A Comparative Sequence Analysis of Herbicide Target Genes across Dozens of Weedy Plant Species

As the price of sequencing has fallen drastically over the past decade, increasing amounts of herbicide target gene sequence data have become publically available to weed researchers.  In an effort to consolidate this information, an online database is now accessible at http://weedscience.org, containing the cDNA sequences of 70+ weed species across seven herbicide target genes.  This dataset provides a rich resource for weed scientists, both as a starting place for further target site resistance work in poorly studied species and as a data source for researchers interested in herbicide resistance evolution.  Towards this second goal, gene and protein comparisons were carried out on each herbicide target gene, starting with the construction of multiple sequence alignments (MSAs) for all seven genes.  These MSAs were superimposed on the protein crystal structure to generate conservation/variability scores at each residue and highlight regions that appear to be prone to mutation.  Known herbicide resistance mutation sites were then identified in each MSA and likelihood scores for these mutations to appear for each weed species were calculated, allowing for a ranking of the species from highest to lowest risk of future herbicide resistance evolution.  The utility of this analysis for weed managers will be discussed as well as other potential uses of the dataset.