The impact of Ty3-gypsy group LTR retrotransposons Fatima on B-genome specificity of polyploid wheats

Abstract

BackgroundTransposable 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.ResultsFISH 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.ConclusionThe B-genome specificity of the gypsy-like Fatima, as determined by FISH, is explained to a great degree by the appearance of a genome-specific element within this family for Ae. speltoides. Moreover, its proliferation mainly occurred in this diploid species before it entered into allopolyploidy.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.

Major repeat components covering one‐third of the ginseng (Panax ginseng C.A. Meyer) genome and evidence for allotetraploidy

“…(Suoniemi et al, 1996;Vicient et al, 1999), wheat (Charles et al, 2008;Salina et al, 2011) and pepper (Park et al, 2011(Park et al, , 2012b, have reported that the genomes expanded and were rearranged by accumulation of LTR-RTs. Our results suggest that LTR-RTs are also the main players in the enlargement and evolution of the ginseng genome.…”

“…This may be representative of heterochromatin structure adjacent to genic regions of the ginseng genome. The accumulation of LTR-RTs around genic regions has been reported in maize (SanMiguel et al, 1998;Kronmiller and Wise, 2009), wheat (Wicker et al, 2001;Salina et al, 2011), barley (Wicker et al, 2005) and pepper (Park et al, 2011(Park et al, , 2012b. In the pepper genome, accumulation of the Ty3/Gypsy elements such as Tat and Athila-like subgroups has resulted in expansion of euchromatic regions by random insertion (Park et al, 2011), while the Del-like subgroup has accumulated in constitutive heterochromatic regions such as pericentromeric regions (Park et al, 2012b).…”

“…Subgenome-specific or subgenome-differential proliferation of transposable elements has been reported in Brassica , cotton (Zhao et al, 1998;Hanson et al, 2000), Oryza (Ammiraju et al, 2008) and wheat (Sabot et al, 2006;Salina et al, 2011). Further inspection of ginseng and related species with PgDel2 and/or other chromosome-specific elements will help authenticate and clarify the origins of the subgenomes, as well as elucidate the evolutionary relationships among Panax species.…”

Genotype- and Cell-Specific Dynamics of Tandem Repeat Patterns in <b><i>Aegilops speltoides</i></b> Tausch (Poaceae, Triticeae)

“…6 B, C). Other kinds of repetitive DNA, such as pSc119.2 [Badaeva et al, 1996;Molnár et al, 2014;present study] and different types of transposable elements [Raskina et al, 2004a[Raskina et al, , b, 2008Salina et al, 2009Salina et al, , 2011, could be the targets for nonhomologous/illegitimate recombination in virtually any area of the chromatin.…”

A Glimpse of Panax ginseng Genome Structure Revealed from Ten BAC Clone Sequences Obtained by SMRT Sequencing Platform

“…The subgenome-specific LTR-RTs distribution was also discovered in other plants such as allopolyploid wheat (Sabot et al 2006;Salina et al 2011). In this study, we found another clue for allopolyploidization event in the ginseng genome.…”