Chromosome-scale genome assembly for sugarcane cultivar SP80-3280

This project focuses on producing a chromosome-resolved assembly of the complex and polyploid sugarcane cultivar SP80-3280, with many chromosomes assembled to telomere-to-telomere continuity. A further goal is to investigate the cultivar’s genomic ancestry by mapping sequence segments against available ancestral-genome resources and public short-read data, particularly for Saccharum spontaneum, S. officinarum, and S. barberi. Together, the assembly and ancestry analysis are intended to provide a framework for studying chromosome structure and the contributions of ancestral lineages to cultivated sugarcane.

The assembly effort has produced a chromosome-resolved representation of SP80-3280, with many chromosomes assembled from telomere to telomere. This level of continuity is especially valuable in sugarcane, where high ploidy and extensive sequence similarity among chromosome copies can make it difficult to distinguish homoeologous chromosomes and resolve their structure. The assembly provides a foundation for examining chromosome-scale organization, gene content, and structural variation while retaining the complexity of the cultivar’s genome. It can also support the ancestry analysis by providing long, continuous sequences in which candidate ancestry signals can be located and compared across chromosomes.

The ancestry component is being developed to work even though reference assemblies are available for only S. officinarum and S. spontaneum. It uses k-mer catalogs derived from public genomics short-read data, then evaluates their containment across sliding windows of the SP80-3280 assembly. A calibrated two-state hidden Markov model is planned to smooth these window-level signals and identify candidate ancestry segments; a four-state model may later be explored to distinguish a broader range of ancestry patterns.