TY - JOUR
T1 - Random sheared fosmid library as a new genomic tool to accelerate complete finishing of rice (Oryza sativa spp. Nipponbare) genome sequence
T2 - Sequencing of gap-specific fosmid clones uncovers new euchromatic portions of the genome
AU - Ammiraju, Jetty S.S.
AU - Yu, Yeisoo
AU - Luo, Meizhong
AU - Kudrna, Dave
AU - Kim, Hye Ran
AU - Goicoechea, Jose L.
AU - Katayose, Yuichi
AU - Matsumoto, Takashi
AU - Wu, Jianzhong
AU - Sasaki, Takuji
AU - Wing, Rod A.
PY - 2005/11
Y1 - 2005/11
N2 - 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.
AB - 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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U2 - 10.1007/s00122-005-0091-3
DO - 10.1007/s00122-005-0091-3
M3 - Article
C2 - 16200416
AN - SCOPUS:27744525806
SN - 0040-5752
VL - 111
SP - 1596
EP - 1607
JO - Theoretical and Applied Genetics
JF - Theoretical and Applied Genetics
IS - 8
ER -