Editorial: mobile elements and plant genome evolution, comparative analyzes and computational tools

Transposable Elements turn out to be functional
Multiple changes that occur constantly in the plant genome allow an organism to develop from a single-celled embryo to a multicellular organism. A significant part of these changes is associated with the recombination activity of numerous classes of interspersed repeats. These numerous families of interspersed repeats were often called “junk DNA” as first, they were not associated with any vital protein-coding processes. Now, more and more clues indicate that such repeated DNA might play major roles in the genome as functional ‘non-coding’ DNA (Pennisi, 2012;Ariel and Manavella, 2021). Transposable elements (TEs), such as DNA transposons and retrotransposons, are the main part of these interspersed repeats (Vitte et al., 2014). The diverse families of retrotransposons are highly abundant genetic elements that are related to retroviruses (Wicker et al., 2007). Although retrotransposons are not ‘true’ mobile elements like DNA transposons – from the comparison of their transposition mechanisms –, retrotransposable elements (RTEs) are notably constitutive of heterochromatin and form a variety of major chromosomal structures such as centromeres (Bennetzen and Wang, 2014) and represent the main intergenic part of the plant genome (Kalendar et al., 2020). RTE mobility is ensured through an RNA intermediate, allowing a Copy-And-Paste approach for their transposition. Their own-encoded RNA is reverse transcribed using their own (or not) encoded enzymes, that will re-create from the single-strand RNA matrix a double-strand DNA at a new location. This reverse transcription can be either through extra-chromosomal DNA within a nucleocapsid (and implies RT/RNAseH + INT enzymes for LTR retrotransposons, e.g.) or directly at the insertion site (Target-Prime Reverse transcription mechanism, with only the RT as a minimal set of enzymes for LINEs and SINEs e.g.) (Wicker et al., 2007). Such Copy-And-Paste mechanisms allow a quick invasion of naive genomes, and is responsible for massive genome increase in a few periods of time (Piegu et al., 2006). Such invasions belong to a few number of initial active copies, called Master copies; however, while these copies must be transcriptionally active (i.e. able to produce RNA), they can be translationally inactive and may rely on other copies for enzymatic activities (Sabot and Schulman, 2006). When recently inserted, neo-copies can be related phylogenetically because of their sequence identity; subsequent mutations (point mutation, recombination, and so on) will then occur and their lineage can then be complex to recompose. Once inserted, each copy has its own evolutionary history and some may acquire biological role (or some part of the copy) and being excepted by their host. Some RTEs can provide evolutionary advantages to the host and were demonstrated to play a significant role in plant adaptation (Song and Cao, 2017). If the fact that TEs can be beneficial to the host is now accepted, recent advances in the field has placed RTEs at the center of the current debate on eukaryotic and notably plant evolution. To advance this important research field, in the Research Topic “Mobile Elements and Plant Genome Evolution, Comparative Analyses, and Computational Tools” we focused on the efficiency of new genomic tools for the discovery of TEs, and highlighted some recent studies on the role of mobile elements in the evolution of the host genome, as well as on genome-wide comparative analysis and profiling of transposable elements.