Near‐T2T genome assembly of Erigeron sumatrensis provides insights into polyploid evolution and the herbicidal efficiency of HPPD inhibitors

Abstract

Species of Erigeron , members of the family Asteraceae, have invaded and adapted to agricultural fields and uncultivated habitats worldwide. Erigeron sumatrensis is one of the most problematic weeds globally. Therefore, generating a near‐telomere‐to‐telomere (T2T), and accurately annotated genome is important for developing improved integrated management strategies for Erigeron species. The resolved 2.05 Gb allohexaploid genome assembly revealed 25 T2T chromosomes and 43 telomeres of the E. sumatrensis . The A, B, and C subgenomes were highly collinear and appear to have experienced a single shared whole‐genome duplication before species divergence. The polyploid genome showed unbalanced expression, with preferential expression of C subgenome, which originated from the most recent common ancestor. In particular, the expression of the herbicide target genes 4‐HPPD4 , 4‐HPPD5 , and 4‐HPPD6 in Clade I was induced by mesotrione treatment, whereas expression of HPPD genes in Clade II was not. Additionally, amino acid substitutions at Lys178 and Gly181 in EsHPPD were found to mediate increased resistance to mesotrione. In conclusion, this high‐quality reference genome reveals detailed information on herbicide–target protein interactions and will facilitate the development of integrated management strategies against invasive weed species.