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

Abstract

Sugarcane (Saccharum hybrid cultivar) ranks among the world's top 10 food crops and annually provides 60À70% of the sugar produced worldwide. Despite its economic importance there has been no large-scale systematics study of genus Saccharum 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 Miscanthus floridulus (first report for this genus), Saccharum spontaneum and Saccharum officinarum allowing us to elucidate the phylogenetic origins of Saccharum s.s. species. We demonstrate that Saccharum s.s. is divided into four species, with S. spontaneum diverging from the remainder of the genus about 1.5 million years ago and S. robustum diverging 750,000 years ago. Two separate lineages, one leading to S. officinarum and the other leading to modern hybrid cultivars diverged from S. robustum 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, S. barberi and S. sinense, cluster as a distinct S. officinarum lineage. This makes modern cultivars a distinct species of genus Saccharum, and we formally propose the name Saccharum cultum for the ancestor of all lineages currently classified as Saccharum hybrid cultivars.

Assembly of 23 Plastid Genomes Provides the Chloroplast View onMiscanthusOrigins

“…The chronogram, Figure 3, which is calibrated to the evolutionary origins of Zea mays. This places the split between Zea and Sorghum at about 6.77 million years ago, which is consistent with our previous studies (Lloyd Evans and Joshi 2016). With more species within Miscanthus in this study, the last common ancestor of Miscanthus and Saccharum was 4.49 million years ago, almost 1.5 million years more ancient than our previous estimate (Lloyd Evans and Joshi 2016).…”

“…The next clade is bounded by Miscanthus olygostachyus at its root. Interestingly, this species is sister to Miscanthus sinensis var Purpurascens and two previously published sequences of M. sinensis and Miscanthus floridulus (Lloyd Evans and Joshi 2016;Nah et al 2016;Tsuruta et al 2017). This would indicate that the M. sinensis forms have either been misidentified or they represent hybrids of M. oligostachyus with M. sinensis.…”

“…In all cases, libraries over 10 Gb in size were reduced to 9 Gb by random selection using seqtk (https://github.com/lh3/seqtk/blob/master/ README.md). All chloroplasts were assembled as described previously (Lloyd Evans and Joshi, 2016), using the newly assembled Miscanthus sinensis 'Andante' chloroplast as a reference.…”

“…Annotation files were downloaded from Verdant in '.tbl' (Verdant native) format. Genes and pseudogenes identified from a previous analysis (Lloyd Evans and Joshi, 2016), and which were not present in the Verdant annotation, were mapped with Exonerate (Slater and Birney 2005) and were placed in a separate '.tbl' format file. A custom BioPerl script was written that integrated the Verdant output and the additional gene output along with data corresponding to gene annotation and cultivar level taxonomies prior to outputting an EMBL format file and a chromosome file that could be automatically uploaded to the EMBL database.…”

“…Miscanthus is a member of the Saccharinae subtribe (as exemplified by sugarcane) and both species lie within the 3.4 million years of divergence where hybridization is possible (Lloyd Evans and Joshi 2016). Sugarcane and Miscanthus floridulus can hybridize in the wild and the introgression of Miscanthus into Saccharum (and Saccharum into Miscanthus) to produce miscanes focussing on biomass and high sucrose is a promising field of study to increase the biomass of Miscanthus and to introduce increased cold tolerance into sugarcane (G lowacka et al 2016 andBurner et al 2015).…”