Genomic insights into herbicide resistance evolution in allopolyploid Monochoria korsakowii

Monochoria korsakowii, a common broadleaf weed in rice paddies, has evolved resistance to acetolactate synthase-inhibiting herbicides (e.g., bensulfuron-methyl [BSM]). However, genomic information for M. korsakowii remains scarce. Here, the first chromosome-scale genome assembly of the allotetraploid M. korsakowii is presented. Comparative genomics reveals a complex genomic architecture that explains its enhanced adaptation to herbicides. No evidence of global subgenome dominance is found; instead, the two subgenomes exhibit functional specialization. Genes preferentially expressed in subgenome A are enriched in pathways related to maintaining energy and physiological homeostasis, whereas those in subgenome B are mainly associated with non-target-site pathways, particularly reactive oxygen species scavenging. Furthermore, sequence analysis shows that tandem duplicates are significantly enriched for herbicide metabolism-related functions, suggesting a potential role for tandem duplication in the evolution of herbicide resistance. Transcriptomic and functional analyses identify a glutathione S-transferase gene (MkoA03G003170) as a key factor conferring metabolic resistance to BSM. This study identifies polyploidy-induced genomic plasticity as a potential factor in resistance, providing a foundational genomic resource for understanding weed adaptation and developing sustainable management strategies.