Sequencing the genespace of leafy spurge

Leafy spurge is an invasive perennial weed that is a significant problem in range and recreational lands throughout much of the northern Great Plains states. An extensive sanger-sequenced EST database was developed that allowed the construction and use of a 23K element microarray. These microarrays were used for several significant studies on bud dormancy, invasiveness, and flowering of leafy spurge. More recently several RNAseq studies have investigated the impact of glyphosate on leafy spurge as well as additional studies on both season dormancy transitions and the transition from paradormancy to growth. These studies have yielded numerous clusters of coordinately regulated genes suitable for promoter analysis. However, leafy spurge lacked genomic sequences containing promoter elements. We have attempted to develop a gene space assembly of leafy spurge using a combination of transcriptome data along with 60X coverage of the leafy spurge genome with 100 and 150 base paired end read libraries. We utilized the Kmer selection program BBNorm to select fragments derived from low copy portions of the genome along with fragments that mapped to known transcribed genes. Initial analysis indicated these fragments contained both coding and non-coding regions of genes. These were assembled using the program Trinity, and Abyss. The Trinity assembly proved the best for with an N50 of 1353 and 102 million contigs.