FHY3/FAR1 transposable elements generate adaptive genetic variation in the Bassia scoparia genome
A near complete genome assembly consisting of 14 scaffolds, a total length of 969.6 Mb, and 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 9 largest scaffolds correspond to the 9 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 of a FHY3/FAR1 gene as an active transposable element and contributes new perspectives on the interaction between transposons and herbicide resistance evolution. Significance StatementIn this work we discover that genes known as FHY3/FAR1, supposed "domesticated transposons", are still actively transposing in the weed Bassia scoparia rearranging the genome in new ways. One rearrangement they are involved in is the tandem duplication of the gene 5-enolpyruvylshikimate-3-phosphate synthase which is the gene that produces the target protein of glyphosate, one of the most important herbicides in the world. This work gives a specific example of the role that transposable elements play in making novel genetics and therefore the role that new genome rearrangements play in adaptative evolution, especially in response to external stress such as herbicides.