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Different histories of two highly variable LTR retrotransposons in sunflower species.
Gene 2017; 634:5-14GENE

Abstract

In the Helianthus genus, very large intra- and interspecific variability related to two specific retrotransposons of Helianthus annuus (Helicopia and SURE) exists. When comparing these two sequences to sunflower sequence databases recently produced by our lab, the Helicopia family was shown to belong to the Maximus/SIRE lineage of the Sirevirus genus of the Copia superfamily, whereas the SURE element (whose superfamily was not even previously identified) was classified as a Gypsy element of the Ogre/Tat lineage of the Metavirus genus. Bioinformatic analysis of the two retrotransposon families revealed their genomic abundance and relative proliferation timing. The genomic abundance of these families differed significantly among 12 Helianthus species. The ratio between the abundance of long terminal repeats and their reverse transcriptases suggested that the SURE family has relatively more solo long terminal repeats than does Helicopia. Pairwise comparisons of Illumina reads encoding the reverse transcriptase domain indicated that SURE amplification may have occurred more recently than that of Helicopia. Finally, the analysis of population structure based on the SURE and Helicopia polymorphisms of 32 Helianthus species evidenced two subpopulations, which roughly corresponded to species of the Helianthus and Divaricati/Ciliares sections. However, a number of species showed an admixed structure, confirming the importance of interspecific hybridisation in the evolution of this genus. In general, these two retrotransposon families differentially contributed to interspecific variability, emphasising the need to refer to specific families when studying genome evolution.

Authors+Show Affiliations

Dept. of Agriculture, Food, and Environment, University of Pisa, Via delBorghetto 80, I-56124 Pisa, Italy.Dept. of Agriculture, Food, and Environment, University of Pisa, Via delBorghetto 80, I-56124 Pisa, Italy.Dept. of Agriculture, Food, and Environment, University of Pisa, Via delBorghetto 80, I-56124 Pisa, Italy.Dept. of Agriculture, Food, and Environment, University of Pisa, Via delBorghetto 80, I-56124 Pisa, Italy. Electronic address: lucia.natali@unipi.it.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

28867564

Citation

Mascagni, Flavia, et al. "Different Histories of Two Highly Variable LTR Retrotransposons in Sunflower Species." Gene, vol. 634, 2017, pp. 5-14.
Mascagni F, Cavallini A, Giordani T, et al. Different histories of two highly variable LTR retrotransposons in sunflower species. Gene. 2017;634:5-14.
Mascagni, F., Cavallini, A., Giordani, T., & Natali, L. (2017). Different histories of two highly variable LTR retrotransposons in sunflower species. Gene, 634, pp. 5-14. doi:10.1016/j.gene.2017.08.014.
Mascagni F, et al. Different Histories of Two Highly Variable LTR Retrotransposons in Sunflower Species. Gene. 2017 Nov 15;634:5-14. PubMed PMID: 28867564.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Different histories of two highly variable LTR retrotransposons in sunflower species. AU - Mascagni,Flavia, AU - Cavallini,Andrea, AU - Giordani,Tommaso, AU - Natali,Lucia, Y1 - 2017/09/01/ PY - 2017/03/13/received PY - 2017/07/15/revised PY - 2017/08/23/accepted PY - 2017/9/5/pubmed PY - 2017/10/3/medline PY - 2017/9/5/entrez KW - Genome evolution KW - Genome variation KW - Helianthus KW - Long-terminal-repeat retrotransposon families KW - Sunflower SP - 5 EP - 14 JF - Gene JO - Gene VL - 634 N2 - In the Helianthus genus, very large intra- and interspecific variability related to two specific retrotransposons of Helianthus annuus (Helicopia and SURE) exists. When comparing these two sequences to sunflower sequence databases recently produced by our lab, the Helicopia family was shown to belong to the Maximus/SIRE lineage of the Sirevirus genus of the Copia superfamily, whereas the SURE element (whose superfamily was not even previously identified) was classified as a Gypsy element of the Ogre/Tat lineage of the Metavirus genus. Bioinformatic analysis of the two retrotransposon families revealed their genomic abundance and relative proliferation timing. The genomic abundance of these families differed significantly among 12 Helianthus species. The ratio between the abundance of long terminal repeats and their reverse transcriptases suggested that the SURE family has relatively more solo long terminal repeats than does Helicopia. Pairwise comparisons of Illumina reads encoding the reverse transcriptase domain indicated that SURE amplification may have occurred more recently than that of Helicopia. Finally, the analysis of population structure based on the SURE and Helicopia polymorphisms of 32 Helianthus species evidenced two subpopulations, which roughly corresponded to species of the Helianthus and Divaricati/Ciliares sections. However, a number of species showed an admixed structure, confirming the importance of interspecific hybridisation in the evolution of this genus. In general, these two retrotransposon families differentially contributed to interspecific variability, emphasising the need to refer to specific families when studying genome evolution. SN - 1879-0038 UR - https://www.unboundmedicine.com/medline/citation/28867564/Different_histories_of_two_highly_variable_LTR_retrotransposons_in_sunflower_species_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0378-1119(17)30664-9 DB - PRIME DP - Unbound Medicine ER -