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Abstract

Transposable elements (TEs) play a crucial role in altering the genomic landscape of all organisms and thereby massively influence the genetic information passed on to succeeding generations (Sundaram & Wysocka, 2020). In the past, TEs were seen as selfish mobile elements populating host genomes to increase their chances for transgenerational transmission over long evolutionary time scales. This notion of selfish elements is slowly changing (Drost & Sanchez, 2019) and a new picture drawing a complex genetic landscape benefitting both, host and TE, emerges whereby novel forms can arise through random shuffling of genetic material. For example, the tomato fruit shape (Benoit et al., 2019), moth adaptive cryptic coloration that occurred during the industrial revolution (Chuong, Elde, & Feschotte, 2017), and inner cell mass development in human embryonic stem cells (Chuong et al., 2017) were all shown to be driven by TE activity. Thus, the impact of these elements on altering morphological traits is imminent and requires new attention in the light of evolvability. However, TEs tend to degenerate their sequence leaving their fragmented copies considered as junk DNA in host genomes, which hamper assembly and annotation of new genomes. Nowadays, the de novo detection of transposable elements is performed by annotation tools specifically designed to capture any type of repeated sequence, TE family, or remnant DNA loci that can be associated with known transposable elements within a genome assembly. The main goal of such efforts is to retrieve a maximum number of loci that can be associated with known TEs. If successful, such annotation can then be used to mask host genomes from TE remnants to simplify genomics studies focusing on host genes. Therefore, there is no automatically performed distinction between complete and potentially active TE and their mutated copies. Here, we introduce the LTRpred pipeline which allows to de novo annotate functional and thus potentially mobile retrotransposons in any given genome assembly. Different from other annotation tools, LTRpred focuses on retrieving structurally intact elements within sequences of genomes rather than characterizing all traces of historic TE activity. Such functional annotation is most useful when trying to spot retrotransposons responsible for recent reshuffling of genetic material in the tree of life. Detecting and further characterization of those active retrotransposons yields the potential to harness them as mutagenesis agents by inducing transposition bursts in a controlled fashion to stimulate genomic reshaping processes towards novel traits.