Background: 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 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 line in Romania and argues the efficiency of long-read sequencing strategies.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.3390/insects16010002 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Enhancing public health outcomes with AI-powered clinical surveillance: Precise detection of COVID-19 variants using qPCR and nanopore sequencing.
J Infect Public Health
January 2025
Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan. Electronic address:
Background: We aimed to evaluate the efficacy of integrating the Varia5 multiplex assay (qPCR) and whole genome sequencing (WGS) for monitoring SARS-CoV-2, focusing on their overall performance in identifying various virus variants.
Methods: This study included 140 naso-pharyngeal swab samples from individuals with suspected COVID-19. We utilized our self-developed Varia5 multiplex assay, which targets five viral genes linked to COVID-19 mutations, in conjunction with comprehensive genomic analysis performed through whole genome sequencing (WGS) using the Oxford Nanopore system.
High-Throughput Oxford Nanopore Sequencing Unveils Complex Viral Population in Kansas Wheat: Implications for Sustainable Virus Management.
Viruses
January 2025
Department of Plant Pathology, Throckmorton Plant Science Center, Kansas State University, Manhattan, KS 66506, USA.
Wheat viruses are major yield-reducing factors, with mixed infections causing substantial economic losses. Determining field virus populations is crucial for effective management and developing virus-resistant cultivars. This study utilized the high-throughput Oxford Nanopore sequencing technique (ONT) to characterize wheat viral populations in major wheat-growing counties of Kansas from 2019 to 2021.
View Article and Find Full Text PDFDynamic Roles of RNA and RNA Epigenetics in HTLV-1 Biology.
Viruses
January 2025
Center for Retrovirus Research, Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA.
Since the discovery of RNA in the early 1900s, scientific understanding of RNA form and function has evolved beyond protein coding. Viruses, particularly retroviruses like human T-cell leukemia virus type 1 (HTLV-1), rely heavily on RNA and RNA post-transcriptional modifications to regulate the viral lifecycle, pathogenesis, and evasion of host immune responses. With the emergence of new sequencing technologies in the last decade, our ability to dissect the intricacies of RNA has flourished.
View Article and Find Full Text PDFThe Impact of Oxford Nanopore Technologies Based Methodologies on the Genome Sequencing and Assembly of Romanian Strains of .
Insects
December 2024
Drosophila Laboratory, Department of Genetics, Faculty of Biology, University of Bucharest, 060101 Bucharest, Romania.
Background: 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 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.
Gene Expression Profiles Reveal Distinct Mechanisms Driving Chronic Obstructive Pulmonary Disease Exacerbations.
Int J Mol Sci
January 2025
Hospital General Universitario de Elche-FISABIO, 03203 Elche, Spain.
Chronic obstructive pulmonary disease (COPD) exacerbations are major contributors to morbidity and mortality, highlighting the need to better understand their molecular mechanisms to improve prevention, diagnosis, and treatment. This study investigated differential gene expression profiles and key biological processes in COPD exacerbations categorized based on sputum microbiome profiling. An observational study was performed on a cohort of 16 COPD patients, who provided blood and sputum samples during exacerbations, along with five stable-state samples as controls.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!