Wheat Zapper: A flexible online tool for colinearity studies in grass genomes

Loai M. Alnemer, Raed I. Seetan, Filippo M. Bassi, Charith Chitraranjan, Adam Helsene, Paul Loree, Steve Bou Goshn, Yong Q. Gu, Ming Cheng Luo, M. Javed Iqbal, Gerard R. Lazo, Anne M. Denton, Shahryar F. Kianian

Research output: Contribution to journalArticlepeer-review

10 Scopus citations


In the course of evolution, the genomes of grasses have maintained an observable degree of gene order conservation. The information available for already sequenced genomes can be used to predict the gene order of nonsequenced species by means of comparative colinearity studies. The "Wheat Zapper" application presented here performs on-demand colinearity analysis between wheat, rice, Sorghum, and Brachypodium in a simple, time efficient, and flexible manner. This application was specifically designed to provide plant scientists with a set of tools, comprising not only synteny inference, but also automated primer design, intron/exon boundaries prediction, visual representation using the graphic tool Circos 0.53, and the possibility of downloading FASTA sequences for downstream applications. Quality of the "Wheat Zapper" prediction was confirmed against the genome of maize, with good correlation (r > 0.83) observed between the gene order predicted on the basis of synteny and their actual position on the genome. Further, the accuracy of "Wheat Zapper" was calculated at 0.65 considering the "Genome Zipper" application as the "gold" standard. The differences between these two tools are amply discussed, making the point that "Wheat Zapper" is an accurate and reliable on-demand tool that is sure to benefit the cereal scientific community. The Wheat Zapper is available at http://wge.ndsu.nodak.edu/wheatzapper/.

Original languageEnglish (US)
Pages (from-to)11-17
Number of pages7
JournalFunctional and Integrative Genomics
Issue number1
StatePublished - Mar 2013

Bibliographical note

Funding Information:
Acknowledgments The authors wish to thank all our beta testers for very insightful suggestions. This work was supported by funding from the National Science Foundation, Plant Genome Research Program (NSF-PGRP) grant no. IOS-0822100 to SFK. FMB was partially supported by Program Master and Back Regione Autonoma della Sardegna and Monsanto Beachell-Borlaug International Scholarship.


  • Brachypodium
  • Fine mapping
  • Microsynteny
  • Rice
  • Sorghum
  • Synteny


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