A comparison of methods for LTR-retrotransposon insertion time profiling in the Populus trichocarpa genome

Retrotransposons in Plant Genomes: Structure, Identification, and Classification through Bioinformatics and Machine Learning

“…Using key features like retrotransposon length, LTR length, ORFs, and motifs such as the TATA box, AATAAA, TDS, and poly-A tails, one it seems possible to build a well-defined ML problem. Using data mining, Arango-López et al (2017) [6] demonstrated that element length and LTR length are important to classify LTR retrotransposons, Benachenhou et al [64] proposed that motifs inside of LTRs are conserved across superfamilies using HMMs, Fischer et al (2018) [222] showed that profile hidden Markov models (pHMMs) are a promising approach to find TEs in genomes, and Orozco-Arias et al (2017) [223] demonstrated the useful of high performance computing to speed up analysis of TEs in large genomes. Finally, Loureiro et al [170] presented evidence that ML can be used to test and improve the identification and classification of TEs using already developed bioinformatics tools.…”

“…Interestingly, LTRs of retrotransposon and retroviruses share comparable function in the initiation of the RNA template, the first step of the movement of the element [37]. Since the RNA template is generated from R to R sections, it contains only one U5 and U3 section, and eventually, two identical LTRs when the DNA copy of the element is inserted into the genome [64]. A short motif TG-5′ and 3′-CA called the Short Inverted Repeat (SIR) initiates and terminates LTRs [65,66].…”

“…LTR-RTs also contain a primer binding site (PBS) and a Poly-Purine Tract (PPT). Both sites can work as primers [64], whereby the first is the (−)-strand priming site for reverse transcription and the second is the (+)-strand priming site for reverse transcription [31,46,68]. In addition, the neo-insertion of LTR retrotransposons creates a short duplication called the target site duplication (TSD) of 4–6 bp at the termini of the element [12,40,69,70] (Figure 1).…”

“…On the other hand, host genomes employ a variety of genome downsizing strategies to mitigate genome expansion caused by TEs [51]. For instance, one strategy is unequal recombination between LTRs of the same or different retrotransposons [49,64,82], which produces solo-LTRs in a single step by deleting one LTR and the internal section of them. Another strategy includes illegitimate recombination that gradually eliminates tracts of LTR retrotransposons and leaves truncated LTR retrotransposons [113,114].…”

Data Integration in Poplar: ‘Omics Layers and Integration Strategies

“…In a recent study by Mascagni et al (2018), insertion ages of LTR TEs were determined in P. trichocarpa by comparing the sequences of the 3′ and 5′ ends of LTRs. This provides an indication of the time since insertion because at the time of insertion, the 3′ and 5′ LTRs are identical, and subsequently accumulate mutations independently after insertion.…”