Complete chloroplast genomes of <i>Saccharum spontaneum</i>, <i>Saccharum officinarum</i> and <i>Miscanthus floridulus</i> (Panicoideae: Andropogoneae) reveal the plastid view on sugarcane origins

<p>Sugarcane (<i>Saccharum</i> hybrid cultivar) ranks among the world's top 10 food crops and annually provides 60–70% of the sugar produced worldwide. Despite its economic importance there has been no large-scale systematics study of genus <i>Saccharum</i> and the existing model of sugarcane origins has remained largely unchallenged for almost 50 years. For the first time, we have assembled the complete plastid genomes of <i>Miscanthus floridulus</i> (first report for this genus), <i>Saccharum spontaneum</i> and <i>Saccharum officinarum</i> allowing us to elucidate the phylogenetic origins of <i>Saccharum s.s</i>. species. We demonstrate that <i>Saccharum s.s.</i> is divided into four species, with <i>S. spontaneum</i> diverging from the remainder of the genus about 1.5 million years ago and <i>S. robustum</i> diverging 750,000 years ago. Two separate lineages, one leading to <i>S. officinarum</i> and the other leading to modern hybrid cultivars diverged from <i>S. robustum</i> 640,000 years ago. These findings overturn all previous hypotheses on sugarcane origins, demonstrating that sugarcane's antecedents could not have arisen by human action. All modern cultivars share a common Polynesian origin, whereas Old World canes, <i>S. barberi</i> and <i>S. sinense</i>, cluster as a distinct <i>S. officinarum</i> lineage. This makes modern cultivars a distinct species of genus <i>Saccharum</i>, and we formally propose the name <i>Saccharum cultum</i> for the ancestor of all lineages currently classified as <i>Saccharum</i> hybrid cultivars.</p