Extracting Whole Chloroplast Genomes from Plant Sequence Data

Plant chloroplast sequence data can be used as a barcode in many studies such as plant identification, purity assessment and phylogenetic analysis. Sequence read mapping and de novo assembly approaches have been used to generate a consensus chloroplast sequence from whole genome shot gun Next Generation Sequence (NGS) data. Use of complete chloroplast genomic sequences provides a better resolution for sequence variation analysis studies. However, the accuracy of the consensus chloroplast sequence generated is important as it provides certainty in obtaining reliable results in applications outlined above. We present data on the use of two sequencing platforms; Illumina and Ion Torrent, and data analysis approaches, read mapping versus de novo assembly, to generate an accurate consensus chloroplast sequence for cultivated rice (cv Nipponbare) and an Australian wild rice plant. Two data analysis tools were used and compared for their robustness in processing the NGS data to generate the consensus chloroplast sequence using both approaches (read mapping versus de novo assembly). The approach has been applied to several different plant species.