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

Overview

Journal Genome Biol Evol

Publisher Oxford University Press

Specialties Biology
Genetics
Molecular Biology

Date 2019 Sep 14

PMID 31518388

Citations 16

Authors

Eric L Patterson

Christopher A Saski

Daniel B Sloan

Patrick J Tranel

Philip Westra

Todd A Gaines

Affiliations

Soon will be listed here.

Abstract

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.

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Subtelomeric 5-enolpyruvylshikimate-3-phosphate synthase copy number variation confers glyphosate resistance in Eleusine indica.

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Subtelomeric 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) copy number variation confers glyphosate resistance in Eleusine indica.

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