FHY3/FAR1 transposable elements generate adaptive genetic variation in the Bassia scoparia genome

A nearly complete genome assembly consisting of 14 scaffolds, a total length of 969.6 Mb, and an N50 scaffold length of 99.88 Mb, was generated to better understand how transposable element activity has led to adaptive evolution in Bassia scoparia (kochia), an agronomically important weed.

The nine largest scaffolds correspond to the nine chromosomes of the close relative, Beta vulgaris. From this assembly, 54 387 protein-coding gene loci were annotated. We determined that genes containing Far-Red Elongated Hypocotyl 3 (FHY3) or Far-Red Impaired Response 1 (FAR1) functional domains have undergone a large, kochia-specific gene family expansion. We discovered that putative Mutator Don-Robertson (MuDR) transposable elements with detectable FHY3/FAR1 domains were tightly associated with segmental duplications of 5-enolpyruvylshikimate-3-phosphate synthase subsequently conferring resistance to the herbicide glyphosate. Further, we characterized a new MuDR subtype, named here as 'Muntjac', which contributes to the evolution of herbicide resistance in kochia through the process of transduplication.

Collectively, our study provides insights into the role FHY3/FAR1 genes as active transposable elements and contributes new perspectives on the interaction between transposons and herbicide resistance evolution. © 2025 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.