scholarly journals Genomic analysis ofPelements in natural populations ofDrosophila melanogaster

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3824 ◽  
Author(s):  
Casey M. Bergman ◽  
Shunhua Han ◽  
Michael G. Nelson ◽  
Vladyslav Bondarenko ◽  
Iryna Kozeretska
Keyword(s):  
Gonadal Dysgenesis ◽  
Natural Populations ◽  
Full Length ◽  
Element Content ◽  
Element Abundance ◽  
North American Population ◽  
Mobile Dna ◽  
Geographic Differences ◽  
Isofemale Strains ◽  
Genomic Basis

TheDrosophila melanogaster Ptransposable element provides one of the best cases of horizontal transfer of a mobile DNA sequence in eukaryotes. Invasion of natural populations by thePelement has led to a syndrome of phenotypes known as P-M hybrid dysgenesis that emerges when strains differing in theirPelement composition mate and produce offspring. Despite extensive research on many aspects ofPelement biology, many questions remain about the genomic basis of variation in P-M dysgenesis phenotypes across populations. Here we compare estimates of genomicPelement content with gonadal dysgenesis phenotypes for isofemale strains obtained from three worldwide populations ofD. melanogasterto illuminate the molecular basis of natural variation in cytotype status. We show thatPelement abundance estimated from genome sequences of isofemale strains is highly correlated across different bioinformatics approaches, but that abundance estimates are sensitive to method and filtering strategies as well as incomplete inbreeding of isofemale strains. We find thatPelement content varies significantly across populations, with strains from a North American population having fewerPelements but a higher proportion of full-length elements than strains from populations sampled in Europe or Africa. Despite these geographic differences inPelement abundance and structure, neither the number ofPelements nor the ratio of full-length to internally-truncated copies is strongly correlated with the degree of gonadal dysgenesis exhibited by an isofemale strain. Thus, variation inPelement abundance and structure across different populations does not necessarily lead to corresponding geographic differences in gonadal dysgenesis phenotypes. Finally, we confirm that population differences in the abundance and structure ofPelements that are observed from isofemale lines can also be observed in pool-seq samples from the same populations. Our work supports the view that genomicPelement content alone is not sufficient to explain variation in gonadal dysgenesis across strains ofD. melanogaster, and informs future efforts to decode the genomic basis of geographic and temporal differences inPelement 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 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 A novel repressor of P element transposition in Drosophila melanogaster

1998 ◽  
Vol 71 (1) ◽  
pp. 21-30 ◽  
Author(s):  
RICHARD M. BADGE ◽  
JOHN F. Y. BROOKFIELD
Keyword(s):  
Drosophila Melanogaster ◽  
Inbred Line ◽  
Gonadal Dysgenesis ◽  
Full Length ◽  
P Element ◽  
Temperature Dependent ◽  
P Elements

We have discovered, in an inbred line (Loua) of Drosophila melanogaster from Zaïre, a third chromosome showing unusual P element repression. Repression of P element transposition by this chromosome, named Loua3, is dominant zygotic and has three unusual properties. Firstly, its repression of the gonadal dysgenesis caused by a strong P haplotype is strongly temperature-dependent, being most evident at higher rearing temperatures. Secondly, subdivision of Loua3 by recombination abolishes repression: the effect is apparently a function of the intact chromosome. Finally, Loua3 also diminishes somatic lethality when chromosomes carrying many ‘ammunition’ elements (Birmingham2) are exposed to the constitutive transposase source Δ2-3(99B). The chromosome has 17 P elements, none full-length, located in at least 12 dispersed positions.

scholarly journals Har-P, a short P-element variant, weaponizes P-transposase to severely impair Drosophila development

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Satyam P Srivastav ◽  
Reazur Rahman ◽  
Qicheng Ma ◽  
Jasmine Pierre ◽  
Saptaparni Bandyopadhyay ◽  
...  
Keyword(s):  
Gonadal Dysgenesis ◽  
De Novo ◽  
Full Length ◽  
P Element ◽  
Drosophila Development ◽  
P Elements ◽  
Transposon Silencing ◽  
Somatic Transposition

Without transposon-silencing Piwi-interacting RNAs (piRNAs), transposition causes an ovarian atrophy syndrome in Drosophila called gonadal dysgenesis (GD). Harwich (Har) strains with P-elements cause severe GD in F1 daughters when Har fathers mate with mothers lacking P-element-piRNAs (i.e. ISO1 strain). To address the mystery of why Har induces severe GD, we bred hybrid Drosophila with Har genomic fragments into the ISO1 background to create HISR-D or HISR-N lines that still cause Dysgenesis or are Non-dysgenic, respectively. In these lines, we discovered a highly truncated P-element variant we named ‘Har-P’ as the most frequent de novo insertion. Although HISR-D lines still contain full-length P-elements, HISR-N lines lost functional P-transposase but retained Har-P’s that when crossed back to P-transposase restores GD induction. Finally, we uncovered P-element-piRNA-directed repression on Har-P’s transmitted paternally to suppress somatic transposition. The Drosophila short Har-P’s and full-length P-elements relationship parallels the MITEs/DNA-transposase in plants and SINEs/LINEs in mammals.

scholarly journals Effects of autosomal inversions on meiotic exchange in distal and proximal regions of the X chromosome in a natural population of Drosophila melanogaster

1994 ◽  
Vol 63 (1) ◽  
pp. 57-62 ◽  
Author(s):  
Paul D. Sniegowski ◽  
Anne Pringle ◽  
Kimberly A. Hughes
Keyword(s):  
Drosophila Melanogaster ◽  
Natural Population ◽  
X Chromosome ◽  
Natural Populations ◽  
Element Abundance ◽  
Recombination Rates ◽  
Interchromosomal Effect ◽  
Naturally Occurring ◽  
Study Population ◽  
Transposable Element Abundance

SummaryWe have investigated the interchromosomal effect of the naturally-occurring paracentric inversions In(2L)t and In(3R)P on meiotic recombination in two regions of the X chromosome in Drosophila melanogaster. Previous authors have suggested that the rate of recombination at the tip of the X chromosome may be substantially higher in some natural populations than values measured in the laboratory, due to the interchromosomal effect of heterozygous autosomal inversions. This suggestion was motivated by observations that transposable elements are not as common at the tip of the X chromosome as predicted by recent research relating reduced meiotic exchange to increased element abundance in D. melanogaster. We examined the effects of heterozygous In(2L)t and In(3R)P on recombination at both the tip and base of the X chromosome on a background of isogenic major chromosomes from a natural population. Both inversions substantially increased the rate of recombination at the base; neither one affected recombination at the tip. The results suggest that the presence of inversions in the study population does not elevate rates of crossing over at the tip of the X chromosome. The relevance of these results to ideas relating transposable element abundance to recombination rates is discussed.

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