The Draft Genome of Kochia scoparia and the Mechanism of Glyphosate Resistance via Transposon-Mediated EPSPS Tandem Gene Duplication

Eric L. Patterson, Christopher A. Saski, Daniel B. Sloan, Patrick J. Tranel, Philip Westra, Todd A. Gaines, Brandon Gaut

Research output: Contribution to journalArticlepeer-review


Increased copy number of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene confers resistance to glyphosate, the world's most-used herbicide. There are typically three to eight EPSPS copies arranged in tandem in glyphosate-resistant populations of the weed kochia (Kochia scoparia). Here, we report a draft genome assembly from a glyphosate-susceptible kochia individual. Additionally, we assembled the EPSPS locus from a glyphosate-resistant kochia plant by sequencing select bacterial artificial chromosomes from a kochia bacterial artificial chromosome library. Comparing the resistant and susceptible EPSPS locus allowed us to reconstruct the history of duplication in the structurally complex EPSPS locus and uncover the genes that are coduplicated with EPSPS, several of which have a corresponding change in transcription. The comparison between the susceptible and resistant assemblies revealed two dominant repeat types. Additionally, we discovered a mobile genetic element with a FHY3/FAR1-like gene predicted in its sequence that is associated with the duplicated EPSPS gene copies in the resistant line. We present a hypothetical model based on unequal crossing over that implicates this mobile element as responsible for the origin of the EPSPS gene duplication event and the evolution of herbicide resistance in this system. These findings add to our understanding of stress resistance evolution and provide an example of rapid resistance evolution to high levels of environmental stress.

Original languageEnglish (US)
Pages (from-to)2927-2940
Number of pages14
JournalGenome biology and evolution
Issue number10
StatePublished - Oct 1 2019


  • gene duplication
  • genomics
  • herbicide resistance
  • mobile genetic element
  • molecular evolution
  • weed biology

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics


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