The Sugarcane Chloroplast Genome: A Next Generation Sequencing Perspective

The sugarcane chloroplast genome sequence and heteroplasmy in sugarcane chloroplast was re-investigated using next generation sequencing.  NGS data from total DNA of sugarcane (Saccharum spp. hybrids) cultivar Q155 was used for chloroplast genome assembly, employing a combined approach of de novo assembly and reference-based mapping. It was found that the chloroplast genome of sugarcane cultivar Q155 is likely to be the chloroplast genome sequence for cultivated sugarcane, as it is the consensus of sequences reported for other two cultivars, NCo310 and SP80-3280. Our finding is consistent within the recent narrow origin of sugarcane in which all modern sugarcane hybrid cultivars were derived from a few selected clones after a few generations within a short-time divergence. We carried out further analysis, using samples with different proportions of nuclear, mitochondrial and chloroplast DNA, to test the potential to distinguish genuine chloroplast heteroplasmy from apparent heteroplasmy due to chloroplast homologues inserted in other cellular genomes. It is revealed that the reported variants were present only at frequencies that could be attributed to non-chloroplast sequences from mitochondria and nucleus. There is no positive evidence from NGS data for heteroplasmy in the sugarcane chloroplast genome. This might also indicate that plant chloroplast genomes do not display heteroplasmy.