Amaranthus tuberculatus Transcriptome

Waterhemp (Amaranthus tuberculatus (Moq.) J.D. Sauer) is a problem weed commonly found in the Midwestern United States that can cause yield losses up to 74% and 56% in maize (Zea mays L.) and soybean [Glycine max (L.) Merr.], respectively. In 2011, p-hydroxyphenylpyruvate-dioxygenase (HPPD, EC 1.13.11.27) inhibitor herbicide resistance was reported in two waterhemp populations. No previous studies have examined genome wide gene expression in herbicide resistant waterhemp. Therefore we conducted an RNA-sequencing (RNA-seq) de novo transcriptome assembly of waterhemp. We treated (mesotrione) and mock-treated two waterhemp populations (HPPD-herbicide resistant and susceptible) and collected leaf samples at three, six, twelve, and twenty-four hours after treatment. We performed a de novo transcriptome assembly using all sample sequences to better represent the waterhemp transcriptome as well as allowing us to identify transcripts specific to a genotype, treatment, or time point. The waterhemp transcriptome, differentially expressed genes and single nucleotide polymorphisms (SNPs) generated in this study, will be a valuable to for the weed science community for future studies.