Copy number of P elements, KP/full-sized P element ratio and their relationships with environmental factors in Brazilian Drosophila melanogaster populations

The Landscape of the DNA Transposons in the Genome of the Horezu_LaPeri Strain of Drosophila melanogaster

Natural transposons (NTs) represent mobile DNA sequences found in both prokaryotic and eukaryotic genomes. Drosophila melanogaster (the fruit fly) is a eukaryotic model organism with NTs standing for about 20% of its genome and has contributed significantly to the understanding of various aspects of transposon biology. Our study describes an accurate approach designed to map class II transposons (DNA transposons) in the genome of the Horezu_LaPeri fruit fly strain, consecutive to Oxford Nanopore Technology sequencing. A whole genome bioinformatics analysis was conducted using Genome ARTIST_v2, LoRTE and RepeatMasker tools to identify DNA transposons insertions. Then, a gene ontology enrichment analysis was performed in order to evaluate the potential adaptive role of some DNA transposons insertions. Herein, we describe DNA transposon insertions specific for the Horezu_LaPeri genome and a predictive functional analysis of some insertional alleles. The PCR validation of P-element insertions specific for this fruit fly strain, along with a putative consensus sequence for the KP element, is also reported. Overall, the genome of the Horezu_LaPeri strain contains several insertions of DNA transposons associated with genes known to be involved in adaptive processes. For some of these genes, insertional alleles obtained via mobilization of the artificial transposons were previously reported. This is a very alluring aspect, as it suggests that insertional mutagenesis experiments conducting adaptive predictions for laboratory strains may be confirmed by mirroring insertions which are expected to be found at least in some natural fruit fly strains.

Paternally Inherited P-Element Copy Number Affects the Magnitude of Hybrid Dysgenesis in Drosophila simulans and D. melanogaster

Transposable elements (TEs) are repetitive regions of DNA that are able to self-replicate and reinsert themselves throughout host genomes. Since the discovery of TEs, a prevalent question has been whether increasing TE copy number has an effect on the fitness of their hosts. P-elements (PEs) in Drosophila are a well-studied TE that has strong phenotypic effects. When a female without PEs (M) is crossed to a male with them (P), the resulting females are often sterile, a phenomenon called hybrid dysgenesis (HD). Here, we used short- and long-read sequencing to infer the number of PEs in the genomes of dozens of isofemale lines from two Drosophila species and measured whether the magnitude of HD was correlated with the number of PEs in the paternal genome. Consistent with previous reports, we find evidence for a positive correlation between the paternal PE copy number and the magnitude of HD in progeny from ♀M × ♂ P crosses for both species. Other crosses are not affected by the number of PE copies. We also find that the correlation between the strength of HD and PE copy number differs between species, which suggests that there are genetic differences that might make some genomes more resilient to the potentially deleterious effects of TEs. Our results suggest that PE copy number interacts with other factors in the genome and the environment to cause HD and that the importance of these interactions is species specific.

Genomic analysis of P elements in natural populations of Drosophila melanogaster

The 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 across populations. Here we compare estimates of genomic P element content with gonadal dysgenesis phenotypes 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 P element 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 that P element content varies significantly across populations, with strains from a North American population having fewer P elements but a higher proportion of full-length elements than strains from populations sampled in Europe or Africa. Despite these geographic differences in P element abundance and structure, neither the number of P elements 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 in P element 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 of P elements that are observed from isofemale lines can also be observed in pool-seq samples from the same populations. Our work supports the view that genomic P element content alone 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.

P element activity and molecular structure in Drosophila melanogaster populations from Firtina Valley, Turkey

In order to study P element dynamics in natural populations of Drosophila melanogaster, 88 isofemale lines were examined from the Firtina Valley, Turkey. The P-M gonadal dysgenesis characteristics and the molecular patterns of P and KP elements were analyzed. Gonadal dysgenesis tests showed a slight variation both for P activity and P susceptibility, however the results showed a predominant M' phenotype for this region. The P and KP element were also characterized by polymerase chain reaction. The molecular analyses showed that all the populations examined had the entire 1.15 kb KP element. The molecular patterns of KP elements were the same for the populations studied. No clear relationship was found between phenotype and genomic P element composition. The correlations between the level of gonadal dysgenesis percentage (as an index for P activity and P susceptibility) and several geoclimatic factors were tested, and no general effects of altitude, temperature, rainfall, or humidity were found. The theoretical P' strain, which is very rare in natural populations, was also recorded for this region.

Long-term patterns of genomic P element content and P-M characteristics of Drosophila melanogaster in eastern Australia

A latitudinal cline in characteristics associated with the P DNA transposable element is well known in eastern Australian populations of Drosophila melanogaster. In order to survey the long-term patterns of P-M system characteristics and genomic P element content, we established 292 isofemale lines from 54 localities in 1996-1997 and evaluated them for gonadal dysgenesis (GD) sterility and the ratio of KP to full-size P elements (KP/FP ratio). The results were compared to those from collections made in 1983-1986 and 1991-1994. Over 10-14 years, 1) the cross A GD scores of the northern-middle populations declined dramatically; 2) the clinal pattern of the cross A* GD scores did not change; 3) the latitudinal pattern of the KP/FP ratio did not change. The results suggest that only a few P elements determine P-M characteristics and that there has been selection for genomes with fewer active P elements, but not for a great change in proportions of size classes.

Prevalence of full-size P and KP elements in North American populations of Drosophila melanogaster

The P transposable element invaded the Drosophila melanogaster genome in the middle of the twentieth century, probably from D. willistoni in the Caribbean or southeastern North America. P elements then spread rapidly and became ubiquitous worldwide in wild populations of D. melanogaster by 1980. To study the dynamics and long-term fate of transposable genetic elements, we examined the molecular profile of genomic P elements and the phenotype in the P-M system of the current North American natural populations collected in 2001-2003. We found that full-size P and KP elements were the two major size classes of P elements present in the genomes of all populations ("FP + KP predominance") and that the P-related phenotypes had largely not changed since the 1980s. Both FP + KP predominance and phenotypic stability were also seen in other populations from other continents. As North American populations did not show many KP elements in earlier samples, we hypothesize that KP elements have spread and multiplied in the last 20 years in North America. We suggest that this may be due to a transpositional advantage of KP elements, rather than to a role in P-element regulation.

Male-killing Spiroplasma naturally infecting Drosophila melanogaster

Elucidation of the mechanism of action of selfish genetic elements is difficult outside species with well-defined genetics. Male-killing, the phenomenon whereby inherited bacteria kill male hosts during embryogenesis, is thus uncharacterized in mechanistic terms despite being common and important in insects. We characterized the prevalence, identity and source of the male-killing infection recently discovered in Drosophila melanogaster in Brazil. Male-killing was found to be present in 2.3% of flies from Recife, Brazil, and was uniquely associated with the presence of Spiroplasma infection. The identity of sequences across part of the 16S and across the 16S-23S ITS region indicated that the male-killing infection of D. melanogaster was very closely related to S. poulsonii, the source of the male-killing infection in willistoni group flies also found in South America. The sequences of two further protein-coding genes indicated the D. melanogaster infection to be most closely related to that found in D. nebulosa, from the willistoni group. Our data suggest that the establishment of D. melanogaster in South America was associated with the movement of male-killing bacteria between species.