The Draft Genome of Kochia scoparia : A Foundation for Studying Adaptive Evolution and Its Impacts on Genome Architecture

Kochia scoparia (kochia) is one of the most important weeds in the western United States and Canada. It currently infests hundreds of thousands of acres of farm and range land across North America and causes millions of dollars in crop loss annually in sugar beet, canola, wheat and corn fields. K. scoparia has evolved resistance to many of the most important herbicides used for its control, including glyphosate, dicamba, and ALS inhibitors. Additionally, K. scoparia is an extremely hardy plant that can tolerate substantial abiotic stress from drought, salt, and both extremes of temperature. This suite of traits all contribute to its success as a weed. Our research aims to make K. scoparia a model organism, not only for weed research but also as a plant extremophile. Initial analysis of Illumina reads suggested that the K. scoparia genome is highly complex. To circumvent problems surrounding highly repetitive regions of the genome we are utilizing a hybrid low coverage PAC-BIO and high coverage Illumina approach. Currently, we have assembled ~83% of the genome with 711 mb in 19,671 scaffolds. Our initial ALL-Paths assembly suggests that K. scoparia contains substantial sequence duplication throughout the genome and that this may lead to rapid genome evolution and increased genetic diversity at key loci involved in abiotic stress response. We begin our exploration by examining the contig that contains the EPSPS gene, a tandemly duplicated gene that provides resistance to glyphosate in some K. scoparia populations.