The impact of Ty3-<it>gypsy </it>group LTR retrotransposons <it>Fatima </it>on B-genome specificity of polyploid wheats
<p>Abstract</p> <p>Background</p> <p>Transposable elements (TEs) are a rapidly evolving fraction of the eukaryotic genomes and the main contributors to genome plasticity and divergence. Recently, occupation of the A- and D-genomes of allopolyploid wheat by specific TE f...
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doaj-7fd02201cddb4e59bf1f0f5951e628492020-11-24T21:20:04ZengBMCBMC Plant Biology1471-22292011-06-011119910.1186/1471-2229-11-99The impact of Ty3-<it>gypsy </it>group LTR retrotransposons <it>Fatima </it>on B-genome specificity of polyploid wheatsHuneau CecileBelcram HarryShcherban Andrey BAdonina Irina GSergeeva Ekaterina MSalina Elena AChalhoub Boulos<p>Abstract</p> <p>Background</p> <p>Transposable elements (TEs) are a rapidly evolving fraction of the eukaryotic genomes and the main contributors to genome plasticity and divergence. Recently, occupation of the A- and D-genomes of allopolyploid wheat by specific TE families was demonstrated. Here, we investigated the impact of the well-represented family of <it>gypsy </it>LTR-retrotransposons, <it>Fatima</it>, on B-genome divergence of allopolyploid wheat using the fluorescent <it>in situ </it>hybridisation (FISH) method and phylogenetic analysis.</p> <p>Results</p> <p>FISH analysis of a BAC clone (BAC_2383A24) initially screened with Spelt1 repeats demonstrated its predominant localisation to chromosomes of the B-genome and its putative diploid progenitor <it>Aegilops speltoides </it>in hexaploid (genomic formula, BBAADD) and tetraploid (genomic formula, BBAA) wheats as well as their diploid progenitors. Analysis of the complete BAC_2383A24 nucleotide sequence (113 605 bp) demonstrated that it contains 55.6% TEs, 0.9% subtelomeric tandem repeats (Spelt1), and five genes. LTR retrotransposons are predominant, representing 50.7% of the total nucleotide sequence. Three elements of the <it>gypsy </it>LTR retrotransposon family <it>Fatima </it>make up 47.2% of all the LTR retrotransposons in this BAC. <it>In situ </it>hybridisation of the <it>Fatima</it>_2383A24-3 subclone suggests that individual representatives of the <it>Fatima </it>family contribute to the majority of the B-genome specific FISH pattern for BAC_2383A24. Phylogenetic analysis of various <it>Fatima </it>elements available from databases in combination with the data on their insertion dates demonstrated that the <it>Fatima </it>elements fall into several groups. One of these groups, containing <it>Fatima</it>_2383A24-3, is more specific to the B-genome and proliferated around 0.5-2.5 MYA, prior to allopolyploid wheat formation.</p> <p>Conclusion</p> <p>The B-genome specificity of the <it>gypsy</it>-like <it>Fatima</it>, as determined by FISH, is explained to a great degree by the appearance of a genome-specific element within this family for <it>Ae. speltoides</it>. Moreover, its proliferation mainly occurred in this diploid species before it entered into allopolyploidy.</p> <p>Most likely, this scenario of emergence and proliferation of the genome-specific variants of retroelements, mainly in the diploid species, is characteristic of the evolution of all three genomes of hexaploid wheat.</p> http://www.biomedcentral.com/1471-2229/11/99 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Huneau Cecile Belcram Harry Shcherban Andrey B Adonina Irina G Sergeeva Ekaterina M Salina Elena A Chalhoub Boulos |
spellingShingle |
Huneau Cecile Belcram Harry Shcherban Andrey B Adonina Irina G Sergeeva Ekaterina M Salina Elena A Chalhoub Boulos The impact of Ty3-<it>gypsy </it>group LTR retrotransposons <it>Fatima </it>on B-genome specificity of polyploid wheats BMC Plant Biology |
author_facet |
Huneau Cecile Belcram Harry Shcherban Andrey B Adonina Irina G Sergeeva Ekaterina M Salina Elena A Chalhoub Boulos |
author_sort |
Huneau Cecile |
title |
The impact of Ty3-<it>gypsy </it>group LTR retrotransposons <it>Fatima </it>on B-genome specificity of polyploid wheats |
title_short |
The impact of Ty3-<it>gypsy </it>group LTR retrotransposons <it>Fatima </it>on B-genome specificity of polyploid wheats |
title_full |
The impact of Ty3-<it>gypsy </it>group LTR retrotransposons <it>Fatima </it>on B-genome specificity of polyploid wheats |
title_fullStr |
The impact of Ty3-<it>gypsy </it>group LTR retrotransposons <it>Fatima </it>on B-genome specificity of polyploid wheats |
title_full_unstemmed |
The impact of Ty3-<it>gypsy </it>group LTR retrotransposons <it>Fatima </it>on B-genome specificity of polyploid wheats |
title_sort |
impact of ty3-<it>gypsy </it>group ltr retrotransposons <it>fatima </it>on b-genome specificity of polyploid wheats |
publisher |
BMC |
series |
BMC Plant Biology |
issn |
1471-2229 |
publishDate |
2011-06-01 |
description |
<p>Abstract</p> <p>Background</p> <p>Transposable elements (TEs) are a rapidly evolving fraction of the eukaryotic genomes and the main contributors to genome plasticity and divergence. Recently, occupation of the A- and D-genomes of allopolyploid wheat by specific TE families was demonstrated. Here, we investigated the impact of the well-represented family of <it>gypsy </it>LTR-retrotransposons, <it>Fatima</it>, on B-genome divergence of allopolyploid wheat using the fluorescent <it>in situ </it>hybridisation (FISH) method and phylogenetic analysis.</p> <p>Results</p> <p>FISH analysis of a BAC clone (BAC_2383A24) initially screened with Spelt1 repeats demonstrated its predominant localisation to chromosomes of the B-genome and its putative diploid progenitor <it>Aegilops speltoides </it>in hexaploid (genomic formula, BBAADD) and tetraploid (genomic formula, BBAA) wheats as well as their diploid progenitors. Analysis of the complete BAC_2383A24 nucleotide sequence (113 605 bp) demonstrated that it contains 55.6% TEs, 0.9% subtelomeric tandem repeats (Spelt1), and five genes. LTR retrotransposons are predominant, representing 50.7% of the total nucleotide sequence. Three elements of the <it>gypsy </it>LTR retrotransposon family <it>Fatima </it>make up 47.2% of all the LTR retrotransposons in this BAC. <it>In situ </it>hybridisation of the <it>Fatima</it>_2383A24-3 subclone suggests that individual representatives of the <it>Fatima </it>family contribute to the majority of the B-genome specific FISH pattern for BAC_2383A24. Phylogenetic analysis of various <it>Fatima </it>elements available from databases in combination with the data on their insertion dates demonstrated that the <it>Fatima </it>elements fall into several groups. One of these groups, containing <it>Fatima</it>_2383A24-3, is more specific to the B-genome and proliferated around 0.5-2.5 MYA, prior to allopolyploid wheat formation.</p> <p>Conclusion</p> <p>The B-genome specificity of the <it>gypsy</it>-like <it>Fatima</it>, as determined by FISH, is explained to a great degree by the appearance of a genome-specific element within this family for <it>Ae. speltoides</it>. Moreover, its proliferation mainly occurred in this diploid species before it entered into allopolyploidy.</p> <p>Most likely, this scenario of emergence and proliferation of the genome-specific variants of retroelements, mainly in the diploid species, is characteristic of the evolution of all three genomes of hexaploid wheat.</p> |
url |
http://www.biomedcentral.com/1471-2229/11/99 |
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