hAT transposable elements and their derivatives: an analysis in the 12 Drosophila genomes

Ortiz, Mauro de Freitas; Lorenzatto, Karina Rodrigues; Corrêa, Bruna; Loreto, Élgion Lúcio Silva

doi:10.1007/s10709-010-9439-y

Cited by 13 publications

(10 citation statements)

References 34 publications

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“…They are short sequences with no coding capacity and conserved TIRs that often reach high copy numbers in the genomes and are found within or near genes (Feschotte and Pritham 2007). They were first discovered in plants (Bureau and Wessler 1992) but are also found in several animal genomes, including Drosophila (Holyoake and Kidwell 2003; Ortiz et al 2010; Dias and Carareto 2011; Deprá et al 2012; Rius et al 2013). The origin of some MITE families is unclear.…”

Section: Introductionmentioning

confidence: 99%

BuT2 Is a Member of the Third Major Group of hAT Transposons and Is Involved in Horizontal Transfer Events in the Genus Drosophila

Rossato

Ludwig

Deprá

et al. 2014

Genome Biology and Evolution

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The hAT superfamily comprises a large and diverse array of DNA transposons found in all supergroups of eukaryotes. Here we characterized the Drosophila buzzatii BuT2 element and found that it harbors a five-exon gene encoding a 643-aa putatively functional transposase. A phylogeny built with 85 hAT transposases yielded, in addition to the two major groups already described, Ac and Buster, a third one comprising 20 sequences that includes BuT2, Tip100, hAT-4_BM, and RP-hAT1. This third group is here named Tip. In addition, we studied the phylogenetic distribution and evolution of BuT2 by in silico searches and molecular approaches. Our data revealed BuT2 was, most often, vertically transmitted during the evolution of genus Drosophila being lost independently in several species. Nevertheless, we propose the occurrence of three horizontal transfer events to explain its distribution and conservation among species. Another aspect of BuT2 evolution and life cycle is the presence of short related sequences, which contain similar 5′ and 3′ regions, including the terminal inverted repeats. These sequences that can be considered as miniature inverted repeat transposable elements probably originated by internal deletion of complete copies and show evidences of recent mobilization.

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Section: Introductionmentioning

confidence: 99%

BuT2 Is a Member of the Third Major Group of hAT Transposons and Is Involved in Horizontal Transfer Events in the Genus Drosophila

Rossato

Ludwig

Deprá

et al. 2014

Genome Biology and Evolution

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“…The analysis of the target site of 28 hAT elements, including derivatives, in 12 Drosophila species revealed a target site specificity requiring the nucleotide residues T and A at positions 2 and 7, respectively (de Freitas et al 2010). This strong specificity of nucleotide positions could not be observed in the sequence logo generated from the TSD of 84 BvhAT and BvhATpin transposons.…”

Section: Discussionmentioning

confidence: 93%

Survey of sugar beet (Beta vulgaris L.) hAT transposons and MITE-like hATpin derivatives

et al. 2012

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Genome-wide analyses of repetitive DNA suggest a significant impact particularly of transposable elements on genome size and evolution of virtually all eukaryotic organisms. In this study, we analyzed the abundance and diversity of the hAT transposon superfamily of the sugar beet (B. vulgaris) genome, using molecular, bioinformatic and cytogenetic approaches. We identified 81 transposase-coding sequences, three of which are part of structurally intact but nonfunctional hAT transposons (BvhAT), in a B. vulgaris BAC library as well as in whole genome sequencing-derived data sets. Additionally, 116 complete and 497 truncated non-autonomous BvhAT derivatives lacking the transposase gene were in silico-detected. The 116 complete derivatives were subdivided into four BvhATpin groups each characterized by a distinct terminal inverted repeat motif. Both BvhAT and BvhATpin transposons are specific for species of the genus Beta and closely related species, showing a localization on B. vulgaris chromosomes predominantely in euchromatic regions. The lack of any BvhAT transposase function together with the high degree of degeneration observed for the BvhAT and the BvhATpin genomic fraction contrasts with the abundance and activity of autonomous and non-autonomous hAT transposons revealed in other plant species. This indicates a possible genus-specific structural and functional repression of the hAT transposon superfamily during Beta diversification and evolution.

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“…Phylogenetic studies showed related elements forming a monophyletic group composed of hAT2_AG and Herves from A. gambiae , hAT-1_Dsi (Drosophila simulans , Drosophila sechellia , Drosophila melanogaster , Drosophila mauritiana and Zaprionus indianus ; this element was also called hosimary by Deprá et al ., (2010)), homo2 (Drosophila mojavensis ), howilli1 (Drosophila willistoni ) and hAT-1DP (Drosophila persimilis and Drosophila pseudoobscura ) (de Freitas Ortiz and Loreto, 2009;Deprá et al ., 2010;de Freitas Ortiz et al ., 2010;Arensburger et al ., 2011). This group will be referred to herein as the Herves -like elements.…”

Section: Introductionmentioning

confidence: 99%

“…The MnRs in the 3′ subterminal region consist of 28 nucleotides. The same array of minisatellites is present in two related hAT elements: hAT1-Dp of D. pseudoobscura and hopers1 of D. persimilis (de Freitas Ortiz et al ., 2010). However, the transposase sequence of the Herves -like TEs present in D. willistoni , D. pseudoobscura and D. persimilis show a general divergence of 0.28, whereas the 5′ MnRs are highly conserved, showing divergence of 0.05.…”

Section: Introductionmentioning

confidence: 99%

Characterization of Herves‐like transposable elements (hATs) in Drosophila species and their evolutionary scenario

Bernardo

Mombach

Loreto

2019

Insect Molecular Biology

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A monophyletic group of Drosophila hAT transposable elements, referred to as Herves‐like, was characterized and found to be present in 46% of 57 screened Drosophila species. A remarkable characteristic of these elements is the presence of a long array of minisatellite repeats (MnRs) in both subterminal extremities of the elements. The copy number of these minisatellites was highly variable between and within populations. Twenty‐three strains of Drosophila willistoni, covering its geographic distribution, were screened for polymorphism in the copy number of 5′ MnRs, showing a variation from 7 to 20 repeat copies. These MnRs are well conserved among Drosophila species and probably function as transposase binding sequences, as provided by short subterminal repeats in other hAT elements. Miniature inverted repeat transposable elements were found in 27% of species carrying Herves‐like elements. Phylogenetic analysis showed incongruences between transposable elements and species phylogenies, suggesting that at least four horizontal transfer events have occurred.

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hAT transposable elements and their derivatives: an analysis in the 12 Drosophila genomes

Cited by 13 publications

References 34 publications

BuT2 Is a Member of the Third Major Group of hAT Transposons and Is Involved in Horizontal Transfer Events in the Genus Drosophila

BuT2 Is a Member of the Third Major Group of hAT Transposons and Is Involved in Horizontal Transfer Events in the Genus Drosophila

Survey of sugar beet (Beta vulgaris L.) hAT transposons and MITE-like hATpin derivatives

Characterization of Herves‐like transposable elements (hATs) in Drosophila species and their evolutionary scenario

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