Skip to main content
Log in

A transposition-active Phyllostachys edulis long terminal repeat (LTR) retrotransposon

  • Regular Paper
  • Published:
Journal of Plant Research Aims and scope Submit manuscript

Abstract

Due to infrequent sexual reproduction, moso bamboo breeding by hybridization is extremely technically difficult. Insertional mutagenesis based on endogenous active transposons may thus serve as an alternative method to create new germplasm of moso bamboo. In the present study, using LTR-STRUC, a full-length intact long terminal repeat (LTR) retrotransposon was identified in the moso bamboo genome and was named PHRE2 (Phyllostachys edulis retrotransposon 2). The 5′ and 3′ LTR sequences of PHRE2 were highly (98.39%) similar. PHRE2 contains all domains necessary for transposition such as gag, pr, rt, rh, and int. The coding frames of these essential domains were complete and had no apparent mutations. In addition, PHRE2 possessed a prime binding site (PBS), a polypurine tract (PPT), and two typical sequences of LTR retrotransposons. A genome-wide scan showed that the moso bamboo genome has only one full-length sequence of PHYRE2. After its transfer to Arabidopsis thaliana, an increase in PHRE2 copy number occurred in the T3 plants compared to in the T2 plants. After moso bamboo seedlings were grown in tissue culture or treated by irradiation or plant hormones, the copy number of PHRE2 significantly increased. These findings indicate that PHRE2 has the capacity for transposition, which can be induced by environmental conditions.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Bechtold N, Ellis J, Pelletier G (1993) In planta Agrobacterium-mediated gene transfer by infiltration of adult Arabidopsis thaliana plants. C R Acad Sci Paris Life Sci 316:1194–1199

    CAS  Google Scholar 

  • Bubner B, Baldwin IT (2004) Use of real-time PCR for determining copy number and zygosity in transgenic plants. Plant Cell Rep 23:263–271

    Article  CAS  PubMed  Google Scholar 

  • Chang W, Schulman AH (2008) BARE retrotransposons produce multiple groups of rarely polyadenylated transcripts from two differentially regulated promoters. Plant J 56:40–50

    Article  CAS  PubMed  Google Scholar 

  • Chen A, Zhou M, Tang D (2017) Effects of treating bamboo seeds with 137 Cs-γRay and 5-azacytidine on methylation level of bamboo seedling. J Nucl Agric Sci 31:218–224

    Google Scholar 

  • Cheng C, Daigen M, Hirochika H (2006) Epigenetic regulation of the rice retrotransposon Tos17. Mol Genet Genom 276:378–390

    Article  CAS  Google Scholar 

  • Ding Y, Wang X, Su L, Zhai J, Cao S, Zhang D, Liu C, Bi Y, Qian Q, Cheng Z, Chu C, Cao X (2007) SDG714, a histone H3K9 methyltransferase, is involved in Tos17 DNA methylation and transposition in rice. Plant Cell 19:9–22

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dong LL, Zhao HS, Wang LL, Sun HY, Lou YF, Gao ZM (2016) Expression and Function of PeSCR Gene from Phyllostachys edulis. Sci Silvae Sin 52:35–42

    Google Scholar 

  • Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Eickbush TH, Jamburuthugoda VK (2008) The diversity of retroelements and the properties of their reverse transcriptases. Virus Res 134:221–234

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Feschotte C, Jiang N, Wessler SR (2002) Plant transposable elements: where genetics meets genomics. Nat Rev Genet 3:329–341

    Article  CAS  PubMed  Google Scholar 

  • Huang CC (2013) Studies on tissue culture of Phyllostachys Pubescens seed. Dissertation. Guangxi Normal University

  • Ingham DJ, Beer S, Money S, Hansen G (2001) Quantitative real-time PCR assay for determining transgene copy number in trans-formed plants. Biotechniques 31:132–140

    CAS  PubMed  Google Scholar 

  • Janzen DH (1976) Why bamboos wait so long to flower. Ann Rev Eco Syst 7:347–391

    Article  Google Scholar 

  • Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

    Article  CAS  PubMed  Google Scholar 

  • La H, Ding B, Mishra GP, Zhou B, Yang H, Bellizzi Mdel R, Chen S, Meyers BC, Peng Z, Zhu JK, Wang GL (2011) A 5-methylcytosine DNA glycosylase/lyase demethylates the retrotransposon Tos17 and promotes its transposition in rice. Proc Natl Acad Sci USA 108:15498–15503

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouzé P, Rombauts S (2002) PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res 30(1):325–327

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu H, Guo X, Wu J, Chen GB, Ying Y (2013) Development of universal genetic markers based on single-copy orthologousb (COS II) genes in Poaeeae. Plant Cell Rep 32:379–388

    Article  CAS  PubMed  Google Scholar 

  • Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2-DDCT method. Methods 25:402–408

    Article  CAS  PubMed  Google Scholar 

  • Llorens C, Fares MA, Moya A (2008) Relationships of gag-pol diversity between Ty3/Gypsy and Retroviridae LTR retroelements and the three kings hypothesis. BMC Evol Biol 8:276–294

    Article  PubMed  PubMed Central  Google Scholar 

  • Llorens C, Futami R, Covelli L, Dominguez-Escriba L, Viu JM, Tamarit D, Aguilar-Rodriguez J, Vicente-Ripolles M, Fuster G, Bernet GP, Maumus F, Munoz-Pomer A, Sempere JM, LaTorre A, Moya A (2011) The Gypsy database (GyDB) of mobile genetic elements: release 2.0. Nucleic Acids Res 39(Database issue):D70–D74

    Article  CAS  PubMed  Google Scholar 

  • Ma J, Jackson SA (2006) Retrotransposon accumulation and satellite amplification mediated by segmental duplication facilitate centromere expansion in rice. Genome Res 16:251–259

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Marí-Ordóñez A, Marchais A, Etcheverry M, Martin A, Colot V, Voinnet O (2013) Reconstructing de novo silencing of an active plant retrotransposon. Nat Genet 45:1029–1039

    Article  PubMed  Google Scholar 

  • McCarthy EM, McDonald JF (2003) LTR_STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics 19:362–367

    Article  CAS  PubMed  Google Scholar 

  • McClintock B (1951) Chromosome organization and genic expression. In: Cold Spring Harbor Symposia on Quantitative Biology. Cold Spring Harbor Lab Press 16:13–47

    Article  CAS  Google Scholar 

  • Mirouze M, Reinders J, Bucher E, Nishimura T, Schneeberger K, Ossowski S, Cao J, Weigel D, Paszkowski J, Mathieu O (2009) Selective epigenetic control of retrotransposition in Arabidopsis. Nature 461:427–430

    Article  CAS  PubMed  Google Scholar 

  • Morgante M, De Paoli E, Radovic S (2007) Transposable elements and the plant pan-genomes. Curr Opin Plant Biol 10:149–155

    Article  CAS  PubMed  Google Scholar 

  • Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4325

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Negi P, Rai AN, Suprasanna P (2016) Moving through the stressed genome: emerging regulatory roles for transposons in plant stress response. Front Plant Sci 7:1448

    PubMed  PubMed Central  Google Scholar 

  • Peng Z, Lu Y, Li L, Zhao Q, Feng Q, Gao Z, Lu H, Hu T, Yao N, Liu K, Li Y, Fan D, Guo Y, Li W, Lu Y, Weng Q, Zhou C, Zhang L, Huang T, Zhao Y, Zhu C, Liu X, Yang X, Wang T, Miao K, Zhuang C, Cao X, Tang W, Liu G, Liu Y, Chen J, Liu Z, Yuan L, Liu Z, Huang X, Lu T, Fei B, Ning Z, Han B, Jiang Z (2013) The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla). Nat Genet 45:456–461

    Article  CAS  PubMed  Google Scholar 

  • Rey O, Danchin E, Mirouze M, Loot C, Blanchet S (2016) Adaptation to global change: a transposable element–epigenetics perspective. Trends Ecol Evol 31:514–526

    Article  PubMed  Google Scholar 

  • Takeda S, Sugimoto K, Otsuki H, Hirochika H (1999) A 13-bp cis-regulatory element in the LTR promoter of the tobacco retrotransposon Tto1 is involved in responsiveness to tissue culture, wounding, methyl jasmonate and fungal eliecitors. Plant J 18:383–393

    Article  CAS  PubMed  Google Scholar 

  • Wang LL, Zhao HS, Sun HY, Dong LL, Lou YF, Gao ZM (2015) Cloning and expression analysis of miR397 and miR1432 in Phyllostachys edulis under stresses. Sci Silvae Sin 51:63–70

    Google Scholar 

  • Watanabe M, Ueda K, Manabe I, Akai T (1982) Flowering, seeding, germination and flowering periodicity of Phyllostachys pubescens. J Jpn For Soc 64:107–111

    Google Scholar 

  • Zhou M-B, Zheng Y, Liu Z-G, Xia X-W, Tang D-Q, Fu Y, Chen M (2016) Endo-1,4-\(\hat{\text{I}}^2\)-glucanase gene involved into the rapid elongation of Phyllostachys heterocycla var. pubescens. Trees 30(4):1259–1274

Download references

Acknowledgements

The National Natural Science Foundation of China (Grant Nos. 31470615 and 31270645) and the Talents Program of Natural Science Foundation of Zhejiang Province (Grant No. LR12C16001) supported this study.

Author information

Authors and Affiliations

Authors

Contributions

M. B. Zhou designated the experiments, identified PHRE2, constructed the vectors, and wrote the paper; L. L. Liang estimated the copy number of PHRE2 and performed Arabidopsis transformation; H. Hänninen revised and edited the paper; all authors read and approved the manuscript.

Corresponding author

Correspondence to Mingbing Zhou.

Ethics declarations

Conflict of interest

None declared.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 1689 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Zhou, M., Liang, L. & Hänninen, H. A transposition-active Phyllostachys edulis long terminal repeat (LTR) retrotransposon. J Plant Res 131, 203–210 (2018). https://doi.org/10.1007/s10265-017-0983-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10265-017-0983-8

Keywords

Navigation