Construction of random sheared fosmid library from Chinese cabbage and its use for Brassica rapa genome sequencing project

Tae-Ho Park; Beom-Seok Park; Jin-A. Kim; Joon Ki Hong; Mina Jin; Young-Joo Seol; Jeong-Hwan Mun

doi:10.1016/j.jcg.2010.12.002

Volume 38 Issue 1

Jan. 2011

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Construction of random sheared fosmid library from Chinese cabbage and its use for Brassica rapa genome sequencing project

doi: 10.1016/j.jcg.2010.12.002

a
Genomics and Functional Bio-Material Division, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
b
The Department of Horticultural Science, Daegu University, Gyeongsan 712-714, Republic of Korea

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Corresponding author: E-mail address: pbeom@korea.kr (Beom-Seok Park)
Received Date: 2010-07-06
Accepted Date: 2010-12-20
Rev Recd Date: 2010-09-27

Available Online: 2011-02-19

Publish Date: 2011-01-20

Abstract

Abstract

As a part of the Multinational Genome Sequencing Project ofBrassica rapa, linkage group R9 and R3 were sequenced using a bacterial artificial chromosome (BAC) by BAC strategy. The current physical contigs are expected to cover approximately 90% euchromatins of both chromosomes. As the project progresses, BAC selection for sequence extension becomes more limited because BAC libraries are restriction enzyme-specific. To support the project, a random sheared fosmid library was constructed. The library consists of 97536 clones with average insert size of approximately 40 kb corresponding to seven genome equivalents, assuming a Chinese cabbage genome size of 550 Mb. The library was screened with primers designed at the end of sequences of nine points of scaffold gaps where BAC clones cannot be selected to extend the physical contigs. The selected positive clones were end-sequenced to check the overlap between the fosmid clones and the adjacent BAC clones. Nine fosmid clones were selected and fully sequenced. The sequences revealed two completed gap filling and seven sequence extensions, which can be used for further selection of BAC clones confirming that the fosmid library will facilitate the sequence completion of B. rapa.
- Chinese cabbage,
- Fosmid library,
- Genome sequencing,
- Physical contig

These authors contributed equally to this work.

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References(33)

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