The impact of Ty3-gypsy group LTR retrotransposons ... - URGV - Inra

Abstract
Background
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 gypsy LTR-retrotransposons,
Fatima, on B-genome divergence of allopolyploid wheat using the fluorescent in situ
hybridisation (FISH) method and phylogenetic analysis.
Results
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 Aegilops speltoides 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
gypsy LTR retrotransposon family Fatima make up 47.2% of all the LTR retrotransposons in
this BAC. In situ hybridisation of the Fatima_2383A24-3 subclone suggests that individual
representatives of the Fatima family contribute to the majority of the B-genome specific FISH
pattern for BAC_2383A24. Phylogenetic analysis of various Fatima elements available from
databases in combination with the data on their insertion dates demonstrated that the Fatima
elements fall into several groups. One of these groups, containing Fatima_2383A24-3, is
more specific to the B-genome and proliferated around 0.5–2.5 MYA, prior to allopolyploid
wheat formation.
Conclusion