Erigeron canadensis cultivar:TN-R Genome sequencing and assembly. Erigeron canadensis cultivar:TN-R

Conyza canadensis, which is a member of the Compositae (Asteraceae) family, was the first broadleaf weed to evolve resistance to glyphosate herbicide and is one of the most problematic weeds in the world. It is a true diploid (2n=2X=18) with the smallest genome of any known agricultural weed (335 Mb). Thus, it is an appropriate candidate to help us understand the genetic and molecular bases of weediness. We undertook a draft de novo genome assembly by combining data from multiple sequencing platforms (454 GS-FLX, Illumina HiSeq 2000 and PacBio RS) using various libraries with different insertion sizes (~350 bp, ~600 bp, ~3 kb and ~10 kb) of a Tennessee-accessed glyphosate-resistant horseweed biotype. From 116.3 Gb (~350x coverage) of data, the genome was assembled into 13,966 scaffolds with N50 =33,561 bp. The assembly covered 92.3% of the genome, including the complete chloroplast genome (~153 Kb) and a nearly-complete mitochondrial genome (~450 Kb in 120 scaffolds). The nuclear genome is comprised of 44,592 protein-coding genes. Simple sequence repeat and single nucleotide polymorphisms were surveyed. Genome re-sequencing of seven other horseweed biotypes was performed. These sequence data were assembled and used for genome variation analysis. Genomic patterns were detected that associated with glyphosate-resistant or –susceptible biotypes. The draft genome should be useful to better understand weediness and the evolution of herbicide resistance, and also be helpful as another reference genome in the Compositae. To our knowledge, this project represents the first published draft genome from an agricultural weed.