Saccharum spontaneum cultivar:AP85-441 Genome sequencing and assembly. Saccharum spontaneum cultivar:AP85-441

Sugarcane is the 5th most valuable crop. Saccharum spontaneum contributed disease resistance to modern hybrid cultivars. The complexity of polyploid interspecific hybrid sugarcane genomes is unprecedented. The haploid S. spontaneum AP85-441 was sequenced and assembled into 32 chromosomes in 8 homologous groups. The reduction of basic chromosome number from 10 to 8 in S. spontaneum is caused by fissions of two ancestral chromosomes followed by translocations to three chromosomes each. The two rounds of whole genome duplication event occurred after the divergence of Saccharum and Miscanthus, and S. spontaneum is autopolyploid. We annotated 35,536 genes with alleles, and 4289, 9792, 14797, and 6647 genes with 4, 3, 2, and 1 alleles, respectively. The subgenomes displayed no global expression dominance, but more than half of gene sets shows allelic dominance. S. spontaneum has an enhanced NADP-ME C4 pathway for photosynthesis. 78% NBS disease genes were located in the rearranged chromosomes. Re-sequencing of 64 S. spontaneum genomes revealed balancing selection in rearranged region and octoploid is the ancestral ploidy. The allele defined Saccharum genome offers new knowledge and resources to accelerate sugarcane improvement.