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.

Keywords: BAC sequencing; LTR retrotransposons; insertion age; next-generation sequencing; olive.

Figure 1.

Number of full-length REs identified in this study, separated according to their superfamily. Each bar in the histogram shows the number of Illumina reads that matched to all REs (height) and the number of REs (width) of each superfamily.

Figure 2.

Box and whiskers plot of RE redundancy (calculated as the number of mapped reads per kb) of olive Copia and Gypsy REs. The boxes represent the 25–75%, whiskers represent the whole range of values, and lines in the box represent the mean values of the distribution.

Figure 3.

Distribution of full-length olive LTR-REs according to the ratio between the number of mapped reads per kb measured separately on LTR and inter-LTR regions.

Figure 4.

Phylogenetic tree obtained from the neighbour-joining analysis of 93 Copia retrotranscriptase sequences. Different Copia families are indicated by different grey tones (different colours in the online version of DNA Research). For each RE, the area of the symbol indicates the redundancy of that element in the olive genome. The bar represents the genetic distance. Asterisks indicate bootstrap values >50%. The letter S indicates a Copia RE with an LTR/inter-LTR ratio of >10.

Figure 5.

Phylogenetic tree obtained from the neighbour-joining analysis of 43 Gypsy retrotranscriptase sequences. Different Gypsy families are indicated by different grey tones (different colours in the online version of DNA Research). For each RE, the area of the symbol indicates the redundancy of that element in the olive genome. The bar represents the genetic distance. Asterisks indicate bootstrap values >50%. The letter S indicates two Gypsy REs with an LTR/inter-LTR ratio of >10.

Figure 6.

Distributions of full-length REs identified in this study, according to their estimated insertion ages (MY). Mean insertion dates are reported in parentheses.

Figure 7.

The relationship between estimated insertion ages (MY) and the redundancy of full-length REs identified in this study.