title: Repetitive DNA and Plant Domestication: Variation in Copy Number and Proximity to Genes of LTR-Retrotransposons among Wild and Cultivated Sunflower (Helianthus annuus) Genotypes.
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.affiliation: Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa, Italy.
authors.forename: Flavia
authors.initials: F
authors.lastname: Mascagni
authors.affiliation: Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa, Italy.
authors.forename: Elena
authors.initials: E
authors.lastname: Barghini
authors.affiliation: Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa, Italy.
authors.forename: Tommaso
authors.initials: T
authors.lastname: Giordani
authors.affiliation: The Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, BC, Canada.
authors.forename: Loren H
authors.initials: LH
authors.lastname: Rieseberg
authors.affiliation: Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Cavallini
authors.affiliation: Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa, Italy lucia.natali@unipi.it.
authors.forename: Lucia
authors.initials: L
authors.lastname: Natali
mesh_terms: D056915:DNA Copy Number Variations; D017343:Genes, Plant; D005838:Genotype; D006368:Helianthus / Q000235:genetics*; D018626:Retroelements; D012641:Selection, Genetic; D020079:Terminal Repeat Sequences
chemical_list: D018626:Retroelements
keywords: Helianthus annuus; long terminal repeat retrotransposons; plant domestication; repetitive DNA; retrotransposon redundancy