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Repetitive DNA and Plant Domestication: Variation in Copy Number and Proximity to Genes of LTR-Retrotransposons among Wild and Cultivated Sunflower (Helianthus annuus) Genotypes.
Genome Biol Evol 2015; 7(12):3368-82GB

Abstract

The sunflower (Helianthus annuus) genome contains a very large proportion of transposable elements, especially long terminal repeat retrotransposons. However, knowledge on the retrotransposon-related variability within this species is still limited. We used next-generation sequencing (NGS) technologies to perform a quantitative and qualitative survey of intraspecific variation of the retrotransposon fraction of the genome across 15 genotypes--7 wild accessions and 8 cultivars--of H. annuus. By mapping the Illumina reads of the 15 genotypes onto a library of sunflower long terminal repeat retrotransposons, we observed considerable variability in redundancy among genotypes, at both superfamily and family levels. In another analysis, we mapped Illumina paired reads to two sets of sequences, that is, long terminal repeat retrotransposons and protein-encoding sequences, and evaluated the extent of retrotransposon proximity to genes in the sunflower genome by counting the number of paired reads in which one read mapped to a retrotransposon and the other to a gene. Large variability among genotypes was also ascertained for retrotransposon proximity to genes. Both long terminal repeat retrotransposon redundancy and proximity to genes varied among retrotransposon families and also between cultivated and wild genotypes. Such differences are discussed in relation to the possible role of long terminal repeat retrotransposons in the domestication of sunflower.

Authors+Show Affiliations

Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa, Italy.Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa, Italy.Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa, Italy.The Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, BC, Canada.Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa, Italy.Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa, Italy lucia.natali@unipi.it.

Pub Type(s)

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

Language

eng

PubMed ID

26608057

Citation

Mascagni, Flavia, et al. "Repetitive DNA and Plant Domestication: Variation in Copy Number and Proximity to Genes of LTR-Retrotransposons Among Wild and Cultivated Sunflower (Helianthus Annuus) Genotypes." Genome Biology and Evolution, vol. 7, no. 12, 2015, pp. 3368-82.
Mascagni F, Barghini E, Giordani T, et al. Repetitive DNA and Plant Domestication: Variation in Copy Number and Proximity to Genes of LTR-Retrotransposons among Wild and Cultivated Sunflower (Helianthus annuus) Genotypes. Genome Biol Evol. 2015;7(12):3368-82.
Mascagni, F., Barghini, E., Giordani, T., Rieseberg, L. H., Cavallini, A., & Natali, L. (2015). Repetitive DNA and Plant Domestication: Variation in Copy Number and Proximity to Genes of LTR-Retrotransposons among Wild and Cultivated Sunflower (Helianthus annuus) Genotypes. Genome Biology and Evolution, 7(12), pp. 3368-82. doi:10.1093/gbe/evv230.
Mascagni F, et al. Repetitive DNA and Plant Domestication: Variation in Copy Number and Proximity to Genes of LTR-Retrotransposons Among Wild and Cultivated Sunflower (Helianthus Annuus) Genotypes. Genome Biol Evol. 2015 Nov 24;7(12):3368-82. PubMed PMID: 26608057.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Repetitive DNA and Plant Domestication: Variation in Copy Number and Proximity to Genes of LTR-Retrotransposons among Wild and Cultivated Sunflower (Helianthus annuus) Genotypes. AU - Mascagni,Flavia, AU - Barghini,Elena, AU - Giordani,Tommaso, AU - Rieseberg,Loren H, AU - Cavallini,Andrea, AU - Natali,Lucia, Y1 - 2015/11/24/ PY - 2015/11/27/entrez PY - 2015/11/27/pubmed PY - 2017/1/11/medline KW - Helianthus annuus KW - long terminal repeat retrotransposons KW - plant domestication KW - repetitive DNA KW - retrotransposon redundancy SP - 3368 EP - 82 JF - Genome biology and evolution JO - Genome Biol Evol VL - 7 IS - 12 N2 - The sunflower (Helianthus annuus) genome contains a very large proportion of transposable elements, especially long terminal repeat retrotransposons. However, knowledge on the retrotransposon-related variability within this species is still limited. We used next-generation sequencing (NGS) technologies to perform a quantitative and qualitative survey of intraspecific variation of the retrotransposon fraction of the genome across 15 genotypes--7 wild accessions and 8 cultivars--of H. annuus. By mapping the Illumina reads of the 15 genotypes onto a library of sunflower long terminal repeat retrotransposons, we observed considerable variability in redundancy among genotypes, at both superfamily and family levels. In another analysis, we mapped Illumina paired reads to two sets of sequences, that is, long terminal repeat retrotransposons and protein-encoding sequences, and evaluated the extent of retrotransposon proximity to genes in the sunflower genome by counting the number of paired reads in which one read mapped to a retrotransposon and the other to a gene. Large variability among genotypes was also ascertained for retrotransposon proximity to genes. Both long terminal repeat retrotransposon redundancy and proximity to genes varied among retrotransposon families and also between cultivated and wild genotypes. Such differences are discussed in relation to the possible role of long terminal repeat retrotransposons in the domestication of sunflower. SN - 1759-6653 UR - https://www.unboundmedicine.com/medline/citation/26608057/Repetitive_DNA_and_Plant_Domestication:_Variation_in_Copy_Number_and_Proximity_to_Genes_of_LTR_Retrotransposons_among_Wild_and_Cultivated_Sunflower__Helianthus_annuus__Genotypes_ L2 - https://academic.oup.com/gbe/article-lookup/doi/10.1093/gbe/evv230 DB - PRIME DP - Unbound Medicine ER -