Sensitive detection of pre-integration intermediates of long terminal repeat retrotransposons in crop plants

Abstract

Retrotransposons have played an important role in the evolution of host genomes1,2. Their impact is mainly deduced from the composition of DNA sequences that have been fixed over evolutionary time2. Such studies provide important ‘snapshots’ reflecting the historical activities of transposons but do not predict current transposition potential. We previously reported sequence-independent retrotransposon trapping (SIRT) as a method that, by identification of extrachromosomal linear DNA (eclDNA), revealed the presence of active long terminal repeat (LTR) retrotransposons in Arabidopsis3. However, SIRT cannot be applied to large and transposon-rich genomes, as found in crop plants. We have developed an alternative approach named ALE-seq (amplification of LTR of eclDNAs followed by sequencing) for such situations. ALE-seq reveals sequences of 5′ LTRs of eclDNAs after two-step amplification: in vitro transcription and subsequent reverse transcription. Using ALE-seq in rice, we detected eclDNAs for a novel Copia family LTR retrotransposon, Go-on, which is activated by heat stress. Sequencing of rice accessions revealed that Go-on has preferentially accumulated in Oryza sativa ssp. indica rice grown at higher temperatures. Furthermore, ALE-seq applied to tomato fruits identified a developmentally regulated Gypsy family of retrotransposons. A bioinformatic pipeline adapted for ALE-seq data analyses is used for the direct and reference-free annotation of new, active retroelements. This pipeline allows assessment of LTR retrotransposon activities in organisms for which genomic sequences and/or reference genomes are either unavailable or of low quality.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Fig. 1: Detection of eclDNA by ALE-seq.
Fig. 2: Sensitivity and specificity of eclDNA detection by ALE-seq.
Fig. 3: Identification of a heat-activated retrotransposon in rice.
Fig. 4: Identification of a tomato retrotransposon activated in fruit pericarp.

Data availability

The next-generation sequencing data that support the findings of this study are available in the Sequence Read Archive (SRA) repository with the identifier SRP155920.

References

  1. 1.

    Lisch, D. How important are transposons for plant evolution? Nat. Rev. Genet. 14, 49–61 (2012).

    Article  Google Scholar 

  2. 2.

    Chuong, E. B., Elde, N. C. & Feschotte, C. Regulatory activities of transposable elements: from conflicts to benefits. Nat. Rev. Genet. 18, 71–86 (2017).

    CAS  Article  Google Scholar 

  3. 3.

    Griffiths, J., Catoni, M., Iwasaki, M. & Paszkowski, J. Sequence-independent identification of active LTR retrotransposons in Arabidopsis. Mol. Plant 11, 508–511 (2017).

    Article  Google Scholar 

  4. 4.

    Ma, J. & Bennetzen, J. L. Rapid recent growth and divergence of rice nuclear genomes. Proc. Natl Acad. Sci. USA 101, 12404–12410 (2004).

    CAS  Article  Google Scholar 

  5. 5.

    Sanchez, D. H., Gaubert, H., Drost, H., Zabet, N. R. & Paszkowski, J. High-frequency recombination between members of an LTR retrotransposon family during transposition bursts. Nat. Commun. 8, 1283 (2017).

    Article  Google Scholar 

  6. 6.

    Picault, N. et al. Identification of an active LTR retrotransposon in rice. Plant J. 58, 754–765 (2009).

    CAS  Article  Google Scholar 

  7. 7.

    Sabot, F. et al. Transpositional landscape of the rice genome revealed by paired-end mapping of high-throughput re-sequencing data. Plant J. 66, 241–246 (2011).

    CAS  Article  Google Scholar 

  8. 8.

    Mirouze, M. et al. Selective epigenetic control of retrotransposition in Arabidopsis. Nature 461, 427–430 (2009).

    CAS  Article  Google Scholar 

  9. 9.

    Ito, H. et al. An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress. Nature 472, 115–119 (2011).

    CAS  Article  Google Scholar 

  10. 10.

    Paszkowski, J. Controlled activation of retrotransposition for plant breeding. Curr. Opin. Biotechnol. 32, 200–206 (2015).

    CAS  Article  Google Scholar 

  11. 11.

    Cavrak, V. V. et al. How a retrotransposon exploits the plant’s heat stress response for its activation. PLoS Genet. 10, e1004115 (2014).

    Article  Google Scholar 

  12. 12.

    Pietzenuk, B. et al. Recurrent evolution of heat-responsiveness in Brassicaceae COPIA elements. Genome Biol. 17, 209 (2016).

    Article  Google Scholar 

  13. 13.

    3K RGP. The 3,000 rice genomes project. Gigascience 3, 7 (2014).

  14. 14.

    Nakagome, M. et al. Transposon insertion finder (TIF): a novel program for detection of de novo transpositions of transposable elements. BMC Bioinform. 15, 71 (2014).

    Article  Google Scholar 

  15. 15.

    Xiong, Z. Y. et al. Latitudinal distribution and differentiation of rice germplasm: its implications in breeding. Crop Sci. 51, 1050–1058 (2011).

    Article  Google Scholar 

  16. 16.

    Zhong, S. et al. Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nat. Biotechnol. 31, 154–159 (2013).

    CAS  Article  Google Scholar 

  17. 17.

    The Tomato Genome Consortium. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485, 635–641 (2012).

  18. 18.

    Eshed, Y. & Zamir, D. An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL. Genetics 141, 1147–1162 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. 19.

    Eshed, Y. & Zamir, D. Less-than-additive epistatic interactions of quantitative trait loci in tomato. Genetics 143, 1807–1817 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. 20.

    Quadrana, L. et al. The Arabidopsis thaliana mobilome and its impact at the species level. eLife 5, e15716 (2016).

    Article  Google Scholar 

  21. 21.

    Stuart, T. et al. Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation. eLife 5, e20777 (2016).

    Article  Google Scholar 

  22. 22.

    Wei, B. et al. Genome-wide characterization of non-reference transposons in crops suggests non-random insertion. BMC Genomics 17, 536 (2016).

    Article  Google Scholar 

  23. 23.

    Lanciano, S. et al. Sequencing the extrachromosomal circular mobilome reveals retrotransposon activity in plants. PLoS Genet. 13, e1006630 (2017).

    Article  Google Scholar 

  24. 24.

    Møller, H. D. et al. Formation of extrachromosomal circular DNA from long terminal repeats of retrotransposons in Saccharomyces cerevisiae. G3 (Bethesda) 6, 453–462 (2015).

    Article  Google Scholar 

  25. 25.

    Møller, H. D., Parsons, L., Jørgensen, T. S., Botstein, D. & Regenberg, B. Extrachromosomal circular DNA is common in yeast. Proc. Natl Acad. Sci. USA 112, 3114–3122 (2015).

    Article  Google Scholar 

  26. 26.

    Cheng, C. et al. Loss of function mutations in the rice chromomethylase OsCMT3a cause a burst of transposition. Plant J. 83, 1069–1081 (2015).

    CAS  Article  Google Scholar 

  27. 27.

    Cui, X. et al. Control of transposon activity by a histone H3K4 demethylase in rice. Proc. Natl Acad. Sci. USA 110, 1953–1958 (2013).

    CAS  Article  Google Scholar 

  28. 28.

    Wang, Z. H. et al. Genomewide variation in an introgression line of rice-zizania revealed by whole-genome re-sequencing. PLoS ONE 8, e74479 (2013).

    CAS  Article  Google Scholar 

  29. 29.

    Li, H., Freeling, M. & Lisch, D. Epigenetic reprogramming during vegetative phase change in maize. Proc. Natl Acad. Sci. USA 107, 22184–22189 (2010).

    CAS  Article  Google Scholar 

  30. 30.

    Slotkin, R. K. et al. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136, 461–472 (2009).

    CAS  Article  Google Scholar 

  31. 31.

    Liu, R. et al. A DEMETER-like DNA demethylase governs tomato fruit ripening. Proc. Natl Acad. Sci. USA 112, 10804–10809 (2015).

    CAS  Article  Google Scholar 

  32. 32.

    Goodier, J. L. Retrotransposition in tumors and brains. Mob. DNA 5, 11 (2014).

    Article  Google Scholar 

  33. 33.

    Baillie, J. K. et al. Somatic retrotransposition alters the genetic landscape of the human brain. Nature 479, 534–537 (2011).

    CAS  Article  Google Scholar 

  34. 34.

    Mullins, C. S. & Linnebacher, M. Human endogenous retroviruses and cancer: causality and therapeutic possibilities. World J. Gastroenterol. 18, 6027–6035 (2012).

    Article  Google Scholar 

  35. 35.

    Cho, J. & Paszkowski, J. Regulation of rice root development by a retrotransposon acting as a microRNA sponge. eLife 6, e30038 (2017).

    Article  Google Scholar 

  36. 36.

    Chan, P. P. & Lowe, T. M. GtRNAdb 2. 0: an expanded database of transfer RNA genes identified in complete and draft genomes. Nucleic Acids Res. 44, 184–189 (2016).

    Article  Google Scholar 

  37. 37.

    Daujat, M. et al. PlantRNA, a database for tRNAs of photosynthetic eukaryotes. Nucleic Acids Res. 41, 273–279 (2012).

    Google Scholar 

  38. 38.

    Finn, R. D. et al. Pfam: the protein families database. Nucleic Acids Res. 42, 222–230 (2014).

    Article  Google Scholar 

  39. 39.

    Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).

    CAS  Article  Google Scholar 

  40. 40.

    Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).

    Article  Google Scholar 

  41. 41.

    Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 516–520 (2010).

    Article  Google Scholar 

  42. 42.

    Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24–26 (2011).

    CAS  Article  Google Scholar 

  43. 43.

    Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2013).

    Article  Google Scholar 

  44. 44.

    Liao, Y., Smyth, G. K. & Shi, W. The subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Res. 41, e108 (2013).

    Article  Google Scholar 

  45. 45.

    Li, W. & Godzik, A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658–1659 (2006).

    CAS  Article  Google Scholar 

  46. 46.

    Catoni, M. et al. DNA sequence properties that predict susceptibility to epiallelic switching. EMBO J. 36, 617–628 (2017).

    CAS  Article  Google Scholar 

  47. 47.

    Krueger, F. & Andrews, S. R. Bismark: a flexible aligner and methylation caller for bisulfite-seq applications. Bioinformatics 27, 1571–1572 (2011).

    CAS  Article  Google Scholar 

  48. 48.

    Catoni, M., Tsang, J. M. F., Greco, A. P. & Zabet, N. R. DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts. Nucleic Acids Res. 46, e114 (2018).

    Article  Google Scholar 

  49. 49.

    Lawrence, M., Gentleman, R. & Carey, V. rtracklayer: an R package for interfacing with genome browsers. Bioinformatics 25, 1841–1842 (2009).

    CAS  Article  Google Scholar 

Download references

Acknowledgements

This work was supported by European Research Council (EVOBREED) grant no. 322621 and a Gatsby Fellowship grant no. AT3273/GLE.

Author information

Affiliations

Authors

Contributions

J.C. and J.P. conceived the research. J.C., M.B., M.C., H.-G.D., A.B. and M.O. performed experiments. J.C., M.B., M.C. and H.-G.D. analysed data. J.C. and J.P. wrote and revised the manuscript.

Corresponding authors

Correspondence to Jungnam Cho or Jerzy Paszkowski.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

Supplementary Figures 1–11 and Supplementary Tables 1–3.

Reporting Summary

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Cho, J., Benoit, M., Catoni, M. et al. Sensitive detection of pre-integration intermediates of long terminal repeat retrotransposons in crop plants. Nature Plants 5, 26–33 (2019). https://doi.org/10.1038/s41477-018-0320-9

Download citation

Further reading