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Genetica

, Volume 138, Issue 8, pp 861–868 | Cite as

Diversity and evolution of Ty1-copia retroelements in representative tribes of Bambusoideae subfamily

  • Ming-bing Zhou
  • Hao Zhong
  • Qin-hui Zhang
  • Ke-Xuan Tang
  • Ding-Qin Tang
Article

Abstract

Ty1-copia retroelements have been found in all major plants and are largely responsible for the huge differences in the genome size. In this study we isolated and sequenced Ty1-copia reverse transcriptase (rt) gene fragments from 44 representative species of bamboo and nine cultivars or forms of Phyllostachys pubescens. Phylogenetic analysis of 72 distinct Ty1-copia rt sequences showed that Ty1-copia retroelements were widespread, diverse and abundant in these species of Bambusoideae subfamily. In addition, a molecular phylogeny of the species of the Bambusoideae subfamily was established by using the internal transcribed spacer sequences of nuclear ribosomal DNA (ITS) sequences. The comparison between ITS- and Ty1-copia rt- based trees is obviously incongruent. The results suggested either the existence of horizontal transfer events between phylogenetically distant species, or an ancestral Ty1-copia retroelement polymorphism followed by different evolution and stochastic losses.

Keywords

Ty1-copia Retroelement Bambusoideae Diversity Evolution 

Notes

Acknowledgements

We are grateful to Ma N. of Research Institute of subtropical forestry and Lin X. of Key Lab for Modern Silvicultural Technology of Zhejiang Province for their advices on sketching the sampling strategies. We are also indebted to Yoshinaga K. of World Bamboos Research Center, Fukuoka, Japan, Zhou C. of Anji Bamboo Museum Garden, Zhao M. of Tianmu Mountain World Biosphere Reserve and ZhouY. of Huaan Bamboo Garden for help in collecting materials tested in study. This work was supported by the grant from the National Natural Science Foundation of China (grant no. 30371181 and 30771753), the grant from Natural Science Foundation of Zhejiang Province (No. Y3080002) and through Talents Program of Natural Science Foundation of Zhejiang Province (grant no. R303420).

Supplementary material

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References

  1. Adachi J, Hasegawa M (1996) MOLPHY: programs for molecular phylogenetics based on maximum likelihood 2.3. The Institute of Statistical Mathematics, TokyoGoogle Scholar
  2. Alix K, Heslop-Harrison JS (2004) The diversity of retroelements in diploid and allotetraploid Brassica species. Plant Mol Biol 54:895–909CrossRefPubMedGoogle Scholar
  3. Alix K, Ryder CR, Moore JM, King G, Heslop-Harrison JS (2005) The genomic organization of retrotransposons in Brassica oleracea. Plant Mol Biol 59:839–851CrossRefPubMedGoogle Scholar
  4. Bennetzen JL (2002) Mechanisms and rates of genome expansion and contraction in flowering plants. Genetica 115:29–36CrossRefPubMedGoogle Scholar
  5. Brosius J (1999) Genomes were forged by massive bombardments with retroelements and retrosequences. Genetica 107:209–238CrossRefPubMedGoogle Scholar
  6. Chen R, Li X, Song W, Liang G, Zhang P, Lin R, Zong W, Chen C, Fung H (2003) Chromosome atlas of major economic plants genome in China, Tomus IV: chromosome atlas of various bamboo species. Science Press, Beijing, pp 275–284Google Scholar
  7. Clayton WD, Harman KT, Williamson H (2006) GrassBase, the online world grass flora. http://www.kew.org/data/grasses-db.html
  8. Das M, Bhattacharya S, Singh P, Filgueiras TS, Pal A (2008) Bamboo taxonomy and diversity in the era of molecular markers. In: Jean-Claude K, Michel D (eds) Advances in botanical research vol 47. Academic Press, London, pp 225–268Google Scholar
  9. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15Google Scholar
  10. Dransfield S, Widjaja EA (1995) Plant resources of South-East Asia No. 7 Bamboos. Backhuys Publishers, LeidenGoogle Scholar
  11. Eickbush T (1994) Origin and evolutionary relationships of retroelements. In: Morse S (ed) The evolutionary biology of viruses. Raven Press, New York, pp 121–157Google Scholar
  12. Ellis THN, Poyser SJ, Knox MR, Vershinin AV, Ambrose MJ (1998) Polymorphism of insertion sites of Ty1-copia class retrotransposons and its use for linkage and diversity analysis in pea. Mol Gen Genet 260:9–19PubMedGoogle Scholar
  13. Feschotte C, Jiang N, Wessler SR (2002) Plant transposable elements: where genetics meets genomics. Nat Rev Genet 3:329–341CrossRefPubMedGoogle Scholar
  14. Flavell AJ, Smith DB, Kumar A (1992) Extreme heterogeneity of Ty1-copia group retrotransposons in plants. Mol Gen Genet 231:233–242PubMedGoogle Scholar
  15. Flavell AJ, Pearce SR, Heslop-Harrison JS, Kumar A (1997) The evolution of Ty1-copia group retrotransposons in eukaryote genomes. Genetica 100:185–195CrossRefPubMedGoogle Scholar
  16. Fortune P, Roulin A, Panaud O (2008) Horizontal transfer of transposable elements in plants. Commun Integr Biol 1(1):74–77CrossRefPubMedGoogle Scholar
  17. Friesen N, Brandes A, Heslop-Harrison JS (2001) Diversity, origin and distribution of retrotransposons (gypsy and Ty1-copia) in conifers. Mol Biol Evol 18:1176–1188PubMedGoogle Scholar
  18. Fu J (2001) Chinese moso bamboo: its importance. Bamboo 22(5):5–7Google Scholar
  19. Geng B, Wang Z (1996) Tomus 9(1) Angiospermae: Monocotyledoneae Graminales (Poaceae): Bambusoideae. Science Press, BeijingGoogle Scholar
  20. Gielis J, Valente P, Bridts C, Verbelen J-P (1997) Estimation of DNA content of bamboos using flow cytometry and confocal laser scanning microscopy. In: Chapman GP (ed) The Bamboos. Academic Press, London, pp 215–223Google Scholar
  21. Gribbon BM, Pearce SR, Kalendar R, Schulman AH, Paulin L, Jack P, Kumar A, Flavell AJ (1999) Phylogeny and transpositional activity of Ty1-copia group retrotransposons in cereal genomes. Mol Gen Genet 261:883–891CrossRefPubMedGoogle Scholar
  22. Gui Y, Sheng W, Quan L, Zhou C, Long S, Zheng H, Jin L, Zhang X, Ma N, Fan L (2007) Genome size and sequence composition of moso bamboo: a comparative study. Sci China Series C Life Sci 50(5):700–705CrossRefGoogle Scholar
  23. Guo ZH, Li DZ (2004) Phylogenetics of the Thamnocalamus group and its allies (Gramineae: Bambusoideae): inference from the sequences of GBSSI gene and ITS spacer. Mol Phylogenet Evol 30:1–12CrossRefPubMedGoogle Scholar
  24. Heslop-Harrison JS, Brandes A, Taketa S, Schmidt T, Vershinin AV, Alkhimova EG, Kamm A, Doudrick RL, Schwarzacher T, Katsiotis A, Kubis S, Kumar A, Pearce SR, Flavell AJ, Harrison GE (1997) The chromosomal distributions of Ty1-copia group retrotransposable elements in higher plants and their implications for genome evolution. Genetica 100:197–204CrossRefPubMedGoogle Scholar
  25. Hirochika H, Hirochika R (1993) Ty1-group retrotransposons as ubiquitous components of plant genomes. Jpn J Genet 68:35–46CrossRefPubMedGoogle Scholar
  26. Hirochika H, Fukuchi A, Kikuchi F (1992) Retrotransposon families in rice plants. Mol Gen Genet 233:209–216CrossRefPubMedGoogle Scholar
  27. Hunziker JH, Wulff AF, Soderstrom TR (1982) Chromosome studies on the Bambusoideae (Gramineae). Brittonia 34(1):30–35CrossRefGoogle Scholar
  28. Kidwell MG (2002) Transposable elements and the evolution of genome size in eukaryotes. Genetica 115:49–63CrossRefPubMedGoogle Scholar
  29. Kumar A, Bennetzen JL (1999) Plant retrotransposons. Annu Rev Genet 33:479–532CrossRefPubMedGoogle Scholar
  30. Le QH, Wright S, Yu Z, Bureau T (2000) Transposon diversity in Arabidopsis thaliana. Proc Natl Acad Sci USA 97:7376–7381CrossRefPubMedGoogle Scholar
  31. Li DZ (1997) The flora of China Bambusoideae project-problems and current understanding of bamboo taxonomy in China. In: Chapman GP (ed) The bamboos. Academic Press, London, pp 61–81Google Scholar
  32. Lin XC, Ruan XS, Lou YF, Guo XQ, Fang W (2009) Genetic similarity among cultivars of Phyllostachys pubescens. Plant Syst Evol 277:67–73CrossRefGoogle Scholar
  33. Matsuoka Y, Tsunewaki K (1999) Evolutionary dynamics of Ty1-copia group retrotransposons in grass shown by reverse transcriptase domain analysis. Mol Biol Evol 16:208–217PubMedGoogle Scholar
  34. Posada D, Crandall K (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817–818CrossRefPubMedGoogle Scholar
  35. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574CrossRefPubMedGoogle Scholar
  36. Soderstrom TR, Ellis RP (1987) The position of bamboo genera and allies in a system of grass classification. In: Soderstrom TR, Hilu KW, Campbell CS, Barkworth ME (eds) Grass systematics and evolution. Smithsonian Institution Press, Washington, pp 225–238Google Scholar
  37. Stuart-Rogers C, Flavell AJ (2001) The evolution of Ty1-copia group retrotransposons in gymnosperms. Mol Biol Evol 18:155–163PubMedGoogle Scholar
  38. Sullivan J, Joyce P (2005) Model selection in phylogenetics. Ann Rev Ecol Evol Syst 36:445–466CrossRefGoogle Scholar
  39. Swofford (2002) DL Swofford, PAUP*, Phylogenetic Analysis Using Parsimony (and other methods), Version 4.10., Illinois Natural History Survey, Champaign, IllinoisGoogle Scholar
  40. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680CrossRefPubMedGoogle Scholar
  41. VanderWiel PL, Voytas DF, Wendel JF (1993) Copia-like retrotransposable element evolution in diploid and polyploid cotton (Gossypium L.). J Mol Evol 36:429–447CrossRefPubMedGoogle Scholar
  42. Voytas DF, Cummings MP, Konieczny A, Ausubel FM, Rodermel SR (1992) Ty1-copia retrotransposons are ubiquitous among plants. Proc Natl Acad Sci USA 89:7124–7128CrossRefPubMedGoogle Scholar
  43. Wang S, Liu N, Peng K, Zhang Q (1999) The distribution and copy number of copia-like retrotransposons in rice (Oryza sativa L.) and their implications in the organization and evolution of the rice genome. Proc Natl Acad Sci USA 96:6824–6828CrossRefPubMedGoogle Scholar
  44. White TJ, Bruns Y, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal RNA genes for phylogenetics. In: Innis M, Gelfand D, Sninsky J, White T (eds) PCR protocols: a guide to methods and applications. Academic Press, San Diego, pp 315–322Google Scholar
  45. Xiong Y, Eickbush TH (1990) Origin and evolution of retroelements based on their reverse transcriptase sequences. EMBO J 9:3353–3362PubMedGoogle Scholar
  46. Yang HQ, Yang JB, Gao J, Yang YM, Peng S, Li DZ (2008) A molecular phylogenetic and fruit evolutionary analysis of the major groups of the paleotropical woody bamboos (Gramineae: Bambusoideae) based on nuclear ITS, GBSSI gene and plastid trnL-F DNA sequences. Mol Phylogenet Evol 48(3):809–824CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  1. 1.School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
  2. 2.The Nurturing Station for the State Key Laboratory of Subtropical SilvicultureZhejiang A & F UniversityLinAn, Zhejiang ProvinceChina

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