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

Barghini, E and Natali, L and Giordani, T and Cossu, RM and Scalabrin, S and Cattonaro, F and Šimková, H and Vrána, J and Doležel, J and Morgante, M and Cavallini, A (2015) LTR retrotransposon dynamics in the evolution of the olive (Olea europaea) genome. DNA Research, 22 (1). pp. 91-100. ISSN 1756-1663

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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.

Item Type: Article
Additional Information: This article has been accepted for publication in DNA Research ©: 2015 The Authors. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.
Uncontrolled Keywords: 0604 Genetics
Subjects: Q Science > QH Natural history > QH301 Biology
Q Science > QH Natural history > QH426 Genetics
Divisions: Natural Sciences and Psychology
Publisher: Oxford University Press
Related URLs:
Date Deposited: 15 Apr 2016 08:29
Last Modified: 15 Apr 2016 09:07
DOI or Identification number: 10.1093/dnares/dsu042
URI: http://researchonline.ljmu.ac.uk/id/eprint/3431

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