Background: Transposable elements (TEs) constitute the vast majority of all eukaryotic DNA, and display extreme diversity, with thousands of families. Given their abundance and diversity, TEs discovery and annotation becomes challengeable. At present, tools and databases have built libraries to mask TEs in genomes based on de novo- and homology-based identification strategies, but no consensus criteria about which tools should be used have been proposed. Results: In the de novo-based strategy, we compared performances of TE libraries developed by four commonly used tools, including RepeatModeler, LTR_FINDER, LTRharvest, and MITE_Hunter, by using a simulated genome as a standard control. The results showed that the performance of RepeatModeler decreased as it was combined with either LTR_FINDER or LTRharvest. Combination of RepeatModeler and MITE_Hunter showed better performance than RepeatModeler and MITE_Hunter alone. In the homology-based strategy, we evaluated different sources from a taxonomic point of view to build an accurate TE library. When we selected a library from databases to identify TEs for Arabidopsis thaliana genome, the library from a genus genetically closer to Arabidopsis achieved better performance than other genera with further genetic distance. Without the Arabidopsis, combination of top three genera closer to Arabidopsis showed better performance than combination of all genera. Conclusion: This study proposes a series of recommendations to perform an accurate TE annotation: 1) For de novo-based strategy, RepeatModeler and MITE_Hunter are suggested to build a TE library; 2) For homology-based strategy, it is recommended to use library of genus genetically close to the species rather than use combined library from all genera.

Transcription is carried out in most eukaryotes by three multimeric complexes (RNA polymerases I, II and III). However, plants contain two additional RNA polymerases (IV and V), which have evolved from RNA polymerase II. RNA polymerases II, IV and V contain both common and specific subunits that may specialize some of their functions. In this study, we conducted a search for the genes that putatively code for the specific subunits of RNA polymerases IV and V, as well as the corresponding of RNA polymerase II in olive. Based on the homology with the genes of Arabidopsis thaliana, we identified 13 genes that putatively code for the specific subunits of polymerases IV and V, and 16 genes that code for the corresponding specific subunits of polymerase II in olive. The transcriptomic analysis by RNA-Seq revealed that the expression of the RNA polymerases IV and V genes was induced during the initial stages of fruit development. Given that RNA polymerases IV and V are involved in the transcription of long non-coding RNAs, we investigated their expression and observed relevant changes in the expression of this type of RNAs. Particularly, the expression of the intergenic and intronic long non-coding RNAs tended to increase in the early steps of fruit development, suggesting their potential role in this process. The positive correlation between the expression of RNA polymerases IV and V subunits and the expression of non-coding RNAs supports the hypothesis that RNA polymerases IV and V may play a role in fruit development throughout the synthesis of this type of RNAs.