ArticleBMC genomics2016
Exploration of the Drosophila buzzatii transposable element content suggests underestimation of repeats in Drosophila genomes.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Sex-biased Expression of Genes and Transposable Elements in Hybrids from Drosophila mojavensis and Drosophila arizonae.Genome biology and evolution · 2026Article
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- Nebulous without white: annotated long-read genome assembly and CRISPR/Cas9 genome engineering in Drosophila nebulosa.G3 (Bethesda, Md.) · 2022Article
- Species-specific chromatin landscape determines how transposable elements shape genome evolution.eLife · 2022Article
- Transposable Element Expression and Regulation Profile in Gonads of Interspecific Hybrids ofCells · 2021Article
- The Worldwide Invasion of Drosophila suzukii Is Accompanied by a Large Increase of Transposable Element Load and a Small Number of Putatively Adaptive Insertions.Molecular biology and evolution · 2021Article
- Structure, Organization, and Evolution of Satellite DNAs: Insights from the Drosophila repleta and D. virilis Species Groups.Progress in molecular and subcellular biology · 2021Article
- Transposable elements inMobile DNA · 2020Review
- The mobilome of Drosophila incompta, a flower-breeding species: comparison of transposable element landscapes among generalist and specialist flies.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2019Article
- Genomic changes associated with adaptation to arid environments in cactophilic Drosophila species.BMC genomics · 2019Article
- Concurrent Duplication of Drosophila Cid and Cenp-C Genes Resulted in Accelerated Evolution and Male Germline-Biased Expression of the New Copies.Journal of molecular evolution · 2018Article
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- Dissecting the Satellite DNA Landscape in Three CactophilicG3 (Bethesda, Md.) · 2017Article
- Transposable Element Misregulation Is Linked to the Divergence between Parental piRNA Pathways in Drosophila Hybrids.Genome biology and evolution · 2017Article
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- Non-canonical Helitrons inMobile DNA · 2016Article
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6 authors.
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Abstract
backgroundMany new Drosophila genomes have been sequenced in recent years using new-generation sequencing platforms and assembly methods. Transposable elements (TEs), being repetitive sequences, are often misassembled, especially in the genomes sequenced with short reads. Consequently, the mobile fraction of many of the new genomes has not been analyzed in detail or compared with that of other genomes sequenced with different methods, which could shed light into the understanding of genome and TE evolution. Here we compare the TE content of three genomes: D. buzzatii st-1, j-19, and D. mojavensis.
resultsWe have sequenced a new D. buzzatii genome (j-19) that complements the D. buzzatii reference genome (st-1) already published, and compared their TE contents with that of D. mojavensis. We found an underestimation of TE sequences in Drosophila genus NGS-genomes when compared to Sanger-genomes. To be able to compare genomes sequenced with different technologies, we developed a coverage-based method and applied it to the D. buzzatii st-1 and j-19 genome. Between 10.85 and 11.16 % of the D. buzzatii st-1 genome is made up of TEs, between 7 and 7,5 % of D. buzzatii j-19 genome, while TEs represent 15.35 % of the D. mojavensis genome. Helitrons are the most abundant order in the three genomes.
conclusionsTEs in D. buzzatii are less abundant than in D. mojavensis, as expected according to the genome size and TE content positive correlation. However, TEs alone do not explain the genome size difference. TEs accumulate in the dot chromosomes and proximal regions of D. buzzatii and D. mojavensis chromosomes. We also report a significantly higher TE density in D. buzzatii and D. mojavensis X chromosomes, which is not expected under the current models. Our easy-to-use correction method allowed us to identify recently active families in D. buzzatii st-1 belonging to the LTR-retrotransposon superfamily Gypsy.
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