articleScienceFeb 5, 2026Closed access

Multiscale pangenome graphs empower the genomic dissection of mixed-ploidy sugarcane species

YHYumin HuangYZYixing ZhangQZQing ZhangGHGui Hua ZhuangCLChunjia Li

Fujian Agriculture and Forestry University · Guangxi University · +2 more institutions

PubMed
Indexed incrossrefpubmed

Abstract

The sugarcane genus Saccharum is characterized by complex genomes with diverse ploidy levels. We developed a multiscale graph–based pangenome representation, which integrates nine genome assemblies into a unified reference, representing modern cultivars and founding species. Each homo(eo)logous (encompasses both homologous and homeologous relationships) chromosome set retains 47 to 57 haplotypes and ~74,000 to 271,000 gene alleles. This framework enables multiomics exploration, encompassing homo(eo)log systems and epigenomic signatures. The pangenome facilitates population genomics analyses of 417 mixed-ploidy Saccharum accessions, revealing convergent selection and identifying the Andropogoneae TB1 homolog…

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11
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20

Topics & keywords

Topics
Keywords
  • Genome
  • Genomics
  • Comparative genomics
  • Polyploid
  • Ploidy
  • Chromosome
  • Selection (genetic algorithm)
  • Population
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