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. 2016 Jan 4;44(D1):D1141-7.
doi: 10.1093/nar/gkv1130. Epub 2015 Nov 2.

PGSB PlantsDB: updates to the database framework for comparative plant genome research

Manuel Spannagl  1 , Thomas Nussbaumer  2 , Kai C Bader  3 , Mihaela M Martis  4 , Michael Seidel  3 , Karl G Kugler  3 , Heidrun Gundlach  3 , Klaus F X Mayer  3
Affiliations

PGSB PlantsDB: updates to the database framework for comparative plant genome research

Manuel Spannagl et al. Nucleic Acids Res. .

Abstract

PGSB (Plant Genome and Systems Biology: formerly MIPS) PlantsDB (http://pgsb.helmholtz-muenchen.de/plant/index.jsp) is a database framework for the comparative analysis and visualization of plant genome data. The resource has been updated with new data sets and types as well as specialized tools and interfaces to address user demands for intuitive access to complex plant genome data. In its latest incarnation, we have re-worked both the layout and navigation structure and implemented new keyword search options and a new BLAST sequence search functionality. Actively involved in corresponding sequencing consortia, PlantsDB has dedicated special efforts to the integration and visualization of complex triticeae genome data, especially for barley, wheat and rye. We enhanced CrowsNest, a tool to visualize syntenic relationships between genomes, with data from the wheat sub-genome progenitor Aegilops tauschii and added functionality to the PGSB RNASeqExpressionBrowser. GenomeZipper results were integrated for the genomes of barley, rye, wheat and perennial ryegrass and interactive access is granted through PlantsDB interfaces. Data exchange and cross-linking between PlantsDB and other plant genome databases is stimulated by the transPLANT project (http://transplantdb.eu/).

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Figures

Figure 1.
Figure 1.
Re-worked PGSB (Plant Genome and Systems Biology; formerly MIPS) PlantsDB search interfaces, providing intuitive keyword searches for gene identifiers, functional gene descriptions and plant genome resources. A new BLAST interface enables sequence similarity searches against genome and CDS/protein sequences from 18 different plant species.
Figure 2.
Figure 2.
PGSB BLAST search results visualization. Homology matches and alignment visualization of one particular bread wheat gene (Traes_7AL_0F8FA764F.1) and homologous regions to selected progenitor genomes and relatives. The colors depict the sequence identity, whereas the numbers in brackets represent the nucleotide length of the transcripts.
Figure 3.
Figure 3.
Project entry page of the RNASeqExpressionBrowser with extended search features for gene-to-group mapping (‘network modules’) and for lists of differentially expressed genes.
See this image and copyright information in PMC

References

    1. International Barley Genome Sequencing, C. Mayer K.F., Waugh R., Brown J.W., Schulman A., Langridge P., Platzer M., Fincher G.B., Muehlbauer G.J., Sato K., et al. A physical, genetic and functional sequence assembly of the barley genome. Nature. 2012;491:711–716. - PubMed
    1. Brenchley R., Spannagl M., Pfeifer M., Barker G.L., D'Amore R., Allen A.M., McKenzie N., Kramer M., Kerhornou A., Bolser D., et al. Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature. 2012;491:705–710. - PMC - PubMed
    1. International Wheat Genome Sequencing, C. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science. 2014;345:1251788. - PubMed
    1. Martis M.M., Zhou R., Haseneyer G., Schmutzer T., Vrana J., Kubalakova M., Konig S., Kugler K.G., Scholz U., Hackauf B., et al. Reticulate evolution of the rye genome. Plant Cell. 2013;25:3685–3698. - PMC - PubMed
    1. Mochida K., Shinozaki K. Unlocking Triticeae genomics to sustainably feed the future. Plant Cell Physiol. 2013;54:1931–1950. - PMC - PubMed

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