Characterization of de novo transcriptome for waterhemp (Amaranthus tuberculatus) using GS‐FLX 454 pyrosequencing and its application for studies of herbicide target‐site genes

• DOI: 10.1002/ps.2006
• Publication Date: 2010-08-15T23:46:07Z
• Authors: Chance W Riggins; Yanhui Peng; C Neal Stewart; Patrick J Tranel
• Keywords: Pyrosequencing

Abstract BACKGROUND: Waterhemp is a model for weed genomics research in part because it possesses many interesting biological characteristics, rapidly evolves resistance to herbicides and has solid foundation of previous genetics work. To develop further the resources waterhemp, transcriptome was sequenced using Roche GS‐FLX 454 pyrosequencing technology. RESULTS: Pyrosequencing produced 483 225 raw reads, which, after quality control assembly, yielded 44 469 unigenes (contigs + singletons). A total 49% these displayed highly significant similarities Arabidopsis proteins were subsequently grouped into gene ontology categories. Blast searches against public custom databases helped identifying obtaining preliminary sequence data all major target‐site genes which waterhemp documented resistance. Moreover, two other herbicide targets [4‐hydroxyphenylpyruvate dioxygenase (HPPD) glutamine synthetase], where not yet been reported any plant, also investigated six related weedy Amaranthus species. CONCLUSION: These results demonstrate enormous value sequencing discovery polymorphism detection species its relatives. Furthermore, merging with from whole genome experiment made possible establish valuable genomic resource science research. Copyright © 2010 Society Chemical Industry