Haplotype-resolved genome assembly sheds light on the evolutionary history of autohexaploid Tripidium arundinaceum

Tripidium arundinaceum, a wild perennial grass with exceptional stress tolerance, has been tested in sugarcane breeding. Its complex polyploid genome has hindered understanding of its evolution and adaptive traits. Here, we present a high-quality, haplotype-resolved reference genome for autohexaploid T. arundinaceum Hainan92-105 (2n = 6x = 60). T. arundinaceum is likely originated from a diploid ancestor approximately 1.31 million years ago and contains abundant repetitive sequences from two major recent bursts of long terminal repeat retrotransposons following polyploidization. Phylogenetic analyses place Saccharum closer to Sorghum bicolor than to T. arundinaceum, indicating that the polyploidizations in these two lineages occurred independently. Population genomics analysis reveals southwestern China (Yunnan) as a diversity center for T. arundinaceum within China. Genotype-environment associations highlight temperature and precipitation as key local adaptation drivers mediated by stress-associated genes. This study provides a genomic resource for understanding polyploid evolution and climate adaptation in T. arundinaceum.