Interactive visualization of orthologous genes and their annotations in plants

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ConferenceThe 3rd Current Opinion Conference on Plant Genome Evolution, Amsterdam, The Netherlands
AbstractFully sequenced genomes of model organisms and staple crops such as Aegilops tauschii, Arabidopsis thaliana, Brachypodium distachyon, Brassica rapa, Hordeum vulgare, Oryza sativa, Sorghum bicolor, Triticum aestivum, Triticum urartu and Zea mays provide a unique opportunity to visually compare their gene order conservation via orthology. The conservation in gene order provides information about gene function and interactions of proteins that are encoded by these genes. While gene order is conserved and well preserved at phylogenetic distances for closely related plant species, it is low or lost during evolution in distantly related species. A good understanding and visual perspective of gene content and gene order similarities and differences across plant species allows researchers and experimentalists to design breeding strategies that lead to resilient next generation crops (e.g. current GM crops), to nutritionally-enhanced foods (e.g. golden rice) or to pharmaceuticals synthesization (e.g. somatotropin in tobacco plants). Here we propose The Plant Orthology Browser (POB)-a web-based orthology and annotation visualization tool which supports 10 plant species and provides highly intuitive and interactive pairwise comparison and visualization of genomic traits via gene orthology. POB currently includes three interconnected modules: (i) a gene order visualization module implementing a highly interactive environment for exploration of gene order between any pair of chromosomes in two different plant species, (ii) a synteny visualization module providing interactive dot-plot representations of orthology relations between a pair of chromosomes in two distinct plant species, and (iii) a search module, which realizes the interconnectivity among all modules via a Google-like customized free-text search capability with online " as-you-type " suggestions and highlighting that allows users to explore various facets of the underlining information without being constrained by interface-dependent search fields.
AffiliationInformation and Communication Technologies; National Research Council Canada
Peer reviewedYes
NPARC number21276406
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Record identifier8ba53e18-7d26-47cf-9478-548b71a0d35d
Record created2015-10-09
Record modified2016-05-09
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