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

Chance W. Riggins, Yanhui Peng, C. Neal Stewart, Patrick J. Tranel

Research output: Contribution to journalArticlepeer-review

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 a solid foundation of previous genetics work. To develop further the genomics resources forwaterhemp, the transcriptomewas sequenced using RocheGS-FLX 454 pyrosequencing technology. RESULTS: Pyrosequencing produced 483 225 raw reads, which, after quality control and assembly, yielded 44 469 unigenes (contigs+singletons).Atotal of49%of these unigenes displayed highly significant similarities to Arabidopsis proteins andwere subsequently grouped into gene ontology categories. Blast searches against public and custom databases helped in identifying and obtaining preliminary sequence data for all of the major target-site genes for whichwaterhemp hasdocumented resistance. Moreover, sequence data for two other herbicide targets [4-hydroxyphenylpyruvate dioxygenase (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. CONCLUSION: 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 made it possible to establish a valuable genomic resource for weed science research.

Original languageEnglish (US)
Pages (from-to)1042-1052
Number of pages11
JournalPest Management Science
Volume66
Issue number10
DOIs
StatePublished - Oct 1 2010

Keywords

  • 4-Hydroxyphenylpyruvate dioxygenase (HPPD)
  • Amaranthus tuberculatus
  • GS-FLX 454 pyrosequencing
  • Herbicide resistance
  • Target-site genes
  • Transcriptome
  • Waterhemp

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Insect Science

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