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Random sheared fosmid library as a new genomic tool to accelerate complete finishing of rice (Oryza sativa spp. Nipponbare) genome sequence: sequencing of gap-specific fosmid clones uncovers new euchromatic portions of the genome

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Abstract

The International Rice Genome Sequencing Project has recently announced the high-quality finished sequence that covers nearly 95% of the japonica rice genome representing 370 Mbp. Nevertheless, the current physical map of japonica rice contains 62 physical gaps corresponding to approximately 5% of the genome, that have not been identified/represented in the comprehensive array of publicly available BAC, PAC and other genomic library resources. Without finishing these gaps, it is impossible to identify the complete complement of genes encoded by rice genome and will also leave us ignorant of some 5% of the genome and its unknown functions. In this article, we report the construction and characterization of a tenfold redundant, 40 kbp insert fosmid library generated by random mechanical shearing. We demonstrated its utility in refining the physical map of rice by identifying and in silico mapping 22 gap-specific fosmid clones with particular emphasis on chromosomes 1, 2, 6, 7, 8, 9 and 10. Further sequencing of 12 of the gap-specific fosmid clones uncovered unique rice genome sequence that was not previously reported in the finished IRGSP sequence and emphasizes the need to complete finishing of the rice genome.

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Authors and Affiliations

  1. Department of Plant Sciences and BIO5 Institute, Arizona Genomics Institute, The University of Arizona, Tucson, AZ, 85721, USA

    Jetty S. S. Ammiraju, Yeisoo Yu, Meizhong Luo, Dave Kudrna, HyeRan Kim, Jose L. Goicoechea & Rod A. Wing

  2. National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan

    Yuichi Katayose, Takashi Matsumoto, Jianzhong Wu & Takuji Sasaki

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  1. Jetty S. S. Ammiraju
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  2. Yeisoo Yu
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  3. Meizhong Luo
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  4. Dave Kudrna
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  5. HyeRan Kim
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  6. Jose L. Goicoechea
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  7. Yuichi Katayose
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  8. Takashi Matsumoto
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  9. Jianzhong Wu
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  10. Takuji Sasaki
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  11. Rod A. Wing
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Correspondence to Rod A. Wing.

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Communicated by Q. Zhang

Fosmid library reported here is publicly available from our web site http://www.genome.arizona.edu/orders

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Ammiraju, J.S.S., Yu, Y., Luo, M. et al. Random sheared fosmid library as a new genomic tool to accelerate complete finishing of rice (Oryza sativa spp. Nipponbare) genome sequence: sequencing of gap-specific fosmid clones uncovers new euchromatic portions of the genome. Theor Appl Genet 111, 1596–1607 (2005). https://doi.org/10.1007/s00122-005-0091-3

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