title: LTR retrotransposon dynamics in the evolution of the olive (Olea europaea) genome.
abstract: Improved knowledge of genome composition, especially of its repetitive component, generates important information for both theoretical and applied research. The olive repetitive component is made up of two main classes of sequences: tandem repeats and retrotransposons (REs). In this study, we provide characterization of a sample of 254 unique full-length long terminal repeat (LTR) REs. In the sample, Ty1-Copia elements were more numerous than Ty3-Gypsy elements. Mapping a large set of Illumina whole-genome shotgun reads onto the identified retroelement set revealed that Gypsy elements are more redundant than Copia elements. The insertion time of intact retroelements was estimated based on sister LTR's divergence. Although some elements inserted relatively recently, the mean insertion age of the isolated retroelements is around 18 million yrs. Gypsy and Copia retroelements showed different waves of transposition, with Gypsy elements especially active between 10 and 25 million yrs ago and nearly inactive in the last 7 million yrs. The occurrence of numerous solo-LTRs related to isolated full-length retroelements was ascertained for two Gypsy elements and one Copia element. Overall, the results reported in this study show that RE activity (both retrotransposition and DNA loss) has impacted the olive genome structure in more ancient times than in other angiosperms.
authors.affiliation: Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa I-56124, Italy.
authors.forename: Elena
authors.initials: E
authors.lastname: Barghini
authors.affiliation: Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa I-56124, Italy.
authors.forename: Lucia
authors.initials: L
authors.lastname: Natali
authors.affiliation: Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa I-56124, Italy.
authors.forename: Tommaso
authors.initials: T
authors.lastname: Giordani
authors.affiliation: Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa I-56124, Italy Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.
authors.forename: Rosa Maria
authors.initials: RM
authors.lastname: Cossu
authors.affiliation: IGA Technology Service, Udine, Italy.
authors.forename: Simone
authors.initials: S
authors.lastname: Scalabrin
authors.affiliation: IGA Technology Service, Udine, Italy.
authors.forename: Federica
authors.initials: F
authors.lastname: Cattonaro
authors.affiliation: Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic.
authors.forename: Hana
authors.initials: H
authors.lastname: Šimková
authors.affiliation: Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic.
authors.forename: Jan
authors.initials: J
authors.lastname: Vrána
authors.affiliation: Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic.
authors.forename: Jaroslav
authors.initials: J
authors.lastname: Doležel
authors.affiliation: Department of Crop and Environmental Sciences, University of Udine, Udine, Italy Institute of Applied Genomics, Udine, Italy.
authors.forename: Michele
authors.initials: M
authors.lastname: Morgante
authors.affiliation: Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa I-56124, Italy andrea.cavallini@unipi.it.
authors.forename: Andrea
authors.initials: A
authors.lastname: Cavallini
mesh_terms: D002874:Chromosome Mapping; D055106:Genome-Wide Association Study; D031658:Olea / Q000235:genetics*; D018626:Retroelements; D020079:Terminal Repeat Sequences
chemical_list: D018626:Retroelements
keywords: BAC sequencing; LTR retrotransposons; insertion age; next-generation sequencing; olive