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LETTER: Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: New functional implications for MITEs
- Hanhui Kuang,
- Chellappan Padmanabhan,
- Feng Li,
- Ayako Kamei,
- Pudota B. Bhaskar,
- Shu Ouyang,
- Jiming Jiang,
- C. Robin Buell,
- and Barbara Baker
Genome Res. January 2009 19: 42-56; Published in Advance November 26, 2008, doi:10.1101/gr.078196.108
...repeats (TIRs) and target site duplications (TSDs). MITEs have amplified to a high copy number in several plant s, as in rice, which contains more than 90,000 MITEs grouped into approximately 100 different families ( Feschotte et al. 2003 ; Jiang et al. 2004b ; Juretic et al. 2004 ). In the rice...
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LETTER: A Fine Physical Map of the Rice Chromosome 4
- Qiang Zhao,
- Yu Zhang,
- Zhukuan Cheng,
- Mingsheng Chen,
- Shengyue Wang,
- Qi Feng,
- Yucheng Huang,
- Ying Li,
- Yesheng Tang,
- Bo Zhou,
- Zhehua Chen,
- Shuliang Yu,
- Jingjie Zhu,
- Xin Hu,
- Jie Mu,
- Kai Ying,
- Pei Hao,
- Lei Zhang,
- Yiqi Lu,
- Lei S. Zhang,
- Yilei Liu,
- Zhen Yu,
- Danlin Fan,
- Qijun Weng,
- Ling Chen,
- Tingting Lu,
- Xiaohui Liu,
- Peixin Jia,
- Tongguo Sun,
- Yongrui Wu,
- Yujun Zhang,
- Ying Lu,
- Can Li,
- Rong Wang,
- Haiyan Lei,
- Tao Li,
- Hao Hu,
- Mei Wu,
- Runquan Zhang,
- Jianping Guan,
- Jia Zhu,
- Gang Fu,
- Minghong Gu,
- Guofan Hong,
- Yongbiao Xue,
- Rod Wing,
- Jiming Jiang,
- and Bin Han
Genome Res. May 1, 2002 12: 817-823; doi:10.1101/gr.48902
.... , Sasinowski M. , Presting G. , Frisch D. , Goff S. , et al. ( 2000 ) Rice transposable elements: A survey of 73,000 sequence-tagged-connectors. Genome Res. 10 : 982 – 990 . ↵ Marra M.A. , Kucaba T.A. , Dietrich N.L. , Green E.D. , Brownstein B. , Wilson R.K. , McDonald K.M. , Hillier L.W. , McPherson J...
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LETTER: Abundance, Distribution, and Transcriptional Activity of Repetitive Elements in the Maize Genome
- Blake C. Meyers,
- Scott V. Tingey,
- and Michele Morgante
Genome Res. October 1, 2001 11: 1660-1676; Published in Advance September 20, 2001, doi:10.1101/gr.188201
...elements from these plant species have not been described. For example, Mao et al. (2000) analyzed 73,000 BAC-end sequences to determine that 4.5% of the rice is comprosed of transposable elements; lacking a set of distinct and well-characterized rice elements, these sequences could only be characterized...
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RESOURCE: Computational and Experimental Analysis of Microsatellites in Rice (Oryza sativa L.): Frequency, Length Variation, Transposon Associations, and Genetic Marker Potential
- Svetlana Temnykh,
- Genevieve DeClerck,
- Angelika Lukashova,
- Leonard Lipovich,
- Samuel Cartinhour,
- and Susan McCouch
Genome Res. August 1, 2001 11: 1441-1452; doi:10.1101/gr.184001
...with the Micropon family of miniature inverted-repeat transposable elements (MITEs) and were difficult to amplify. A set of 200 Class I SSR markers was developed and integrated into the existing microsatellite map of rice, providing immediate links between the genetic, physical, and sequence-based maps...
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RESOURCE: The Oryza bacterial artificial chromosome library resource: Construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza
- Jetty S.S. Ammiraju,
- Meizhong Luo,
- José L. Goicoechea,
- Wenming Wang,
- Dave Kudrna,
- Christopher Mueller,
- Jayson Talag,
- HyeRan Kim,
- Nicholas B. Sisneros,
- Barbara Blackmon,
- Eric Fang,
- Jeffery B. Tomkins,
- Darshan Brar,
- David MacKill,
- Susan McCouch,
- Nori Kurata,
- Georgina Lambert,
- David W. Galbraith,
- K. Arumuganathan,
- Kiran Rao,
- Jason G. Walling,
- Navdeep Gill,
- Yeisoo Yu,
- Phillip SanMiguel,
- Carol Soderlund,
- Scott Jackson,
- and Rod A. Wing
Genome Res. January 2006 16: 140-147; Published in Advance December 12, 2005, doi:10.1101/gr.3766306
...., Frisch, D., Goff, S., et al. 2000 . Rice transposable elements: A survey of 73,000 sequence-tagged-connectors. Genome Res. 10 : 982 -990. ↵ Martinez, C.P., Arumuganathan, K., Kikuchi, H., and Earle, E.D. 1994 . Nuclear DNA content of ten rice species as determined by flow cytometry. Jpn. J. Genet. 69...
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LETTER: Mosaic Organization of Orthologous Sequences in Grass Genomes
- Rentao Song,
- Victor Llaca,
- and Joachim Messing
Genome Res. October 1, 2002 12: 1549-1555; Published in Advance September 13, 2002, doi:10.1101/gr.268302
.... Sci. 95 : 370 – 375 . ↵ Mao L. , Wood T.C. , Yu Y. , Budiman M.A. , Tomkins J. , Woo S. , Sasinowski M. , Presting G. , Frisch D. , Goff S. , et al. ( 2000 ) Rice transposable elements: A survey of 73,000 sequence-tagged-connectors. Genome Res. 7 : 982 – 990 . ↵ Messing J. ( 2001 ) Do plants have more...
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RESOURCE: Internet Contig Explorer (iCE)—A Tool for Visualizing Clone Fingerprint Maps
- Christopher D. Fjell,
- Ian Bosdet,
- Jacqueline E. Schein,
- Steven J.M. Jones,
- and Marco A. Marra
Genome Res. June 2003 13: 1244-1249; doi:10.1101/gr.819303
..., M.A., Tomkins, J., Woo, S., Sasinowski, M., Presting, G., Frisch, D., Goff, S., et al. 2000 . Rice transposable elements: A survey of 73,000 sequence-tagged-connectors Genome Res. 10 : 982 –990. ↵ Marra, M.A., Kucaba, T.A., Dietrich, N.L., Green, E.D., Brownstein, B., Wilson, R.K., McDonald, K...
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Methods: Locating Sequence on FPC Maps and Selecting a Minimal Tiling Path
- Friedrich W. Engler,
- James Hatfield,
- William Nelson,
- and Carol A. Soderlund
Genome Res. September 2003 13: 2152-2163; Published in Advance January 1, 2003, doi:10.1101/gr.1068603
...is BAC end sequences, the results can be used to select many clones for a minimal tiling path at once. The third tool, pickMTP, automates the majority of this last usage of BSS. Results are presented using the rice FPC map, BAC end sequences, and whole-genome shotgun from Syngenta. Footnotes...
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METHODS: RePS: A Sequence Assembler That Masks Exact Repeats Identified from the Shotgun Data
- Jun Wang,
- Gane Ka-Shu Wong,
- Peixiang Ni,
- Yujun Han,
- Xiangang Huang,
- Jianguo Zhang,
- Chen Ye,
- Yong Zhang,
- Jianfei Hu,
- Kunlin Zhang,
- Xin Xu,
- Lijuan Cong,
- Hong Lu,
- Xide Ren,
- Xiaoyu Ren,
- Jun He,
- Lin Tao,
- Douglas A. Passey,
- Jian Wang,
- Huanming Yang,
- Jun Yu,
- and Songgang Li
Genome Res. May 1, 2002 12: 824-831; doi:10.1101/gr.165102
...in the human . Curr. Opin. Genet. Dev. 6 : 743 – 748 . ↵ Staden R. , Beal K.F. , Bonfield J.K. ( 2000 ) The Staden package, 1998. Comput. Methods Mol. Biol. 132 : 115 – 130 . ↵ Turcotte K. , Srinivasan S. , Bureau T. ( 2001 ) Survey of transposable elements from rice genomic sequences. Plant J. 25 : 169 – 179...
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RESOURCE: A Deep-Coverage Tomato BAC Library and Prospects Toward Development of an STC Framework for Genome Sequencing
- Muhammad A. Budiman,
- Long Mao,
- Todd C. Wood,
- and Rod A. Wing
Genome Res. January 1, 2000 10: 129-136; doi:10.1101/gr.10.1.129
...hybridization with anchored markers ( Mozo et al. 1999 ). The STC and fingerprinting strategy has been widely adopted and is presently being used for the human, Arabidopsis , and rice sequencing projects. In this study we report the construction and characterization of a comprehensive BAC library...

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