Characterization of de novo transcriptome for waterhemp (Amaranthus tuberculatus) using GS-FLX 454 pyrosequencing

Waterhemp is a model for weed genomics research in part because it possesses many interesting biological characteristics, rapidly evolves resistance to herbicides, and has a solid foundation of previous genetics work. To further develop genomics resources for waterhemp, we sequenced the transcriptome using Roche GS-FLX 454 pyrosequencing technology. Pyrosequencing produced 483,225 raw reads, which after quality control and assembly, yielded 44,469 unigenes (contigs + singletons). Forty-nine percent of these unigenes displayed highly significant similarities to Arabidopsis proteins and were subsequently grouped into gene ontology categories. BLAST searches against public and custom databases helped us identify and obtain preliminary sequence data for all of the major target-site genes for which waterhemp has documented resistance. Moreover, sequence data for two other herbicide targets (HPPD and glutamine synthetase), where resistance has not yet been reported in any plant, were also investigated in waterhemp and six related weedy Amaranthus species. These results demonstrate the enormous value of 454 sequencing for gene discovery and polymorphism detection in a major weed species and its relatives. Furthermore, the merging of the 454 transcriptome data with results from a previous whole genome 454 sequencing experiment has enabled us to establish a valuable genomic resource for weed science research.