Saccharum spontaneum isolate:Np-X Genome sequencing and assembly

S. spontaneum is a founding Saccharum species that contributes stress resistance to the genetic background of modern sugarcane cultivars. Here, we have assembled the autopolyploid S. spontaneum Np-X genome with ancestral form into 40 pseudo-chromosomes in 10 homologous groups, revealing the recent chromosome reduction and polyploidization that occurred in Saccharum. The Saccharum chromosomes underwent a paleo-duplication event in the Poaceae and some of them underwent fission accompanied by centromeric spreading around 0.80 Mya before evolving into their current forms with basic chromosome numbers x = 8 and x = 9 in S. spontaneum. Highly diverse chromatin structures exist among homologous chromosomes despite their high collinearity and some chromosomal regions exhibit functional redundancy. WGDs occurred independently in Saccharum species around 1.5 Mya. Resequencing of 102 accessions elucidated that the S. spontaneum originated from North India and that the basic chromosome numbers x = 8, x = 9, and x = 10 originated independently. Recent chromosome reduction rather than polyploidization has contributed to the adaptive evolution of Saccharum. Our study provides genomic resources and suggests new directions for accelerating sugarcane improvement and advances our knowledge of the evolution of auto-polyploidy.