The Landscape of the DNA Transposons in the Genome of the Horezu_LaPeri Strain of <i>Drosophila melanogaster</i>
Natural transposons (NTs) represent mobile DNA sequences found in both prokaryotic and eukaryotic genomes. <i>Drosophila melanogaster</i> (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...
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MDPI AG
2023-05-01
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| Series: | Insects |
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| Online Access: | https://www.mdpi.com/2075-4450/14/6/494 |
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| author | Alexandru Marian Bologa Ileana Stoica Nicoleta Denisa Constantin Alexandru Al. Ecovoiu |
| author_facet | Alexandru Marian Bologa Ileana Stoica Nicoleta Denisa Constantin Alexandru Al. Ecovoiu |
| author_sort | Alexandru Marian Bologa |
| collection | DOAJ |
| description | Natural transposons (NTs) represent mobile DNA sequences found in both prokaryotic and eukaryotic genomes. <i>Drosophila melanogaster</i> (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. |
| first_indexed | 2024-03-11T02:19:11Z |
| format | Article |
| id | doaj.art-382dde395e73414192a1aec247dd57a9 |
| institution | Directory Open Access Journal |
| issn | 2075-4450 |
| language | English |
| last_indexed | 2024-03-11T02:19:11Z |
| publishDate | 2023-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Insects |
| spelling | doaj.art-382dde395e73414192a1aec247dd57a92023-11-18T10:55:37ZengMDPI AGInsects2075-44502023-05-0114649410.3390/insects14060494The Landscape of the DNA Transposons in the Genome of the Horezu_LaPeri Strain of <i>Drosophila melanogaster</i>Alexandru Marian Bologa0Ileana Stoica1Nicoleta Denisa Constantin2Alexandru Al. Ecovoiu3Department of Genetics, Faculty of Biology, University of Bucharest, 060101 Bucharest, RomaniaDepartment of Genetics, Faculty of Biology, University of Bucharest, 060101 Bucharest, RomaniaDepartment of Genetics, Faculty of Biology, University of Bucharest, 060101 Bucharest, RomaniaDepartment of Genetics, Faculty of Biology, University of Bucharest, 060101 Bucharest, RomaniaNatural transposons (NTs) represent mobile DNA sequences found in both prokaryotic and eukaryotic genomes. <i>Drosophila melanogaster</i> (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.https://www.mdpi.com/2075-4450/14/6/494transposable elementsDNA natural transposons<i>Drosophila melanogaster</i>P-elementheterochromatinbioinformatics |
| spellingShingle | Alexandru Marian Bologa Ileana Stoica Nicoleta Denisa Constantin Alexandru Al. Ecovoiu The Landscape of the DNA Transposons in the Genome of the Horezu_LaPeri Strain of <i>Drosophila melanogaster</i> Insects transposable elements DNA natural transposons <i>Drosophila melanogaster</i> P-element heterochromatin bioinformatics |
| title | The Landscape of the DNA Transposons in the Genome of the Horezu_LaPeri Strain of <i>Drosophila melanogaster</i> |
| title_full | The Landscape of the DNA Transposons in the Genome of the Horezu_LaPeri Strain of <i>Drosophila melanogaster</i> |
| title_fullStr | The Landscape of the DNA Transposons in the Genome of the Horezu_LaPeri Strain of <i>Drosophila melanogaster</i> |
| title_full_unstemmed | The Landscape of the DNA Transposons in the Genome of the Horezu_LaPeri Strain of <i>Drosophila melanogaster</i> |
| title_short | The Landscape of the DNA Transposons in the Genome of the Horezu_LaPeri Strain of <i>Drosophila melanogaster</i> |
| title_sort | landscape of the dna transposons in the genome of the horezu laperi strain of i drosophila melanogaster i |
| topic | transposable elements DNA natural transposons <i>Drosophila melanogaster</i> P-element heterochromatin bioinformatics |
| url | https://www.mdpi.com/2075-4450/14/6/494 |
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