Comparative Analysis Of Orthologous Sequences Between Saccharum officinarum and Saccharum spontaneum

Modern sugarcane cultivars are derived from interspecific hybridization between S. officinarum and S. spontaneum with 70-80% of the genome from S. officinarum, 10-20% of the genome from S. spontaneum, and 10% recombinants. We have constructed two bacterial artificial chromosome (BAC) libraries of the modern sugarcane ancestral genomes, S. officinarum and S. spontaneum to serve as the foundation to reveal complex genome structure of sugarcane. These two BAC libraries have been used to screen for the major genes involved in sucrose, lignin, and cellulose biosynthesis pathways. We selected and sequenced 29 BAC clones from S. officinarum and 19 BAC clones from S. spontaneum for comparative analysis to trace the evolutionary history of Saccharum species. A total of 2.8 Mb sequence from S. officinarum and 1.8 Mb sequence from S. spontaneum were generated. Comparative analysis of orthologous sequences between S. officinarum and S. spontaneum revealed extensive genome rearrangements, including inversions, deletions, and translocations. Among the 48 sequenced BACs, 14 of them contain sucrose-phosphate synthase (SPS) genes. Analysis of sequence divergence among the 5 families of SPS genes between S. officinarum and S. spontaneum revealed the greatest divergence in SPS C genes and the lowest in SPS D2 genes. Haplotype analysis of BAC sequences within each species can be used in quality control of genome assemblies for sequencing these autopolyploid genomes.