Genome ARTIST_v2—An Autonomous Bioinformatics Tool for Annotation of Natural Transposons in Sequenced Genomes

Ecovoiu, Alexandru Al.; Bologa, Alexandru Marian; Chifiriuc, David Ioan Mihail; Ciuca, Andrei Mihai; Constantin, Nicoleta; Ghionoiu, Iulian Constantin; Ghita, Iulian Cristian; Rațiu, Attila Cristian

doi:10.3390/ijms232012686

Cited by 2 publications

(9 citation statements)

References 22 publications

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“…GA_v2 runs with bash scripts that allow for the extraction of TIRs from contigs along with their flanking sequence (the sequence in the immediate vicinity of the transposon), which is elemental for the mapping of each NT. We collected 3000 nucleotides long flanking sequences using parameters described elsewhere [ 21 ]. The extracted sequences are represented as Junction Queries (JQs) because they represent genome–transposon junctions and were used as queries in WF2 from GA_v2.…”

Section: Resultsmentioning

confidence: 99%

“…Only the insertions with TSDs ( Supplementary Table S3 ) were PCR checked, and the obtained amplicons were migrated in agarose gel ( Supplementary Figure S1 ). Some of the tested insertions were identified using the Canu assembly analyzed in this paper, while three other P-element insertions (in Ac13E , in retn and near stv ) with identical TSDs were identified in alternative assemblies described elsewhere [ 21 , 24 ]. The PCR primers are specific to the sequences that flank the insertions of the P elements ( Supplementary Table S1 ) and together with the MM11 primer (specific for TIRs of the P-element) were used to amplify the genome–transposon junction, thus testing the presence of the insertions.…”

Section: Resultsmentioning

confidence: 99%

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The Landscape of the DNA Transposons in the Genome of the Horezu_LaPeri Strain of Drosophila melanogaster

Bologa

Stoica

Constantin

et al. 2023

Insects

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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 Horezul_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 Horezul_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.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

The Landscape of the DNA Transposons in the Genome of the Horezu_LaPeri Strain of Drosophila melanogaster

Bologa

Stoica

Constantin

et al. 2023

Insects

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“…The comparative analysis considered the evaluation of the total content in NTs with RepeatMasker version 4.1.2 (relying on rmblastn version 2.10.0+ and CONS-Dfam_withRBRM_3.3) [ 19 ]. We also mapped mdg1 retroelement (an LTR transposon from the Gypsy group) in these assemblies using Genome ARTIST (GA_v2) software [ 20 ].…”

Section: Resultsmentioning

confidence: 99%

“…In order to test this assumption, we considered mdg1 retroelement, since it is potentially active and may occur as full-length copies in the genome of D. melanogaster [ 22 , 23 ]. The mapping was performed with GA_v2 tool, using a strategy described elsewhere [ 20 ]. The majority of mdg1 insertions were mapped at nucleotide level relative to the D. melanogaster reference genome (r6.48), either in intergenic regions or in specific genes ( Tables S3–S7 ).…”

Section: Resultsmentioning

confidence: 99%

“…The program was run using the alignment application rmblastn version 2.10.0+ and NTs consensus database Dfam 3.3. To identify and analyze the insertions of mdg1 retroelement in the D. melanogaster Horezu genotype, we used Genome ARTIST (GA) v2 software (accessed on 01 November 2022) [ 20 ]. Genome sequencing, preprocessing and data analysis were performed in the Drosophila laboratory of the Department of Genetics, Faculty of Biology, University of Bucharest.…”

Section: Methodsmentioning

confidence: 99%

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ONT-Based Alternative Assemblies Impact on the Annotations of Unique versus Repetitive Features in the Genome of a Romanian Strain of Drosophila melanogaster

Bologa

Stoica

Rațiu

et al. 2022

IJMS

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To date, different strategies of whole-genome sequencing (WGS) have been developed in order to understand the genome structure and functions. However, the analysis of genomic sequences obtained from natural populations is challenging and the biological interpretation of sequencing data remains the main issue. The MinION device developed by Oxford Nanopore Technologies (ONT) is able to generate long reads with minimal costs and time requirements. These valuable assets qualify it as a suitable method for performing WGS, especially in small laboratories. The long reads resulted using this sequencing approach can cover large structural variants and repetitive sequences commonly present in the genomes of eukaryotes. Using MinION, we performed two WGS assessments of a Romanian local strain of Drosophila melanogaster, referred to as Horezu_LaPeri (Horezu). In total, 1,317,857 reads with a size of 8.9 gigabytes (Gb) were generated. Canu and Flye de novo assembly tools were employed to obtain four distinct assemblies with both unfiltered and filtered reads, achieving maximum reference genome coverages of 94.8% (Canu) and 91.4% (Flye). In order to test the quality of these assemblies, we performed a two-step evaluation. Firstly, we considered the BUSCO scores and inquired for a supplemental set of genes using BLAST. Subsequently, we appraised the total content of natural transposons (NTs) relative to the reference genome (ISO1 strain) and mapped the mdg1 retroelement as a resolution assayer. Our results reveal that filtered data provide only slightly enhanced results when considering genes identification, but the use of unfiltered data had a consistent positive impact on the global evaluation of the NTs content. Our comparative studies also revealed differences between Flye and Canu assemblies regarding the annotation of unique versus repetitive genomic features. In our hands, Flye proved to be moderately better for gene identification, while Canu clearly outperformed Flye for NTs analysis. Data concerning the NTs content were compared to those obtained with ONT for the D. melanogaster ISO1 strain, revealing that our strategy conducted better results. Additionally, the parameters of our ONT reads and assemblies are similar to those reported for ONT experiments performed on various model organisms, revealing that our assembly data are appropriate for a proficient annotation of the Horezu genome.

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Genome ARTIST_v2—An Autonomous Bioinformatics Tool for Annotation of Natural Transposons in Sequenced Genomes

Cited by 2 publications

References 22 publications

The Landscape of the DNA Transposons in the Genome of the Horezu_LaPeri Strain of Drosophila melanogaster

The Landscape of the DNA Transposons in the Genome of the Horezu_LaPeri Strain of Drosophila melanogaster

ONT-Based Alternative Assemblies Impact on the Annotations of Unique versus Repetitive Features in the Genome of a Romanian Strain of Drosophila melanogaster

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