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

Abstract

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.

Keywords: DNA natural transposons; Drosophila melanogaster; P-element; bioinformatics; heterochromatin; transposable elements; transposon annotation.

Figure 1

Example of visualization of genes and transposons annotations in the GA_v2 graphic interface. The reference genome is marked with blue, and the sequence of the transposable element is marked with red. The green boxes show the annotations, revealing that this insertion of the P-element has an internal deletion between positions 806 and 2561 (KP element) in the overlapping genes ebd2 and CG32436.

Figure 2

Multiple alignment of 11 KP elements extracted from Canu contigs of the Horezu_LaPeri genome using ClustalX v2.1 application. The stars indicate the number of completely conserved columns in the multiple alignment.

Figure 3

Frequency distributions of considered DNA NTs in reference genome (A) of D. melanogaster (r6.48) and in the Horezu_LaPeri genome (B). All DNA NTs from the Horezu_LaPeri genome were identified using GA_v2 software. DNA NTs from the reference genome include both the FlyBase-annotated NTs and the unannotated NTs identified with GA_v2 in this study.

Figure 4

The frequency of DNA NTs obtained with LoRTE for the ONT reads generated via sequencing of the Horezu_LaPeri genome. The y-axis shows the number of copies of NTs, while on the x-axis are represented the transposons’ families. The color code is associated with the annotations generated using LoRTE for each analyzed element.

Figure 5

NTs’ landscape divergence diagrams computed with RepeatMasker for: (A) the proportion of repetitive elements in the reference genome of D. melanogaster (dm3); (B) the total number of repetitive elements in the Horezu_LaPeri genome. The y-axis represents genome coverage for each transposon type, and the x-axis represents Kimura distances.

Figure 6

The distribution of the P-element and Bari1 NTs in the Horezu_LaPeri genome. The red triangles represent the insertions of the P-element, while the green triangles represent insertions of the Bari1 element, an NT found in both genomes. The green triangles with an asterisk (*) stand for Bari1 insertions which were detected only in the Horezu_LaPeri genome. P-element insertions in/near to Ac13E, retn and stv genes were mapped using an alternative assembly. Created with BioRender.com (accessed on 15 May 2023).