This article is part of the Research Topic The Brassica Genome

Methods ARTICLE

Front. Plant Sci., 08 November 2012 | doi: 10.3389/fpls.2012.00243

Sequencing of chloroplast genome using whole cellular DNA and Solexa sequencing technology

  • 1Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
  • 2Department of Horticulture, Plant Genome Research Institute, Chungnam National University, Daejeon, South Korea

Sequencing of the chloroplast (cp) genome using traditional sequencing methods has been difficult because of its size (>120 kb) and the complicated procedures required to prepare templates. To explore the feasibility of sequencing the cp genome using DNA extracted from whole cells and Solexa sequencing technology, we sequenced whole cellular DNA isolated from leaves of three Brassica rapa accessions with one lane per accession. In total, 246, 362, and 361 Mb sequence data were generated for the three accessions Chiifu-401-42, Z16, and FT, respectively. Micro-reads were assembled by reference-guided assembly using the cpDNA sequences of B. rapa, Arabidopsis thaliana, and Nicotiana tabacum. We achieved coverage of more than 99.96% of the cp genome in the three tested accessions using the B. rapa sequence as the reference. When A. thaliana or N. tabacum sequences were used as references, 99.7–99.8 or 95.5–99.7% of the B. rapa cp genome was covered, respectively. These results demonstrated that sequencing of whole cellular DNA isolated from young leaves using the Illumina Genome Analyzer is an efficient method for high-throughput sequencing of cp genome.

Keywords: chloroplast genome, sequencing, Solexa sequencing technology, whole cellular DNA, Brassica rapa

Citation: Wu J, Liu B, Cheng F, Ramchiary N, Choi SR, Lim YP and Wang X-W (2012) Sequencing of chloroplast genome using whole cellular DNA and Solexa sequencing technology. Front. Plant Sci. 3:243. doi: 10.3389/fpls.2012.00243

Received: 16 July 2012; Accepted: 12 October 2012;
Published online: 08 November 2012.

Edited by:

Michael Freeling, University of California Berkeley, USA

Reviewed by:

Eduard Akhunov, Kansas State University, USA
Xiyin Wang, Hebei United University, China

Copyright: © 2012 Wu, Liu, Cheng, Ramchiary, Choi, Lim and Wang. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc.

*Correspondence: Xiao-Wu Wang, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nan Da Jie 12, Beijing 100081, China. e-mail: wangxw@mail.caas.net.cn

Jian Wu and Bo Liu have contributed equally to this work.

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