The SoyBase Genome Browser: A Cross-legume Discovery Tool

Legumes form the third largest plant family, with members distributed from the tropics to the tundra.   Many legume species function as anchor species in their ecological niches.  For humans, many legume species serve as a dietary mainstay and provide a significant amount of their total protein intake.  Soybean, Glycine max, along with Medicago truncatula, and Lotus japonicus, are model legume species with published genome sequences. The SoyBase soybean genome browser and the Legume Information System browsers for Lotus and Medicago are integrated via synteny tracks. The SoyBase soybean pseudochromosomes are extensively annotated with other legume data tracks, including EST and unigene sets from 11 legume species.  Soybean expression data from transcriptome sequencing projects, allows users to visualize expression in different plant tissues and developmental time points as well as gene expression during seed development.  The SoyBase genome browser is also linked to the soybean genetic map using sequence based genetically mapped markers.  This linkage allows users to leverage the considerable genetic data for soybean in the form of QTL data for agronomic traits with the genomic sequence data presented in the genome browser.  Thus researchers of other legume species can discover homologous sequences in soybean and observe the soybean genetic map for agronomic traits that may be associated with their genes of interest.  By visualizing the results of the transcriptome sequencing projects the researcher could also observe in what tissues as well as time points their genes may be expressed.  Examples of the data and user interface will be presented.