TE-nester: a recursive software tool for structure-based discovery of nested transposable elements

Lexa, Matej; Lapar, Radovan; Jedlička, Pavel; Vanat, I.; Cervennansky, Michal; Kejnovský, Eduard

doi:10.1109/bibm.2018.8621071

Cited by 2 publications

(4 citation statements)

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“…We searched 12 plant genomes (see Methods) for LTR retrotransposons nested into pre-existing LTR retrotransposons using our newly developed TE-nester tool [26, 27]. In a pair of nested elements, the younger inserted element was named “nested” and the pre-existing element was called “original”.…”

Section: Resultsmentioning

confidence: 99%

“…The 12 species and their respective genome versions included Arabidopsis lyrata ([54], Alyrata_384_v1.fa), Arabidopsis thaliana ([55], Athaliana_167_TAIR9.fa), Brachypodium distachyon ([56], Bdistachyon_314_v3.0.fa), Glycine max ([14], Gmax_275_v2.0.fa), Gossypium raimondii ([57], Graimondii_221_v2.0.fa), Lotus japonicus ([58],, Lj2.5_genome_contigs.fna.gz), Medicago truncatula ([59], Mtruncatula_285_Mt4.0.fa), Oryza sativa ([60], Osativa_323_v7.0.fa), Physcomitrella patens ([61], Ppatens_318_v3.fa), Sorghum bicolor ([62], Sbicolor_313_v3.0.fa), Solanum lycopersicum ([63], Slycopersicum_390_v2.5.fa) and Solanum tuberosum ([64], Stuberosum_448_v4.03.fa). Unmasked sequences were analysed with TE-nester [26, 27]. TE-nester in its latest version relies upon LTR Finder [65] to identify full-length LTR retroelements.…”

Section: Methodsmentioning

confidence: 99%

“…Subsequences of interest (LTR, RT domain, insertion sites) were extracted from downloaded genome sequences using bedtools package [66]. Moreover, TE-nester also retrieves sequences of all annotated TEs in ‘fasta’ format [26].…”

Section: Methodsmentioning

confidence: 99%

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Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study

et al. 2019

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BackgroundNesting is common in LTR retrotransposons, especially in large genomes containing a high number of elements.ResultsWe analyzed 12 plant genomes and obtained 1491 pairs of nested and original (pre-existing) LTR retrotransposons. We systematically analyzed mutual nesting of individual LTR retrotransposons and found that certain families, more often belonging to the Ty3/gypsy than Ty1/copia superfamilies, showed a higher nesting frequency as well as a higher preference for older copies of the same family (“autoinsertions”). Nested LTR retrotransposons were preferentially located in the 3’UTR of other LTR retrotransposons, while coding and regulatory regions (LTRs) are not commonly targeted. Insertions displayed a weak preference for palindromes and were associated with a strong positional pattern of higher predicted nucleosome occupancy. Deviation from randomness in target site choice was also found in 13,983 non-nested plant LTR retrotransposons.ConclusionsWe reveal that nesting of LTR retrotransposons is not random. Integration is correlated with sequence composition, secondary structure and the chromatin environment. Insertion into retrotransposon positions with a low negative impact on family fitness supports the concept of the genome being viewed as an ecosystem of various elements.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study

et al. 2019

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“…The complete workflow of our analysis is visualized as a step-by-step flowchart in Supplementary Figure S1. Unmasked sequences were analyzed with TE-greedy-nester (Lexa et al, 2018). TE-greedy-nester in its latest version relies upon LTR Finder (Xu and Wang, 2007) to identify full-length LTR retroelements.…”

Section: Genomic Sequence Sources and Te Annotationmentioning

confidence: 99%

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

2020

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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.

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TE-nester: a recursive software tool for structure-based discovery of nested transposable elements

Cited by 2 publications

References 9 publications

Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study

Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study

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

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