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

Jetty S S Ammiraju, Yeisoo Yu, Meizhong Luo, David A Kudrna, HyeRan Kim, Jose L. Goicoechea, Yuichi Katayose, Takashi Matsumoto, Jianzhong Wu, Takuji Sasaki, Rod A Wing

Research output: Contribution to journalArticle

28 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)1596-1607
Number of pages12
JournalTheoretical And Applied Genetics
Volume111
Issue number8
DOIs
StatePublished - Nov 2005

Fingerprint

Libraries
finishing
Oryza sativa
Clone Cells
Genome
clones
genomics
rice
genome
physical chromosome mapping
Chromosomes, Human, Pair 2
Genomic Library
Chromosomes, Human, Pair 1
genomic libraries
refining
Oryza
Computer Simulation
complement
chromosomes
Genes

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Horticulture
  • Plant Science
  • Genetics
  • Genetics(clinical)

Cite this

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. / Ammiraju, Jetty S S; Yu, Yeisoo; Luo, Meizhong; Kudrna, David A; Kim, HyeRan; Goicoechea, Jose L.; Katayose, Yuichi; Matsumoto, Takashi; Wu, Jianzhong; Sasaki, Takuji; Wing, Rod A.

In: Theoretical And Applied Genetics, Vol. 111, No. 8, 11.2005, p. 1596-1607.

Research output: Contribution to journalArticle

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