What Can Long Terminal Repeats Tell Us About the Age of LTR Retrotransposons, Gene Conversion and Ectopic Recombination?

Pavel Jedlicka,Eduard Kejnovsky,Matej Lexa

doi:10.3389/fpls.2020.00644

Abstract

LTR retrotransposons constitute a significant part of plant genomes and their evolutionary dynamics play an important role in genome size changes. Current methods of LTR retrotransposon age estimation are based only on LTR (long terminal repeat) divergence. This has prompted us to analyze sequence similarity of LTRs in 25,144 LTR retrotransposons from fifteen plant species as well as formation of solo LTRs. We found that approximately one fourth of nested retrotransposons showed a higher LTR divergence than the pre-existing retrotransposons into which they had been inserted. Moreover, LTR similarity was correlated with LTR length. We propose that gene conversion can contribute to this phenomenon. Gene conversion prediction in LTRs showed potential converted regions in 25% of LTR pairs. Gene conversion was higher in species with smaller genomes while the proportion of solo LTRs did not change with genome size in analyzed species. The negative correlation between the extent of gene conversion and the abundance of solo LTRs suggests interference between gene conversion and ectopic recombination. Since such phenomena limit the traditional methods of LTR retrotransposon age estimation, we recommend an improved approach based on the exclusion of regions affected by gene conversion.

Highlights

Transposable elements (TEs) are abundant structural and functional genome components inhabiting genomes throughout the course of life evolution
The evolutionarily dynamics of the same LTR retrotransposon family varied in a number of plant species - some families showed short recent expansion in one species while in another species it had continual moderate activity (Figure 1)
We found that the number of LTR retrotransposons exhibiting signs of gene conversion negatively correlated with the proportion of solo LTRs i.e., families exhibiting stronger signs of gene conversion had a lower proportion of solo LTRs (Pearson’s r = −0.5428 with p-value = 1.784e-11; Figure 8)

Summary

Introduction

Transposable elements (TEs) are abundant structural and functional genome components inhabiting genomes throughout the course of life evolution. The activity of transposable elements is dependent on the developmental stage, is tissue-specific, epigenetically regulated and often induced by stress This is evident especially in plants (that are sessile) where TEs represent in large genomes like maize, barley or wheat often more than 85% of the genome (Charles et al, 2008; Schnable et al, 2009; Wicker et al, 2018). LTR retrotransposons are ancient genome inhabitants present in the genomes of all major taxonomic groups, being abundant especially in plants (Feschotte et al, 2002; Kejnovsky et al, 2012) They exhibit waves of explosive amplification during the evolution of host species that often predate the speciation events (Kim et al, 2004).

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