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Title: Wheat Zapper: a flexible online tool for colinearity studies in plants

Author
item ALNEMER, L - University Of Jordan
item SEETAN, R - North Dakota State University
item BASSI, F - North Dakota State University
item CHITARANJAN, C - North Dakota State University
item HELSENE, A - North Dakota State University
item LOREE, P - North Dakota State University
item GOSHN, S - North Dakota State University
item Gu, Yong
item LUO, M - University Of California
item IQBAL, M - North Dakota State University
item Lazo, Gerard
item KIANIAN, S - North Dakota State University
item DENTON, A - North Dakota State University

Submitted to: Functional and Integrative Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/12/2013
Publication Date: 3/10/2013
Citation: Alnemer, L.M., Seetan, R., Bassi, F.M., Chitaranjan, C., Helsene, A., Loree, P., Goshn, S.B., Gu, Y.Q., Luo, M.C., Iqbal, M., Lazo, G.R., Kianian, S.F., Denton, A.M. 2013. Wheat Zapper: a flexible online tool for colinearity studies in plants. Functional and Integrative Genomics. 13:11-17.

Interpretive Summary: A fully sequenced genome represents a valuable resource for molecular and genetic studies of a species. Wheat is the single most important source of plant calories and protein in the human diet. Due to the complexity and size of its genome, its full reference sequence is not expected to become available in the near future. However, random sequencing of genomic DNA has generated large sequence data. The resource can be well utilized by molecular biologists and breeders if proper bioinformatics tools are available. Therefore, we developed such a tool termed the WheatZapper. The WheatZapper tool allows for extracting sequence reads related to the gene of your interest based on a comparative analysis method with other sequenced plant genomes.

Technical Abstract: 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 “WheatZapper” 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 28 position on the genome. Further, the accuracy of the “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 the “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/.