Publications

Brookfield JF (1991). Models of repression of transposition in P-M hybrid dysgenesis by P cytotype and by zygotically encoded repressor proteins. Genetics 128: 471-486. PMid:1649073    PMCid:1204483 Capy P, Bazin C, Higuet D and Langin T (1998). Dynamics and Evolution of Transposable Elements. Springer-Verlag, Austin. http://dx.doi.org/10.1007/978-94-011-4898-6 Casola C, Lawing AM, Betran E and Feschotte C (2007). PIF-like transposons are common in Drosophila and have been repeatedly domesticated to generate new host genes. Mol. Biol. Evol. 24: 1872-1888. http://dx.doi.org/10.1093/molbev/msm116 PMid:17556756 Doyle JJ and Doyle JL (1987). A rapid isolation procedure for small quantities of fresh leaf materials. Phytochem. Bull. 19: 11-15. Feschotte C, Jiang N and Wessler SR (2002a). Plant TEs: where genetics meets genomics. Nat. Rev. Genet. 3: 329-341. http://dx.doi.org/10.1038/nrg793 PMid:11988759 Feschotte C, Zhang X and Wessler SR (2002b). Miniature Inverted-Repeat Transposable Elements (MITEs) and their Relationship with Established DNA Transposons. In: Mobile DNA II (Craig NL, Craigie R, Gellert M and Lambowitz AM, eds.). Society for Microbiology Press, Washington, 1147-1158. Finnegan DJ (1992). Transposable Elements. In: The Genome of Drosophila melanogaster (Lindsley DL and Zimm G, eds.). Academic Press, New York, 1096-1107. Hartl DL, Lohe AR and Lozovskaya ER (1997a). Modern thoughts on an ancyent marinere: function, evolution, regulation. Annu. Rev. Genet. 31: 337-358. http://dx.doi.org/10.1146/annurev.genet.31.1.337 PMid:9442899 Hartl DL, Lozovskaya ER, Nurminsky DI and Lohe AR (1997b). What restricts the activity of mariner-like TEs? Trends Genet. 13: 197-201. http://dx.doi.org/10.1016/S0168-9525(97)01087-1 Holligan D, Zhang XY, Jiang N and Pritham EJ (2006). The transposable element landscape of the model legume Lotus japonicus. Genetics 174: 2215-2228. http://dx.doi.org/10.1534/genetics.106.062752 PMid:17028332    PMCid:1698628 Jiang N, Bao Z, Zhang X, Hirochika H, et al. (2003). An active DNA transposon family in rice. Nature 421: 163-167. http://dx.doi.org/10.1038/nature01214 PMid:12520302 Kapitonov VV and Jurka J (1999). Molecular paleontology of transposable elements from Arabidopsis thaliana. Genetica 107: 27-37. http://dx.doi.org/10.1023/A:1004030922447 PMid:10952195 Le QH, Wright S, Yu ZH and Bureau T (2000). Transposon diversity in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U. S. A. 97: 7376-7381. http://dx.doi.org/10.1073/pnas.97.13.7376 Le QH, Turcotte K and Bureau T (2001). Tc8, a Tourist-like transposon in Caenorhabditis elegans. Genetics 158: 1081- 1088. PMid:11454757    PMCid:1461737 Montgomery EA, Charlesworth B and Langley CH (1987). A test for the role of natural selection in the stabilization of transposable element copy number in a population of Drosophila melanogaster. Genet. Res. 49: 31-41. http://dx.doi.org/10.1017/S0016672300026707 Pritham EJ (2009). Transposable elements and factors influencing their success in eukaryotes. Heredity J. 100: 648-655. http://dx.doi.org/10.1093/jhered/esp065 PMid:19666747    PMCid:2877548 Roux KH (1995). Optimization and troubleshooting in PCR. PCR Methods Appl. 4: S185-S194. PMid:7580907 Sambrook J, Fritsch EF and Maniatis T (1987). Molecular Cloning: A Laboratory Manual. 2nd edn. Cold Spring Harbor Laboratory, Cold Spring Harbor. Siebert PD, Chenchik A, Kellogg DE, Lukyanov KA, et al. (1995). An improved PCR method for walking in uncloned genomic DNA. Nucleic Acids Res. 23: 1087-1088. http://dx.doi.org/10.1093/nar/23.6.1087 PMid:7731798    PMCid:306810 Swofford DL (2002). PAUP: Phylogenetic Analysis Using Parsimony (*and other Methods). Version 4.0b 10. Sinauer Associates, Sunderland. Tang DQ (2009). Genomic sequencing and its application for biological and evolutional research in bamboo. Bamboo J. 26: 1-10. Thompson JD, Higgins DG and Gibson TJ (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680. http://dx.doi.org/10.1093/nar/22.22.4673 PMid:7984417    PMCid:308517 Walker EL, Eggleston WB, Demopulos D, Kermicle J, et al. (1997). Insertions of a novel class of transposable elements with a strong target site preference at their locus of maize. Genetics 146: 681-693. PMid:9178016    PMCid:1208007 Zhang X, Feschotte C, Zhang Q, Jiang N, et al. (2001). P instability factor: an active maize transposon system associated with the amplification of Tourist-like MITEs and a new superfamily of transposases. Proc. Natl. Acad. Sci. U. S. A. 98: 12572-12577. http://dx.doi.org/10.1073/pnas.211442198 PMid:11675493    PMCid:60095 Zhang X, Jiang N, Feschotte C and Wessler SR (2004). PIF- and Pong-like transposable elements: distribution, evolution and relationship with Tourist-like miniature inverted-repeat transposable elements. Genetics 166: 971-986. http://dx.doi.org/10.1534/genetics.166.2.971 PMid:15020481    PMCid:1470744 Zhou MB, Lu JJ, Zhong H and Tang DQ (2010). Distribution and diversity of PIF-like transposable elements in the Bambusoideae subfamily. Plant Sci. 179: 257-266. http://dx.doi.org/10.1016/j.plantsci.2010.05.012

Akagi H, Yokozeki Y, Inagaki A, Mori K, et al. (2001). Micron, a microsatellite-targeting transposable element in the rice genome. Mol. Genet. Genomics 266: 471-480. http://dx.doi.org/10.1007/s004380100563 PMid:11713677 Barker NP, Clark LG, Davis JI, Duvall MR, et al. (2001). Phylogeny and subfamilial classification of the grasses (Poaceae). Ann. Missouri Bot. Garden 88: 373-457. http://dx.doi.org/10.2307/3298585 Bennetzen JL (2002). Mechanisms and rates of genome expansion and contraction in flowering plants. Genetica 115: 29-36. http://dx.doi.org/10.1023/A:1016015913350 PMid:12188046 Clark LG (1996). Diversity, Biogeography and Evolution of Chusquea. In: International Symposium on Bamboos (Chapman GP, ed.). Academic Press Ltd., London, 33-44. Dransfield S and Widjaja EA (1995). Plant Resources of South-East Asia No. 7 Bamboos. Backhuys Publishers, Leiden. Feschotte C (2008). TEs and the evolution of regulatory networks. Nat. Rev. Genet. 9: 397-405. http://dx.doi.org/10.1038/nrg2337 PMid:18368054    PMCid:2596197 Feschotte C, Jiang N and Wessler SR (2002). Plant transposable elements: where genetics meets genomics. Nat. Rev. Genet. 3: 329-341. http://dx.doi.org/10.1038/nrg793 PMid:11988759 Fu J (2001). Chinese Moso Bamboo: Its importance. Bamboo 22: 5-7. Geilis J, Everaert I and De Loose M (1997). Genetic Variability and Relationships in Phyllostachys Using Random Amplified Polymorphic DNA. In: The Bamboos (Chapman GP, ed.). Linnean Society Symposium, Academic Press, London, 107-124. Gui Y, Wang S, Quan L, Zhou C, et al. (2007). Genome size and sequence composition of moso bamboo: a comparative study. Sci. China C Life Sci. 50: 700-705. http://dx.doi.org/10.1007/s11427-007-0081-6 PMid:17879070 Guo ZH and Li DZ (2002). Advances in the systematics and biogeography of the Bambusoideae (Gramineae) with remarks on some remaining problems. Acta Bot. Yunnanica 24: 431-438. Huang X and Madan A (1999). CAP3: A DNA sequence assembly program. Genome Res. 9: 868-877. http://dx.doi.org/10.1101/gr.9.9.868 PMid:10508846    PMCid:310812 Jiao Y and Deng XW (2007). A genome-wide transcriptional activity survey of rice transposable element-related genes. Genome Biol. 8: R28. http://dx.doi.org/10.1186/gb-2007-8-2-r28 PMid:17326825    PMCid:1852403 Jordan IK, Rogozin IB, Glazko GV and Koonin EV (2003). Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends Genet. 19: 68-72. http://dx.doi.org/10.1016/S0168-9525(02)00006-9 Kellogg EA (2001). Evolutionary history of the grasses. Plant Physiol. 125: 1198-1205. http://dx.doi.org/10.1104/pp.125.3.1198 PMid:11244101    PMCid:1539375 Klinkenborg V (2001). Bamboo for Gardens. Times Book Rev, New York. Lander ES, Linton LM, Birren B, Nusbaum C, et al. (2001). Initial sequencing and analysis of the human genome. Nature 409: 860-921. http://dx.doi.org/10.1038/35057062 PMid:11237011 Lockton S and Gaut BS (2009). The contribution of transposable elements to expressed coding sequence in Arabidopsis thaliana. J. Mol. Evol. 68: 80-89. http://dx.doi.org/10.1007/s00239-008-9190-5 PMid:19125217 Marino-Ramirez L, Lewis KC, Landsman D and Jordan IK (2005). Transposable elements donate lineage-specific regulatory sequences to host genomes. Cytogenet. Genome Res. 110: 333-341. http://dx.doi.org/10.1159/000084965 Matsuoka Y and Tsunewaki K (1999). Evolutionary dynamics of Ty1-copia group retrotransposons in grass shown by reverse transcriptase domain analysis. Mol. Biol. Evol. 16: 208-217. PMid:10028288 Naito K, Zhang F, Tsukiyama T, Saito H, et al. (2009). Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Nature 461: 1130-1134. http://dx.doi.org/10.1038/nature08479 PMid:19847266 Peng Z, Lu T, Li L, Liu X, et al. (2010). Genome-wide characterization of the biggest grass, bamboo, based on 10,608 putative full-length cDNA sequences. BMC Plant Biol. 10: 116. http://dx.doi.org/10.1186/1471-2229-10-116 PMid:20565830    PMCid:3017805 Pritham EJ (2009). TEs and factors influencing their success in eukaryotes. J. Heredity 100: 648-655. http://dx.doi.org/10.1093/jhered/esp065 PMid:19666747    PMCid:2877548 Ramsay L, Macaulay M, Cardle L, Morgante M, et al. (1999). Intimate association of microsatellite repeats with retrotransposons and other dispersed repetitive elements in barley. Plant J. 17: 415-425. http://dx.doi.org/10.1046/j.1365-313X.1999.00392.x PMid:10205898 Richard GF, Kerrest A and Dujon B (2008). Comparative genomics and molecular dynamics of DNA repeats in eukaryotes. Micr. Mol. Bio. Rev. 72: 686-727. http://dx.doi.org/10.1128/MMBR.00011-08 PMid:19052325    PMCid:2593564 SanMiguel P and Bennetzen JL (1998). Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Ann. Bot. 82: 37-44. http://dx.doi.org/10.1006/anbo.1998.0746 Scherer S (2008). A Short Guide to the Human Genome. Cold Spring Harbor University Press, Cold Spring, New York. Schnable PS, Ware D, Fulton RS, Stein JC, et al. (2009). The B73 maize genome: complexity, diversity, and dynamics. Science 326: 1112-1115. http://dx.doi.org/10.1126/science.1178534 PMid:19965430 Sinzelle L, Izsvak Z and Ivics Z (2009). Molecular domestication of transposable elements: from detrimental parasites to useful host genes. Cell Mol. Life Sci. 66: 1073-1093. http://dx.doi.org/10.1007/s00018-009-8376-3 PMid:19132291 Skibbe DS, Fernandes JF, Medzihradszky KF, Burlingame AL, et al. (2009). Mutator transposon activity reprograms the transcriptomes and proteomes of developing maize anthers. Plant J. 59: 622-633. http://dx.doi.org/10.1111/j.1365-313X.2009.03901.x PMid:19453454 Soderstrom TR and Ellis RP (1987). The Position of Bamboo Genera and Allies in a System of Grass Classification. In: Grass Systematics and Evolution (Soderstrom TR, Hilu KW, Campbell CS and Barkworth ME, eds.). Smithsonian Institution Press, New York, 225-238. Swofford DL (2002). PAUP: Phylogenetic Analysis Using Parsimony (*and other methods). Version 4.0b 10. Sinauer Associates, Sunderland. Tang DQ (2009). Genomic sequencing and its application for biological and evolutional research in bamboo. Bamboo J. 26: 1-10. Temnykh S, DeClerck G, Lukashova A, Lipovich L, et al. (2001). Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res. 11: 1441-1452. http://dx.doi.org/10.1101/gr.184001 PMid:11483586    PMCid:311097 Thompson JD, Higgins DG and Gibson TJ (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680. http://dx.doi.org/10.1093/nar/22.22.4673 PMid:7984417    PMCid:308517 Turcotte K, Srinivasan S and Bureau T (2001). Survey of transposable elements from rice genomic sequences. Plant J. 25: 169-179. http://dx.doi.org/10.1046/j.1365-313x.2001.00945.x PMid:11169193 Zhong H, Zhou M, Xu C and Tang DQ (2010). Diversity and evolution of Pong-like elements in Bambusoideae subfamily. Biochem. Syst. Ecol. 38: 750-758. http://dx.doi.org/10.1016/j.bse.2010.06.010 Zhou MB, Lu JJ, Zhong H, Liu XM, et al. (2010a). Distribution and diversity of PIF-like transposable elements in the Bambusoideae subfamily. Plant Sci. 179: 257-266. http://dx.doi.org/10.1016/j.plantsci.2010.05.012 Zhou MB, Lu JJ, Zhong H, Tang KX, et al. (2010b). Distribution and polymorphism of mariner-like elements in the Bambusoideae subfamily. Plant Syst. Evol. 289: 1-11. http://dx.doi.org/10.1007/s00606-010-0323-0 Zhou MB, Zhong H, Zhang QH, Tang KX, et al. (2010c). Diversity and evolution of Ty1-copia retroelements in representative tribes of Bambusoideae subfamily. Genetica 138: 861-868. http://dx.doi.org/10.1007/s10709-010-9469-5 PMid:20577895