Chromosome-Scale Draft Genomes of Common and Giant Ragweed Reveal a Potential Mechanism of Glyphosate Resistance

Ambrosia artemisiifolia L. (common ragweed) and Ambrosia trifida L. (giant ragweed) are two of the most widely distributed and economically important pest species in the world. Across their native North American ranges these species are important weeds of agriculture that cause significant yield losses when left uncontrolled. Both species have developed resistance to many of the most commonly utilized herbicides, including inhibitors of acetolactate synthase (ALS) and enolpyruvyl shikimate 3-phosphate synthase (EPSPS). Although rare, A. artemisiifolia and A. trifida have also been observed to hybridize, with hybrid individuals reported to contain 30 chromosomes, 18 from A. artemisiifolia and 12 from A. trifida. In this research, chromosome scale draft genomes of A. artemisiifolia and A. trifida were produced via a trio binning approach whereby the haploid genomes of hybrid ragweed as well as the diploid genomes of the parental species were sequenced using Pacific Bioscience long read technology. The genomes of the parental species were assembled individually and these results served as reference to sort the sequence reads of the hybrid into 2 groups, referring to the origin of the chromosomes, and therefore permitting the resolution of haplotypes for both species. Genomic assemblies of A. artemisiifolia and A. trifida facilitated the production of complete sequences of herbicide target site genes, including the three copies of EPSPS. These results revealed a previously unreported Proline to Serine mutation at position 106 (P106S) of EPSP2S in both A. artemisiifolia and A. trifida. While this mutation has been reported to confer resistance to glyphosate in several other weed species, it is unclear at present what contribution this mutation may make to the level of glyphosate resistance observed in these species.