Barghini, E., Natali, L., Giordani, T., Cossu, R.M., Scalabrin, S., Cattonaro, F., Šimková, H., Vrána, J., Doležel, J., Morgante, M., Cavallini, A.
DNA RESEARCH
22:
91-100,
2015
Keywords:
LTR retrotransposons, next-generation sequencing, olive, insertion age, BAC sequencing
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.
Fulltext: contact IEB authors
IEB authors: Jaroslav Doležel,
Hana Šimková,
Jan Vrána
Čeština
English