A strategy to recover a high-quality, complete plastid sequence from low-coverage whole-genome sequencing.
ABSTRACT. Premise of the study:We developed a bioinformatic strategy to recover and assemble a chloroplast genome using data derived from low-coverage 454 GS FLX/Roche whole-genome sequencing. Methods:A comparative genomics approach was applied to obtain the complete chloroplast genome from a weedy biotype of rice from Uruguay. We also applied appropriate filters to discriminate reads representing novel DNA transfer events between the chloroplast and nuclear genomes. Results:From a set of 295,159 reads (96 Mb data), we assembled the chloroplast genome into two contigs.