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

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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 “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/.

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Abbreviations

EST:

Expressed sequence tags

Brachypodium :

Brachypodium distachyon

TC:

Tentative consensus sequence

WZ:

Wheat Zapper

GZ:

Genome Zipper

BLAST:

Basic Local Alignment Search Tool

BLASTn:

Basic Local Alignment Search Tool for nucleotides

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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.

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Authors and Affiliations

  1. Computer Information Systems Department, The University of Jordan, Amman, 11942, Jordan

    Loai M. Alnemer

  2. Department of Computer Science, North Dakota State University, Fargo, ND, 58102, USA

    Raed I. Seetan, Charith Chitraranjan, Adam Helsene, Paul Loree, Steve Bou Goshn & Anne M. Denton

  3. Department of Plant Sciences, North Dakota State University, Fargo, ND, 58102, USA

    Filippo M. Bassi, M. Javed Iqbal & Shahryar F. Kianian

  4. USDA- Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA

    Yong Q. Gu & Gerard R. Lazo

  5. Department of Plant Sciences, University of California, Davis, CA, 95616, USA

    Ming-Cheng Luo

  6. NDSU Department 7670, P.O. Box 6050, Fargo, ND, 58108-6050, USA

    Shahryar F. Kianian

Authors
  1. Loai M. Alnemer
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  2. Raed I. Seetan
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  3. Filippo M. Bassi
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  4. Charith Chitraranjan
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  5. Adam Helsene
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  9. Ming-Cheng Luo
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  10. M. Javed Iqbal
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  11. Gerard R. Lazo
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  12. Anne M. Denton
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  13. Shahryar F. Kianian
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Corresponding author

Correspondence to Shahryar F. Kianian.

Additional information

Loai M. Alnemer, Raed I. Seetan, and Filippo M. Bassi contributed equally to this paper.

Electronic supplementary material

Supplementary information provides a precise description of the Intron/Exon prediction algorithm and data supporting the evaluation of ‘Wheat Zapper’ against the genome of maize (Fig. S1 and Table S1).

ESM 1

DOCX 31 kb

Table S2

Spread sheet for the evaluation of synteny prediction calculated by ‘Wheat Zapper’. a Provides a comparison between the predictions of ‘Wheat Zapper’ and ‘Genome Zipper’ for the synteny relationships between Brachypodium, Sorghum, and wheat chromosome 5A. b Provides a list of orthologus genes predicted to be located within the Q gene interval, including the causal locus (highlighted in green; (XLSX 22 kb)

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Alnemer, L.M., Seetan, R.I., Bassi, F.M. et al. Wheat Zapper: a flexible online tool for colinearity studies in grass genomes. Funct Integr Genomics 13, 11–17 (2013). https://doi.org/10.1007/s10142-013-0317-4

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  • DOI: https://doi.org/10.1007/s10142-013-0317-4

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