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. 2014 Dec 10:14:348.
doi: 10.1186/s12870-014-0348-6.

chromoWIZ: a web tool to query and visualize chromosome-anchored genes from cereal and model genomes

Thomas Nussbaumer, Karl G Kugler, Wolfgang Schweiger, Kai C Bader, Heidrun Gundlach, Manuel Spannagl, Naser Poursarebani, Matthias Pfeifer, Klaus F X Mayer

chromoWIZ: a web tool to query and visualize chromosome-anchored genes from cereal and model genomes

Thomas Nussbaumer et al. BMC Plant Biol. .

Abstract

Background: Over the last years reference genome sequences of several economically and scientifically important cereals and model plants became available. Despite the agricultural significance of these crops only a small number of tools exist that allow users to inspect and visualize the genomic position of genes of interest in an interactive manner.

Description: We present chromoWIZ, a web tool that allows visualizing the genomic positions of relevant genes and comparing these data between different plant genomes. Genes can be queried using gene identifiers, functional annotations, or sequence homology in four grass species (Triticum aestivum, Hordeum vulgare, Brachypodium distachyon, Oryza sativa). The distribution of the anchored genes is visualized along the chromosomes by using heat maps. Custom gene expression measurements, differential expression information, and gene-to-group mappings can be uploaded and can be used for further filtering.

Conclusions: This tool is mainly designed for breeders and plant researchers, who are interested in the location and the distribution of candidate genes as well as in the syntenic relationships between different grass species. chromoWIZ is freely available and online accessible at http://mips.helmholtz-muenchen.de/plant/chromoWIZ/index.jsp.

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Figures

Figure 1
Figure 1
Heat map visualization of gene density. chromoWIZ visualizes the gene distribution of (A) all genes anchored as compared to (B) the number of genes matching the query criteria. The tooltip reports the relative and absolute number of tagged genes per bin.
Figure 2
Figure 2
Integration of gene expression information. Gene expression information, lists of differentially genes, and/or gene-to-group mapping data can be uploaded for enabling expression-based querying of genes. The different color codes highlight the search options, which become available after uploading the corresponding data.
Figure 3
Figure 3
Synteny between bread wheat chromosome 4A, Brachypodium and barley. Using chromoWIZ, genes from the bread wheat chromosome 4A were mapped against Brachypodium (A) and against barley (B) in order to highlight syntenic regions.
Figure 4
Figure 4
Chromosome (−arm) enrichment of genes responsive to a fungal pathogen. Bread wheat chromosome (−arm) enrichment for genes, which were responsive to Fusarium graminearum. Chromosome (−arms) 3B, 5BL, and 7DL are found to be significantly enriched for these genes.
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