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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MDPI AG
2024-12-01
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| Series: | Insects |
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| Online Access: | https://www.mdpi.com/2075-4450/16/1/2 |
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| author | Attila Cristian Ratiu Adrian Ionascu Nicoleta Denisa Constantin |
| author_facet | Attila Cristian Ratiu Adrian Ionascu Nicoleta Denisa Constantin |
| author_sort | Attila Cristian Ratiu |
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| description | 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. |
| format | Article |
| id | doaj-art-490d6fbb9b7f44b68af2128e0ce4a668 |
| institution | Kabale University |
| issn | 2075-4450 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Insects |
| spelling | doaj-art-490d6fbb9b7f44b68af2128e0ce4a6682025-01-24T13:35:32ZengMDPI AGInsects2075-44502024-12-01161210.3390/insects16010002The Impact of Oxford Nanopore Technologies Based Methodologies on the Genome Sequencing and Assembly of Romanian Strains of <i>Drosophila suzukii</i>Attila Cristian Ratiu0Adrian Ionascu1Nicoleta Denisa Constantin2<i>Drosophila</i> Laboratory, Department of Genetics, Faculty of Biology, University of Bucharest, 060101 Bucharest, Romania<i>Drosophila</i> Laboratory, Department of Genetics, Faculty of Biology, University of Bucharest, 060101 Bucharest, Romania<i>Drosophila</i> Laboratory, Department of Genetics, Faculty of Biology, University of Bucharest, 060101 Bucharest, RomaniaBackground: <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.https://www.mdpi.com/2075-4450/16/1/2<i>Drosophila suzukii</i>ONT sequencinggenome assemblygenome scaffoldingnatural population |
| spellingShingle | Attila Cristian Ratiu Adrian Ionascu Nicoleta Denisa Constantin The Impact of Oxford Nanopore Technologies Based Methodologies on the Genome Sequencing and Assembly of Romanian Strains of <i>Drosophila suzukii</i> Insects <i>Drosophila suzukii</i> ONT sequencing genome assembly genome scaffolding natural population |
| title | The Impact of Oxford Nanopore Technologies Based Methodologies on the Genome Sequencing and Assembly of Romanian Strains of <i>Drosophila suzukii</i> |
| title_full | The Impact of Oxford Nanopore Technologies Based Methodologies on the Genome Sequencing and Assembly of Romanian Strains of <i>Drosophila suzukii</i> |
| title_fullStr | The Impact of Oxford Nanopore Technologies Based Methodologies on the Genome Sequencing and Assembly of Romanian Strains of <i>Drosophila suzukii</i> |
| title_full_unstemmed | The Impact of Oxford Nanopore Technologies Based Methodologies on the Genome Sequencing and Assembly of Romanian Strains of <i>Drosophila suzukii</i> |
| title_short | The Impact of Oxford Nanopore Technologies Based Methodologies on the Genome Sequencing and Assembly of Romanian Strains of <i>Drosophila suzukii</i> |
| title_sort | impact of oxford nanopore technologies based methodologies on the genome sequencing and assembly of romanian strains of i drosophila suzukii i |
| topic | <i>Drosophila suzukii</i> ONT sequencing genome assembly genome scaffolding natural population |
| url | https://www.mdpi.com/2075-4450/16/1/2 |
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