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DNA Res. 2015 Feb;22(1):91-100. doi: 10.1093/dnares/dsu042. Epub 2014 Nov 26.

LTR retrotransposon dynamics in the evolution of the olive (Olea europaea) genome.

Author information

1
Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa I-56124, Italy.
2
Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa I-56124, Italy Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.
3
IGA Technology Service, Udine, Italy.
4
Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic.
5
Department of Crop and Environmental Sciences, University of Udine, Udine, Italy Institute of Applied Genomics, Udine, Italy.
6
Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa I-56124, Italy andrea.cavallini@unipi.it.

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.

KEYWORDS:

BAC sequencing; LTR retrotransposons; insertion age; next-generation sequencing; olive

PMID:
25428895
PMCID:
PMC4379980
DOI:
10.1093/dnares/dsu042
[Indexed for MEDLINE]
Free PMC Article

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