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LTR retrotransposon dynamics in the evolution of the olive (Olea europaea) genome
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SYSNO ASEP 0446262 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title LTR retrotransposon dynamics in the evolution of the olive (Olea europaea) genome Author(s) Barghini, E. (IT)
Natali, L. (IT)
Giordani, T. (IT)
Cossu, R.M. (IT)
Scalabrin, S. (IT)
Cattonaro, F. (IT)
Šimková, Hana (UEB-Q) RID, ORCID
Vrána, Jan (UEB-Q) RID, ORCID
Doležel, Jaroslav (UEB-Q) RID, ORCID
Morgante, M. (IT)
Cavallini, A. (IT)Source Title Dna Research. - : Oxford University Press - ISSN 1340-2838
Roč. 22, č. 1 (2015), s. 91-100Number of pages 10 s. Language eng - English Country GB - United Kingdom Keywords LTR retrotransposons ; next-generation sequencing ; olive Subject RIV EB - Genetics ; Molecular Biology R&D Projects GBP501/12/G090 GA ČR - Czech Science Foundation (CSF) LO1204 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) Institutional support UEB-Q - RVO:61389030 UT WOS 000350442100009 DOI 10.1093/dnares/dsu042 Annotation 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. Workplace Institute of Experimental Botany Contact David Klier, knihovna@ueb.cas.cz, Tel.: 220 390 469 Year of Publishing 2016
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