A goal of the LIS and LegumeFederation team is to create resources for legume research and advancement of legume trait improvement. One resource we updated recently is the Genome Context Viewer (GCV), which visualizes regions of genomes considered primarily with respect to the ordering and orientation of their annotated genes. Medicago truncatula Genome Database (MTGD), a Legume Federation genomic data portal (GDP), added links to the Medicago genes presented in the Genome Context Viewer and the LIS gene family phylogram. By clicking on any Medicago genes you can view the links for MedicMine, MTGD gene page and MTGD JBrowse.
Other updates to the GCV include:

  • Inclusion of full set of tracks with macrosyntenic relationships to query track; those chromosomes having synteny to the region displayed in the microsynteny view are still featured at the top of the display, ordered in accordance with the microsynteny track ordering
  • Color legend for species in macrosynteny (consistent with taxon coloring scheme used in our phylotree and GIS views)
  • Shading of backgrounds to help differentiate between chromosomes
  • Resizable split pane dividers between the macrosynteny or microsynteny panes and their respective legends

Legume Federation and LIS have released a new Legume Mine: ChickpeaMine. This version of ChickpeaMine contains the same two chickpea genomes that are available on LIS. Chickpea desi (version ICC4958 v2.0) and chickpea kabuli (version CDC Frontier v1.0). Here are some examples on how use the ChickpeaMine and other Mines:

  • Example: Search and Create list
    • Use the keyword search box to search for a gene, ID or keyword Example Search: seed protein
    • Use the Categories box on the left side to sort through the search results Example: Hits by Category Gene
    • Create list from sorted search results by first selecting the genes you want in your list, then clicking on the "create list" button
  • Example: Gene Expression

The LIS and Legume Federation team will continue to add more data and resources. Check the LIS and Legume Federation websites for more updates.