of reference P strains (Harwich and Texas 007) are not impaired by Su(var)205 mutations. Su(var)205 encodes Heterochromatin Protein 1 (HP1). These results suggest that the HP1 dosage effect on the P element properties is sitedependent and could involve the structure of the chromatin.

scholarly journals A quantitative genetic analysis of fitness and its components in Drosophila melanogaster

1986 ◽  
Vol 47 (1) ◽  
pp. 59-70 ◽  
Author(s):  
Trudy F. C. Mackay
Keyword(s):  
Drosophila Melanogaster ◽  
Natural Populations ◽  
Strongly Correlated ◽  
Wild Type ◽  
Relative Contribution ◽  
Quantitative Characters ◽  
Quantitative Genetic ◽  
Bristle Number ◽  
Metric Traits ◽  
Average Fitness

SummaryForty-one third chromosomes extracted from a natural population of Drosophila melanogaster were assessed for net fitness and for the quantitative characters viability, net fertility, female productivity, male weight, abdominal bristle number, and sternopleural bristle number. Net homozygous and heterozygous fitness of the third chromosomes was estimated by competition against a marked balancer third chromosome. Average fitness of the homozygous lines relative to wild-type heterozygotes was 0·13, indicating substantial inbreeding depression for net fitness. All significant correlations of quantitative characters with fitness and with each other were high and positive. Homozygous fitness is strongly correlated with net fertility, viability, and female productivity, moderately associated with male weight, and not significantly associated with bristle traits. The combination of metric traits which best predicts homozygous fitness is the simple multiple of viability and female productivity. Heterozygous fitness is not correlated with homozygous fitness; furthermore, the relative contribution of metric traits to fitness in a heterozygous population is likely to be different from that deduced from homozygous lines. These observations are consistent with a model of genetic variation for fitness in natural populations caused by segregation of rare deleterious recessive alleles.

scholarly journals Polymorphism in distribution and structure of P elements in natural populations of Drosophila melanogaster in and around Japan.

1984 ◽  
Vol 59 (5) ◽  
pp. 441-451 ◽  
Author(s):  
Takeshi TODO ◽  
Yasuhiko SAKOYAMA ◽  
Sadao I. CHIGUSA ◽  
Akihiro FUKUNAGA ◽  
Tasuku HONJO ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Natural Populations ◽  
P Elements

scholarly journals Accumulation of P elements in minority inversions in natural populations of Drosophila melanogaster

1992 ◽  
Vol 59 (1) ◽  
pp. 1-9 ◽  
Author(s):  
Walter F. Eanes ◽  
Cedric Wesley ◽  
Brian Charlesworth
Keyword(s):  
Mathematical Model ◽  
Drosophila Melanogaster ◽  
Copy Number ◽  
Natural Populations ◽  
P Element ◽  
P Elements ◽  
Chromosomal Inversions ◽  
Associated Production ◽  
African Populations ◽  
Parameter Values

SummaryThe accumulation of a transposable element inside chromosomal inversions is examined theoretically by a mathematical model, and empirically by counts of P elements associated with inversion polymorphisms in natural populations of Drosophila melanogaster. The model demonstrates that, if heterozygosity for an inversion effectively reduces element associated production of detrimental chromosome rearrangements, a differential accumulation of elements is expected, with increased copy number inside the minority inversion. Several-fold differential accumulations are possible with certain parameter values. We present data on P element counts for inversion polymorphisms on all five chromosome arms of 157 haploid genomes from two African populations. Our observations show significantly increased numbers of elements within the regions associated with the least common, or minority arrangements, in natural inversion polymorphisms.

scholarly journals The P-element strikes again: the recent invasion of naturalDrosophila simulanspopulations

2015 ◽  
Author(s):  
Robert Kofler ◽  
Tom Hill ◽  
Viola Nolte ◽  
Andrea Betancourt ◽  
Christian Schlötterer
Keyword(s):  
Drosophila Melanogaster ◽  
Defense Mechanisms ◽  
Natural Populations ◽  
Genomic Data ◽  
P Element ◽  
Expression Data ◽  
Transfer Event ◽  
P Elements ◽  
Origins Of Replication ◽  
Close Relatives

The P-element is one of the best understood eukaryotic transposable elements. It invadedDrosophila melanogasterpopulations within a few decades, but was thought to be absent from close relatives, includingD. simulans. Five decades after the spread inD. melanogaster, we provide evidence that the P-element has also invadedD. simulans. P-elements inD. simulansappear to have been acquired recently fromD. melanogasterprobably via a single horizontal transfer event. Expression data indicate that the P-element is processed in the germline ofD. simulans, and genomic data show an enrichment of P-element insertions in putative origins of replication, similar to that seen inD. melanogaster. This ongoing spread of the P-element in natural populations provides an unique opportunity to understand the dynamics of transposable element spreads and the associated piRNA defense mechanisms.

scholarly journals Genomic analysis of European Drosophila melanogaster populations reveals longitudinal structure, continent-wide selection, and previously unknown DNA viruses

2018 ◽  
Author(s):  
Martin Kapun ◽  
Maite G. Barrón ◽  
Fabian Staubach ◽  
Darren J. Obbard ◽  
R. Axel W. Wiberg ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Variation ◽  
Climate Adaptation ◽  
Natural Populations ◽  
Genomic Analysis ◽  
Short Term ◽  
Dna Viruses ◽  
Local Climate ◽  
Term Evolution ◽  
Spatio Temporal

AbstractGenetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatio-temporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. Here, we address these issues using a collaborative approach, sequencing 48 pooled population samples from 32 locations, and perform the first continent-wide genomic analysis of genetic variation in European Drosophila melanogaster. Our analyses uncover longitudinal population structure, provide evidence for continent-wide selective sweeps, identify candidate genes for local climate adaptation, and document clines in chromosomal inversion and transposable element frequencies. We also characterise variation among populations in the composition of the fly microbiome, and identify five new DNA viruses in our samples.

scholarly journals Transposable element-induced fitness mutations in Drosophila melanogaster

1986 ◽  
Vol 48 (2) ◽  
pp. 77-87 ◽  
Author(s):  
Trudy F. C. Mackay
Keyword(s):  
Drosophila Melanogaster ◽  
Extraction Procedure ◽  
Natural Populations ◽  
P Element ◽  
Recessive Lethal ◽  
P Elements ◽  
Fitness Traits ◽  
Mutational Effect ◽  
Evolution Of Transposable Elements ◽  
Mutational Variance

SummaryP element mutagenesis was used to contaminate M strain second chromosomes with P elements. The contaminated lines were compared to uncontaminated control lines for homozygous and heterozygous fitness and its components. Mean homozygous fitness, viability and fertility of chromosome lines contaminated with P elements is decreased relative to the uncontaminated control lines by, respectively, 55, 28 and 40%. Variance among contaminated homozygous lines of total fitness increases by a factor of 1·5, variance of viability by a factor of 5·9, and variance of fertility by a factor of 1·9, compared to variance of these traits among the population of uncontaminated homozygous chromosomes. Estimates of P-element-induced mutational variance among second chromosome lines for homozygous fitness, viability and fertility are, respectively, 2 × 10−2, 5 × 10−2 and 2 × 10−2. This magnitude of mutational effect is equivalent, in terms of incidence of induced recessive lethal chromosomes and D:L ratio, to a dose of approximately 1·0–2·5 × 10−3 m EMS. The distributions of fitness traits among M-derived second chromosome homozygous lines contaminated with P elements are remarkably similar in many regards to distributions of fitness and viability of chromosomal homozygotes derived from natural Drosophila populations. It is possible that a proportion of the fitness variation previously observed (reviewed by Simmons & Crow, 1977) following homozygosis of wild chromosomes was not present in the natural populations, but was generated by P-element transposition during the chromosome extraction procedure. P-element-induced fitness mutations appear to be completely recessive. Implications for models of evolution of transposable elements are discussed.

scholarly journals Disgenesia do híbrido em populações naturais de Drosophila melanogaster.

1999 ◽  
Vol 21 (21) ◽  
pp. 51 ◽  
Author(s):  
Chirlei Cintia Klein ◽  
Liliana Essi ◽  
Ronaldo Medeiros Golombieski ◽  
Élgion Lúcio da Silva Loreto
Keyword(s):  
Drosophila Melanogaster ◽  
Molecular Analysis ◽  
Natural Populations ◽  
Rio Grande ◽  
P Element ◽  
Rio Grande Do Sul ◽  
Genetic Traits ◽  
P Elements ◽  
Regulatory Capacity ◽  
Element Activity

Hybrid dysgenesis has been defined as a remarkable syndrome of correlated genetic traits that are produced in some particular crosses between certain strains. The present study main objective was classify recently collected Drosophila melanogaster strains in relation to P element activity and regulatory capacity. Our results to natural populations trapped from Rio Grande do Sul, Brazil and Colombia shows that it fell on Q class, since all examinated strains has showed P elements by molecular analysis and low P activity. In the same way, these strains shows low susceptibility to P element action. The bigger values found in the colombian population are in agreement with the clinal hypothesis to P element activity.

scholarly journals P elements and P-M characteristics in natural populations of Drosophila melanogaster in the southernmost islands of Japan and in Taiwan

Heredity ◽  
2001 ◽  
Vol 86 (2) ◽  
pp. 206-212 ◽  
Author(s):  
Masanobu Itoh ◽  
Nobuhiro Sasai ◽  
Yutaka Inoue ◽  
Masayoshi Watada
Keyword(s):  
Drosophila Melanogaster ◽  
Natural Populations ◽  
P Elements
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