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.

Background: Drosophila suzukii is a worldwide invasive species with serious economic impacts. Herein, we are presenting the first project of sequencing and assembling the whole genomes of two lines of D. suzukii derived from Romanian local populations using exclusively Oxford Nanopore Technologies data. Methods: We implemented both MinION and Flongle flow-cells and tested the impact of various basecalling models and assembly strategies on the quality of the sought-after representative genome assemblies. Results: We demonstrate that the sup-basecalling model significantly improved the read quality and that adding a relatively small collection of reads had a significant positive impact over the assembly quality. The novel dScaff bioinformatics prototype tool allowed us to perform sequence-level quality tests, as well as to represent assembly selections and display both the contig redundancy and the repeats-enriched genomic sub-sequences. Moreover, we used dScaff to propose a minimal assembly variant corresponding to one of our lines, GB-ls-coga4, which assured a basic linear coverage of the genome and exhibited quality parameters comparable with those particular to the current reference genome assembly. Conclusions: The study presents the first sequencing and assembly of a D. suzukii line in Romania and argues the efficiency of long-read sequencing strategies.

The annotation of transposable elements (transposons) is a very dynamic field of genomics and various tools assigned to support this bioinformatics endeavor have been developed and described. Genome ARTIST v1.19 (GA_v1.19) software was conceived for mapping artificial transposons mobilized during insertional mutagenesis projects, but the new functions of GA_v2 qualify it as a tool for the mapping and annotation of natural transposons (NTs) in long reads, contigs and assembled genomes. The tabular export of mapping and annotation data for high-throughput data analysis, the generation of a list of flanking sequences around the coordinates of insertion or around the target site duplications and the computing of a consensus sequence for the flanking sequences are all key assets of GA_v2. Additionally, we developed a set of scripts that enable the user to annotate NTs, to harness annotations offered by FlyBase for Drosophila melanogaster genome, to convert sequence files from .fasta to .raw, and to extract junction query sequences essential for NTs mapping. Herein, we present the applicability of GA_v2 for a preliminary annotation of P-element and hobo class II NTs and copia retrotransposon in the genome of D. melanogaster strain Horezu_LaPeri (Horezu), Romania, which was sequenced with Nanopore technology in our laboratory. We used contigs assembled with Flye tool and a Q10 quality filter of the reads. Our results suggest that GA_v2 is a reliable autonomous tool able to perform mapping and annotation of NTs in genomes sequenced by long sequencing technology. GA_v2 is open-source software compatible with Linux, Mac OS and Windows and is available at GitHub repository and dedicated website.

Rapid evolution of long-read sequencing technologies requires accurate, fast and user-friendly genome assembly and scaffolding tools. In this article we present Digital Scaffolding (dScaff), a bioinformatics tool that performs scaffolding of de novo genome assemblies based on reference scaffolds or chromosomes. dScaff makes use of a series of bash and R scripts in order to create a minimal complete scaffold from a genome assembly, with future features to be implemented. Herein, we demonstrate the functionality of dScaff on a novel genome assembly pertaining to a recently sequenced local strain of Drosophila suzukii .

Multiplexed 16S rRNA gene sequencing using Oxford Nanopore Technologies frequently results in a significant proportion of reads being categorized as "unclassified" by the standard Dorado demultiplexer. We present a fully automated Bash-based pipeline designed to recover and accurately re-attribute these unclassified reads to their corresponding barcode. By implementing iterative sequence-based alignment via BLASTn and size-filtering constraints, our tool improves data utilization and taxonomic depth. Preliminary testing demonstrates a robust recovery of previously discarded sequences, providing a cost-effective solution for improving the resolution of microbiome studies.

Drosophila suzukii is a successful invasive insect species responsible for agricultural losses. The key to its prowess is the ability to swiftly adapt to new environments through various genetic mechanisms, including fast accommodation of mutations and gene expression fine-tuning. Piezo and nanchung (nan) genes are linked to circadian clock-related behaviors and, therefore, are expected to readily respond to stress stimuli. Herein, we compared the DNA sequences of Piezo, nan, and αTubulin at 67C, a highly conserved housekeeping gene, in ICDPP-ams-1, a Romanian local population of D. suzukii, and two well-annotated reference populations from the United States of America and Japan. Our results imply that short-term evolutionary accumulated single nucleotide and indel variants are overrepresented within introns, a propensity evaluated through the mutation accumulation tendency (MAT) original parameter. Piezo and nan gene expression under photoperiodicity changes challenges were assessed in a series of experiments on three groups of individuals from ICDPP-ams-1. We found that both genes are upregulated in females if their customary circadian rhythm is affected, a trend seemingly reverting if, after an initial perturbation, the circadian clock is reset to its initial timing. In conclusion, we found that both highly conserved and adaptability-related genes are rapidly evolving and that Piezo and nan have a fast functional reaction to circadian clock changes by modifying their gene expression profiles.