Whole organelle genomes from total plant DNA sequencing

Short gun sequencing of whole plant DNA preparations provides short reads that includes good coverage of organelle genomes. Whole chloroplast and mitochondrial genome sequences can be easily obtained by alignment with reference genomes if closely related species sequences are available. De novo assembly of sequences in a more difficult approach to obtaining a complete organelle sequence but provides very useful data for less well know species. This technology will find many applications in plant biology. Using this approach a single base error was found in the published Sanger chloroplast sequence for rice. Chloroplast sequences of wild rice relatives have revealed the relationships of these species to cultivated rice. Chloroplast diversity in hybrid sugarcane and progenitor species has been examined. Phylogenetic relationships in the complex Eucalypt group have been investigated at the whole chloroplast genome sequence level. Relative rates of chloroplast, mitochondrial and nuclear genome evolution can now be examined at the whole genome level.