Abstract
Mariner-like elements (MLEs) are class II transposable elements found in almost all eukaryotic genomes including those of plants, from which hundreds of complete and partial sequences have been elucidated. We have characterized 82 amplification fragments representing MLEs derived from diverse members of the Bambusoideae subfamily. Phylogenetic analysis of MLE transposase sequences shows that MLEs are widespread, diverse and abundant in the Bambusoideae. In addition, a molecular phylogeny of the Bambusoideae subfamily was established by using the internal transcribed spacer sequences of nuclear ribosomal DNA (ITS) information. The phylogenetic tree constructed using MLE fragment sequences was incongruent with a second tree based on ITS information. These results suggest horizontal transfer between distantly related species or the existence of an ancestral MLE polymorphism followed by divergent evolution and stochastic loss.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Adachi J, Hasegawa M (1996) MOLPHY: Programs for molecular phylogenetics based on maximum likelihood 2.3. The Institute of Statistical Mathematics, Tokyo
Bennetzen JL (2002) Mechanisms and rates of genome expansion and contraction in flowering plants. Genetica 115:29–36
Bui QT, Casse N, Leignel V, Nicolas V, Chenais B (2008) Widespread occurrence of mariner transposons in coastal crabs. Mol Phylogenet Evol 47(3):1181–1189
Capy P, Anxolabéhère D, Langin T (1994a) The strange phylogenies of transposable elements: are horizontal transfers the only explanation? Trends Genet 10:7–12
Capy P, Langin T, Bigot Y, Brunet F, Daboussi MJ, Périquet G, David JR, Hartl DL (1994b) Horizontal transmission versus ancient origin: mariner in the witness box. Genetica 93:161–170
Capy P, Bazin C, Higuet D, Langin T (1998) Dynamics and evolution of transposable elements. Springer, Austin
Clayton WD, Harman KT, Williamson H (2006) Grassbase, the online world grass flora. http://www.kew.org/data/grasses-db.html
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, New York, pp 225–268
Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15
Dransfield S, Widjaja EA (1995) Plant resources of South-East Asia No. 7 Bamboos. Backhuys Publishers, Leiden
Feschotte C, Wessler SR (2002) Mariner-like transposases are widespread and diverse in flowering plants. Proc Natl Acad Sci USA 99:280–285
Feschotte C, Jiang N, Wessler SR (2002) Plant transposable elements: where genetics meets genomics. Nat Rev Genet 3:329–341
Feschotte C, Swamy L, Wessler SR (2003) Genome-wide analysis of mariner-like transposable elements in rice reveals complex relationships with Stowaway MITEs. Genetics 163:747–758
Fortune P, Roulin A, Panaud O (2008) Horizontal transfer of transposable elements in plants. Commun Integr Biol 1(1):74–77
Fu J (2001) Chinese Moso Bamboo: its importance. Bamboo 22(5):5–7
Gaut BS (2002) Evolutionary dynamics of grass genomes. New Phytol 154:15–28
Geng B, Wang Z (1996) Tomus 9(1) Angiospermae: Monocotyledoneae Graminales (Poaceae): Bambusoideae. Science Press, Beijing, pp 189–304
Gielis J, Valente P, Bridts C et al (1997) Estimation of DNA content of bamboos using flow cytometry and confocal laser scanning microscopy. The Bamboos. Academic Press, London, pp 215–223
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 C: Life Sci 50(5):700–705
Guo ZH, Li DZ (2002) Advances in the systematics and biogeography of the Bambusoideae (Gramineae) with remarks on some remaining problems. Acta Bot Yunn 24(4):431–438
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 30:1–12
Hartl DL (2001) Discovery of the transposable element mariner. Genetics 157:471–476
Hartl DL, Lohe AR, Lozovskaya ER (1997) Modern thoughts on an ancient mariner: function, evolution, regulation. Ann Rev Genet 31:337–358
Hui CC, Yang YM (2003) Studies on the bamboo diversity and its conservation in Yunnan, China. Scientia Silvae Sin 39:145–152
Jarvik T, Lark KG (1998) Characterization of Soymar1, a mariner-like element in soybean. Genetics 149:1569–1574
Kellogg EA (2001) Evolutionary history of the grasses. Plant Physiol 125:1198–1205
Lampe DJ, Witherspoon DJ, Soto-Adames FN, Robertson HM (2003) Recent horizontal transfer of mellifera subfamily mariner transposons into insect clades representing four different orders shows that selection acts only during horizontal transfer. Mol Biol Evol 20:554–562
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 61–81
Lin XC, Ruan XS, Lou YF, Guo XQ, Fang W (2009) Genetic similarity among cultivars of Phyllostachys pubescens. Plant Syst Evol 277:67–73
Medhora MM, MacPeek AH, Hartl DL (1988) Excision of the Drosophila transposable element mariner: identification and characterization of the Mos factor. EMBO J 7:2185–2189
Plasterk RHA, van Luenen HGAM (2002) The Tc1/Mariner family of transposable elements. In: Craig NL, Craigie R, Geller M, Lambowitz AM (eds) Mobile DNA II. American Society for Microbiology Press, Washington, pp 519–532
Plasterk RHA, Izsvak Z, Ivics Z (1999) Resident aliens: the Tc1/mariner superfamily of transposable elements. Trends Genet 15:326–332
Posada D, Crandall K (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817–818
Prud’homme N, Gans M, Masson M, Terzian C, Bucheton A (1995) flamenco, a gene controlling the gypsy retrovirus of Drosophila melanogaster. Genetics 139(2):697–711
Robertson HM, Soto-Adames FN, Walden KO, Avancini RM, Lampe DJ (1998) The mariner transposons of animals: horizontally jumping genes. In: Syvanen M, Kido CI (eds) Horizontal Gene Transfer. Chapman & Hall, London, pp 268–284
Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574
Silva JC, Loreto EL, Clark JB (2004) Factors that affect the horizontal transfer of transposable elements. Curr Issues Mol Biol 6:57–72
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, New York, pp 225–238
Sullivan J, Joyce P (2005) Model selection in phylogenetics. Ann Rev Ecol Evol Syst 36:445–466
Swofford D (2002) PAUP phylogenetic analysis using parsimony (*and other methods), Version 4.0b 10. Sinauer Associates, Sunderland
Tang DQ, Lu JJ, Fang W, Zhang S, Zhou MB (2010) Development, characterization and utilization of GenBank microsatellite markers in Phyllostachys pubescens and related species. Mol Breed 25:299–311
Tarchini R, Biddle P, Wineland R, Tingey S, Rafalski A (2000) The complete sequence of 340 kb of DNA around the rice Adh1-Adh2 region reveals interrupted colinearity with maize chromosome 4. Plant Cell 12:391–441
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 22:4673–4680
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 315–322
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):809–824
Acknowledgments
We are grateful to N. Ma of the Research Institute of Subtropical Forestry and X. Lin of the Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, for their advice on sketching the sampling strategies. We are also indebted to K. Yoshinaga of the World Bamboos Research Center, Fukuoka, Japan, C. Zhou of Anji Bamboo Museum Garden, M. Zhao of Tianmu Mountain World Biosphere Reserve, and Y. Zhou of Huaan Bamboo Garden for help in collecting the bamboo materials tested in study. This work was supported by special grants from the National Natural Science Foundation of China (nos 30371181 and 30771753) and the Talents Program of Natural Science Foundation of Zhejiang Province (no. R303420).
Author information
Authors and Affiliations
Corresponding authors
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Zhou, MB., Lu, JJ., Zhong, H. et al. Distribution and polymorphism of Mariner-like elements in the Bambusoideae subfamily. Plant Syst Evol 289, 1–11 (2010). https://doi.org/10.1007/s00606-010-0323-0
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00606-010-0323-0