Construction and utility of 10-kb libraries for efficient clone-gap closure for rice genome sequencing

Tae Jin Yang, Yeisoo Yu, Gyoungju Nah, Michael Atkins, Seunghee Lee, David A. Frisch, Rod A Wing

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

Rice is an important crop and a model system for monocot genomics, and is a target for whole genome sequencing by the International Rice Genome Sequencing Project (IRGSP). The IRGSP is using a clone by clone approach to sequence rice based on minimum tiles of BAC or PAC clones. For chromosomes 10 and 3 we are using an integrated physical map based on two finger-printed and end-sequenced BAC libraries to identifying a minimum tiling path of clones. In this study we constructed and tested two rice genomic libraries with an average insert size of 10 kb (10-kb library) to support the gap closure and finishing phases of the rice genome sequencing project. The HaeIII library contains 166,752 clones covering approximately 4.6x rice genome equivalents with an average insert size of 10.5 kb. The Sau3AI library contains 138,960 clones covering 4.2x genome equivalents with an average insert size of 11.6 kb. Both libraries were gridded in duplicate onto 11 high-density filters in a 5 × 5 pattern to facilitate screening by hybridization. The libraries contain an unbiased coverage of the rice genome with less than 5% contamination by clones containing organelle DNA or no insert. An efficient method was developed, consisting of pooled overgo hybridization, the selection of 10-kb gap spanning clones using end sequences, transposon sequencing and utilization of in silico draft sequence, to close relatively small gaps between sequenced BAC clones. Using this method we were able to close a majority of the gaps (up to approximately 50 kb) identified during the finishing phase of chromosome-10 sequencing. This method represents a useful way to close clone gaps and thus to complete the entire rice genome.

Original languageEnglish (US)
Pages (from-to)652-660
Number of pages9
JournalTheoretical And Applied Genetics
Volume107
Issue number4
DOIs
StatePublished - Aug 1 2003

Fingerprint

Libraries
Clone Cells
Genome
clones
rice
genome
Chromosomes, Human, Pair 10
finishing
hybridization
Oryza
chromosomes
Chromosomes, Human, Pair 3
Genomic Library
physical chromosome mapping
tiles
genomic libraries
Genomics
Liliopsida
transposons
Organelles

Keywords

  • 10-kb Library
  • Gap closure
  • Rice genome sequencing

ASJC Scopus subject areas

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

Cite this

Construction and utility of 10-kb libraries for efficient clone-gap closure for rice genome sequencing. / Yang, Tae Jin; Yu, Yeisoo; Nah, Gyoungju; Atkins, Michael; Lee, Seunghee; Frisch, David A.; Wing, Rod A.

In: Theoretical And Applied Genetics, Vol. 107, No. 4, 01.08.2003, p. 652-660.

Research output: Contribution to journalArticle

Yang, Tae Jin ; Yu, Yeisoo ; Nah, Gyoungju ; Atkins, Michael ; Lee, Seunghee ; Frisch, David A. ; Wing, Rod A. / Construction and utility of 10-kb libraries for efficient clone-gap closure for rice genome sequencing. In: Theoretical And Applied Genetics. 2003 ; Vol. 107, No. 4. pp. 652-660.
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