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

@article{1768016,
   author = {Jedlicka, Pavel and Lexa, Matej and Kejnovský, Eduard},
   article_location = {Lausanne (Switzerland)},
   article_number = {644},
   doi = {http://dx.doi.org/10.3389/fpls.2020.00644},
   keywords = {transposable elements; LTR retrotransposons; nesting; age estimation; gene conversion; ectopic recombination; plants},
   language = {eng},
   issn = {1664-462X},
   journal = {Frontiers in Plant Science},
   title = {What Can Long Terminal Repeats Tell Us About the Age of LTR Retrotransposons, Gene Conversion and Ectopic Recombination?},
   url = {https://www.frontiersin.org/articles/10.3389/fpls.2020.00644/full},
   volume = {11},
   year = {2020}
}

TY  - JOUR
ID  - 1768016
AU  - Jedlicka, Pavel - Lexa, Matej - Kejnovský, Eduard
PY  - 2020
TI  - What Can Long Terminal Repeats Tell Us About the Age of LTR Retrotransposons, Gene Conversion and Ectopic Recombination?
JF  - Frontiers in Plant Science
VL  - 11
IS  - 644
SP  - 1-15
EP  - 1-15
PB  - Frontiers Media SA
SN  - 1664462X
KW  - transposable elements
KW  - LTR retrotransposons
KW  - nesting
KW  - age estimation
KW  - gene conversion
KW  - ectopic recombination
KW  - plants
UR  - https://www.frontiersin.org/articles/10.3389/fpls.2020.00644/full
N2  - 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.
ER  - 

JEDLICKA, Pavel, Matej LEXA a Eduard KEJNOVSKÝ. What Can Long Terminal Repeats Tell Us About the Age of LTR Retrotransposons, Gene Conversion and Ectopic Recombination? \textit{Frontiers in Plant Science}. Lausanne (Switzerland): Frontiers Media SA, 2020, roč.~11, č.~644, s.~1-15. ISSN~1664-462X. Dostupné z: https://dx.doi.org/10.3389/fpls.2020.00644.