De Novo Genome Assembly For The Economically-Important Weed Conyza canadensis From Multiple Integrated Next-Generation Sequencing Data

Conyza canadensis, which is in the Compositae (Asteraceae) family, was the first broadleaf weed to evolve glyphosate resistance and is now a problematic weed worldwide. It is a true diploid (2n=2X=18) with the smallest genome of any agricultural weed (335 Mb) and thus among the best model weed candidates for genomic studies. C. canadensis populations are highly self-fertilizing and homozygous. Individual plants can produce over 200,000 wind-dispersed seeds and are easily grown under experimental conditions. In addition, we have developed a plant transformation and regeneration method that allows analyses of overexpression and silencing of potential genes. The reference genome would be not only useful to elucidate the herbicide resistance mechanism, but also beneficial for the study of other economically important plants in the family. We performed 454 and Illumina HiSeq transcriptome runs of resistant and susceptible horseweed samples, which generated ~45,000 unique gene sequences that are being mined for potential resistance genes. Known repeat elements were analyzed; the results show horseweed has a very compact genome structure and suggested the de novo assembly could be easier than initially expected. For the genome assembly, we combined data from multiplex platforms (454 GS-FLX, Illumina HiSeq 2000 and PacBio RS) and various libraries (shotgun, paired-end and mate-paired) of different sizes (~350 bp, ~600 bp, ~3 kb and ~10 kb) to generate comprehensive reads. Two plates of 454 runs of three shotgun libraries produced 2,238,807 raw reads with an average read length of ~390 bp, for a yield total of ~860 Mb data. Two lanes of HiSeq 2000 runs (2 x 100 bp) of two short paired-end libraries produced 786,389,990 raw reads, for a yield total of ~77 Gb data. One lane of HiSeq 2000 run (2x 100 bp) of one 3 Kb mate-paired library produced 381,844,926 raw reads, for a yield total of ~37 Gb data. Ten SMRT cell of PacBio runs produced 513,084 sequences with an average read length of 3.1 Kb, for a yield total of 1.44 Gb data.  From de novo assembly of these data, we have obtained an accurate whole chloroplast genome (~153 Kb), most of the mitochondrial genome (~450 Kb), and 99% of the whole genome assembled into draft scaffolds. Taken together, these resources should enable gene discovery and basic research of weeds and their relatives in the Compositae.