AUTHOR=Wu Jian , Liu Bo , Cheng Feng , Ramchiary Nirala , Choi Su-Ryun , Lim Yong Pyo , Wang Xiaowu 

TITLE=Sequencing of Chloroplast Genome Using Whole Cellular DNA and Solexa Sequencing Technology

JOURNAL=Frontiers in Plant Science

VOLUME=3

YEAR=2012

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2012.00243

DOI=10.3389/fpls.2012.00243

ISSN=1664-462X

ABSTRACT=<p>Sequencing of the chloroplast (cp) genome using traditional sequencing methods has been difficult because of its size (&gt;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 <italic>Brassica</italic><italic>rapa</italic> 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 <italic>B. rapa</italic>, <italic>Arabidopsis thaliana</italic>, and <italic>Nicotiana tabacum</italic>. We achieved coverage of more than 99.96% of the cp genome in the three tested accessions using the <italic>B. rapa</italic> sequence as the reference. When <italic>A. thaliana</italic> or <italic>N. tabacum</italic> sequences were used as references, 99.7–99.8 or 95.5–99.7% of the <italic>B. rapa</italic> 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.</p>