Multiscale Super-Pangenome Graphs Empower the Genomic Dissection of Mixed-Ploidy Saccharum Species

The graph pangenome is a powerful tool for integrative genomic research. In this study, we analyze both epigenomic and transcriptomic data within a graph pangenome framework. We pioneered the development of a multiscale graph pangenome strategy that integrates nine genome assemblies into a unified reference, representing both modern cultivars and their ancestral species. This framework enables comprehensive multi-omics analyses, capturing homoeologous relationships and epigenomic signatures across the genome.