A Duplication Lost In Sugarcane Hybrids Revealed By Chloroplast Genome Assembly Of Wild Species Saccharum officinarum

Sugarcane is a crop of paramount importance for sustainable energy. Modern sugarcane cultivars are derived from interspecific crosses between the two wild species Saccharum officinarum and Saccharum spontaneum and this event occurred very early in the sugarcane domestication history. This hybridization allowed the generation of cultivars with complex aneuploidy genomes containing 100-130 chromosomes that are unequally inherited - ~80% from S. officinarum, ~10% from S. spontaneum and ~10% from inter-specific crosses. Several studies have highlighted the importance of chloroplast genomes (cpDNA) to investigate hybridization events in plant lineages. Few sugarcane cpDNAs have been assembled and published, including those from sugarcane hybrids. However, cpDNAs of wild Saccharum species remains unexplored. In the present study, we used whole-genome sequencing data to survey the chloroplast genome of the wild sugarcane species S. officinarum. Illumina sequencing technology was used for assembly 142,234 bp of S.officinarum cpDNA with 2,065,893 reads and 1043x of coverage. The analysis of the S. officinarum cpDNA revealed a notable difference in the LSC region of wild and cultivated sugarcanes. Chloroplasts of sugarcane cultivars showed a loss of a duplicated fragment with 1,031 bp in the beginning of the LSC region, which decreased the chloroplast gene content in hybrids. Based on these results, we propose the comparative analysis of organelle genomes as a very important tool for deciphering and understanding hybrid Saccharum lineages.