De novo Chloroplast Genome Assembly

Genome sequencing was performed using HiSeqX at Macrogen Inc., Korea, from the extracted DNA of the Korean A. thaliana de novo assembly, with confirmation accomplished with Velvet 1.2.10 [33 (link)] after filtering raw reads using Trimmomatic 0.33 [34 (link)]. After obtaining the first draft of the chloroplast genome sequences, gaps were filled with GapCloser 1.12 [35 (link)] and all bases from the assembled sequences were confirmed by checking each base in the alignment (tview mode in SAMtools 1.9 [36 (link)]) against the assembled chloroplast genome generated with BWA 0.7.17 [37 ]. All these bioinformatic processes were conducted under the environment of Genome Information System (GeIS; http://geis.infoboss.co.kr/; Park et al., in preparation).