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In silico Phylogenetic Analysis of hAT Transposable Elements in Plants

1
Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir 35340, Turkey
2
Izmir International Biomedicine and Genome Center (IBG), Izmir 35340, Turkey
*
Author to whom correspondence should be addressed.
Genes 2018, 9(6), 284; https://doi.org/10.3390/genes9060284
Received: 27 March 2018 / Revised: 16 May 2018 / Accepted: 4 June 2018 / Published: 6 June 2018
(This article belongs to the Special Issue DNA Damage Responses in Plants)
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Abstract

Transposable elements of the hAT family exhibit a cross-kingdom distribution. The plant hAT transposons are proposed to play a critical role in plant adaptive evolution and DNA damage repair. The sequencing of an increasing number of plant genomes has facilitated the discovery of a plethora of hAT elements. This enabled us to perform an in-depth phylogenetic analysis of consensus hAT sequences in the fully-sequenced genomes of 11 plant species that represent diverse taxonomic divisions. Four putative nucleotide sequences were detected in cottonwood that were similar to the corresponding animal hAT elements, which are possibly sequence artifacts. Phylogenetic trees were constructed based both on the known and putative hAT sequences, by employing two different methods of phylogenetic inference. On the basis of the reconstructed phylogeny, plant hAT elements have rather evolved through kingdom-specific vertical gene transfer and gene amplifications within eudicotyledons, monocotyledons, and chlorophytes. Furthermore, the plant hAT sequences were searched for conserved DNA and amino acid sequence features. In this way, diagnostic sequence patterns were detected which allowed us to assign functional annotations to the plant hAT sequences. View Full-Text
Keywords: hAT transposable elements; plants; phylogeny; terminal inverted repeats; transposase hAT transposable elements; plants; phylogeny; terminal inverted repeats; transposase
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Karakülah, G.; Pavlopoulou, A. In silico Phylogenetic Analysis of hAT Transposable Elements in Plants. Genes 2018, 9, 284.

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