The Impact of Oxford Nanopore Technologies Based Methodologies on the Genome Sequencing and Assembly of Romanian Strains of <i>Drosophila suzukii</i>
Background: <i>Drosophila suzukii</i> 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 <i>D. suzukii</i> derived from Romanian local populations using excl...
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| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2024-12-01
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| Series: | Insects |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2075-4450/16/1/2 |
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| Summary: | Background: <i>Drosophila suzukii</i> 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 <i>D. suzukii</i> 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 <i>D. suzukii</i> line in Romania and argues the efficiency of long-read sequencing strategies. |
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| ISSN: | 2075-4450 |