Long terminal repeat retrotransposons in Angiosperm evolution.

Background The high phenotypic variability of Angiosperms is due to the plasticity of their genomes, which is largely determined by transposable elements with their mutagenic and regulatory abilities. The majority of transposable elements in the plant genome are LTR retrotransposons (LTR-TE) which replicate via an RNA intermediate. The LTR-TE composition of individual genomes appears to be the aggregate of past amplification/deletion events, thus forming a unique profile. Results In this research, a comprehensive study of LTR-TE profiles and their transformations along the life-tree of Angiosperms utilizing DANTE and DANTE_LTR pipelines was performed. Analysis of 601 assembled genomes (including the majority of model genomes) from “NCBI Datasets” database covering the 51 of the totally 64 Angiosperm orders and their comparison with five non-angiosperm genomes revealed several trends in LTR-TE profile changes in the Angiosperm clade. Conclusions (i) Comparison of the Angiosperm and non-angiosperm LTR-TE composition showed that the angiosperm-specific LTR-TE landscape was formed gradually, and quantitively remains fairly stable within the clade for at least 140 Myr; (ii) the Ale Ty1/ Copia retrotransposon appears to be the most quantitatively variable in the flowering plants; (iii) additionally, in Angiosperm branches, there were several other highly variable (presumably active) LTR-TE lineages and monocots were most diverse in this character; (iv) it was revealed that several basal Angiosperm orders may possess an ancestral LTR-TE landscape towards the younger orders of the clade; and (v) LTR-TE average profiles of Angiosperm orders essentially fit the APG IV phylogeny in several key points, thereby testifying in favor of the hypothesis that transposable elements activity may be connected with the formation of taxonomic groups, and has therefore been associated with major evolutionary events in the past.