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Journal of Plant Research

, Volume 131, Issue 2, pp 203–210 | Cite as

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

  • Mingbing Zhou
  • Linlin Liang
  • Heikki Hänninen
Regular Paper

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.

Keywords

Long terminal repeat (LTR) retrotransposons Moso bamboo [Phyllostachys edulis (Carrière) J. Houz] Arabidopsis Transposition activation 

Notes

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 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.

Compliance with ethical standards

Conflict of interest

None declared.

Supplementary material

10265_2017_983_MOESM1_ESM.pdf (1.6 mb)
Supplementary material 1 (PDF 1689 KB)

References

  1. 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 316:1194–1199Google Scholar
  2. Bubner B, Baldwin IT (2004) Use of real-time PCR for determining copy number and zygosity in transgenic plants. Plant Cell Rep 23:263–271CrossRefPubMedGoogle Scholar
  3. Chang W, Schulman AH (2008) BARE retrotransposons produce multiple groups of rarely polyadenylated transcripts from two differentially regulated promoters. Plant J 56:40–50CrossRefPubMedGoogle Scholar
  4. 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 31:218–224Google Scholar
  5. Cheng C, Daigen M, Hirochika H (2006) Epigenetic regulation of the rice retrotransposon Tos17. Mol Genet Genom 276:378–390CrossRefGoogle Scholar
  6. 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 19:9–22CrossRefPubMedPubMedCentralGoogle Scholar
  7. 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 52:35–42Google Scholar
  8. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797CrossRefPubMedPubMedCentralGoogle Scholar
  9. Eickbush TH, Jamburuthugoda VK (2008) The diversity of retroelements and the properties of their reverse transcriptases. Virus Res 134:221–234CrossRefPubMedPubMedCentralGoogle Scholar
  10. Feschotte C, Jiang N, Wessler SR (2002) Plant transposable elements: where genetics meets genomics. Nat Rev Genet 3:329–341CrossRefPubMedGoogle Scholar
  11. Huang CC (2013) Studies on tissue culture of Phyllostachys Pubescens seed. Dissertation. Guangxi Normal UniversityGoogle Scholar
  12. Ingham DJ, Beer S, Money S, Hansen G (2001) Quantitative real-time PCR assay for determining transgene copy number in trans-formed plants. Biotechniques 31:132–140PubMedGoogle Scholar
  13. Janzen DH (1976) Why bamboos wait so long to flower. Ann Rev Eco Syst 7:347–391CrossRefGoogle Scholar
  14. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874CrossRefPubMedGoogle Scholar
  15. 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 108:15498–15503CrossRefPubMedPubMedCentralGoogle Scholar
  16. 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):325–327CrossRefPubMedPubMedCentralGoogle Scholar
  17. 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 32:379–388CrossRefPubMedGoogle Scholar
  18. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2-DDCT method. Methods 25:402–408CrossRefPubMedGoogle Scholar
  19. 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 8:276–294CrossRefPubMedPubMedCentralGoogle Scholar
  20. 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–D74CrossRefPubMedGoogle Scholar
  21. Ma J, Jackson SA (2006) Retrotransposon accumulation and satellite amplification mediated by segmental duplication facilitate centromere expansion in rice. Genome Res 16:251–259CrossRefPubMedPubMedCentralGoogle Scholar
  22. 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 45:1029–1039CrossRefPubMedGoogle Scholar
  23. McCarthy EM, McDonald JF (2003) LTR_STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics 19:362–367CrossRefPubMedGoogle Scholar
  24. McClintock B (1951) Chromosome organization and genic expression. In: Cold Spring Harbor Symposia on Quantitative Biology. Cold Spring Harbor Lab Press 16:13–47CrossRefGoogle Scholar
  25. 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 461:427–430CrossRefPubMedGoogle Scholar
  26. Morgante M, De Paoli E, Radovic S (2007) Transposable elements and the plant pan-genomes. Curr Opin Plant Biol 10:149–155CrossRefPubMedGoogle Scholar
  27. Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4325CrossRefPubMedPubMedCentralGoogle Scholar
  28. Negi P, Rai AN, Suprasanna P (2016) Moving through the stressed genome: emerging regulatory roles for transposons in plant stress response. Front Plant Sci 7:1448PubMedPubMedCentralGoogle Scholar
  29. 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 45:456–461CrossRefPubMedGoogle Scholar
  30. Rey O, Danchin E, Mirouze M, Loot C, Blanchet S (2016) Adaptation to global change: a transposable element–epigenetics perspective. Trends Ecol Evol 31:514–526CrossRefPubMedGoogle Scholar
  31. 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 18:383–393CrossRefPubMedGoogle Scholar
  32. 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 51:63–70Google Scholar
  33. Watanabe M, Ueda K, Manabe I, Akai T (1982) Flowering, seeding, germination and flowering periodicity of Phyllostachys pubescens. J Jpn For Soc 64:107–111Google Scholar
  34. 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):1259–1274Google Scholar

Copyright information

© The Botanical Society of Japan and Springer Japan KK 2017

Authors and Affiliations

  • Mingbing Zhou
    • 1
    • 2
  • Linlin Liang
    • 1
  • Heikki Hänninen
    • 1
  1. 1.State Key Laboratory of Subtropical SilvicultureZhejiang A & F UniversityLinanPeople’s Republic of China
  2. 2.Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-efficiency UtilizationZhejiang A & F UniversityLinanPeople’s Republic of China

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