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The impact of Ty3-gypsy group LTR retrotransposons Fatima on B-genome specificity of polyploid wheats.
BMC Plant Biol. 2011 Jun 03; 11:99.BP

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

The 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.

Authors+Show Affiliations

Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Lavrentieva ave, 10, Novosibirsk, 630090, Russia. salina@bionet.nsc.ruNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

21635794

Citation

Salina, Elena A., et al. "The Impact of Ty3-gypsy Group LTR Retrotransposons Fatima On B-genome Specificity of Polyploid Wheats." BMC Plant Biology, vol. 11, 2011, p. 99.
Salina EA, Sergeeva EM, Adonina IG, et al. The impact of Ty3-gypsy group LTR retrotransposons Fatima on B-genome specificity of polyploid wheats. BMC Plant Biol. 2011;11:99.
Salina, E. A., Sergeeva, E. M., Adonina, I. G., Shcherban, A. B., Belcram, H., Huneau, C., & Chalhoub, B. (2011). The impact of Ty3-gypsy group LTR retrotransposons Fatima on B-genome specificity of polyploid wheats. BMC Plant Biology, 11, 99. https://doi.org/10.1186/1471-2229-11-99
Salina EA, et al. The Impact of Ty3-gypsy Group LTR Retrotransposons Fatima On B-genome Specificity of Polyploid Wheats. BMC Plant Biol. 2011 Jun 3;11:99. PubMed PMID: 21635794.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - The impact of Ty3-gypsy group LTR retrotransposons Fatima on B-genome specificity of polyploid wheats. AU - Salina,Elena A, AU - Sergeeva,Ekaterina M, AU - Adonina,Irina G, AU - Shcherban,Andrey B, AU - Belcram,Harry, AU - Huneau,Cecile, AU - Chalhoub,Boulos, Y1 - 2011/06/03/ PY - 2010/10/20/received PY - 2011/06/03/accepted PY - 2011/6/4/entrez PY - 2011/6/4/pubmed PY - 2011/10/1/medline SP - 99 EP - 99 JF - BMC plant biology JO - BMC Plant Biol. VL - 11 N2 - 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: The 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. SN - 1471-2229 UR - https://www.unboundmedicine.com/medline/citation/21635794/The_impact_of_Ty3_gypsy_group_LTR_retrotransposons_Fatima_on_B_genome_specificity_of_polyploid_wheats_ L2 - https://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-11-99 DB - PRIME DP - Unbound Medicine ER -