• Mt5.0, the latest Medicago genome:
    The latest version of the Medicago truncatula genome, Mt5.0 has now been incorporated into the legumeinfo datastore: assembly, annotations.
    A full transition to using Mt5.0 in legumeinfo hosted resources is ongoing, but you can see the comparisons of Mt5.0 gene content with the Mt4.0 version (and with other annotated legume genomes) using an instance of the Legume Federation Genome Context Viewer (GCV) here:
    As described in his LegumeFederation blog post, Dr. Nevin Young decided to take GCV out for a test-drive to help answer the question, "Are symbiosis genes, clustered together in the Medicago truncatula genome into so-called ‘symbiotic islands’, also conserved, syntenic and co-linear in the genomes of other legume species?” The study provided insights into symbiotic islands, strengths and limitations of GCV – and also the challenges of comparative genomics based on sequence assemblies coming from diverse sources. More details here:

    Note that clicking on Mt5.0 genes in the GCV will offer links to resources for Mt5.0 developed by the group at the Laboratory of Plant-Microbe Interactions who produced and published this new version of the Jemalong A17 genome assembly (Pecrix, et al. 2018 Nature Plants (4(12) 1017-1025),). The Mt5.0 genome also has a JBrowse instance set up at the http://medicagohapmap2.org site, featuring a plugin developed at JCVI for highlighting features relevant to gene structure in a text display of the sequence (similar to the TAIR “SeqViewer Nucleotide View”). To access this feature, right click a gene and ask to View Sequence. We have heard Medicago users requesting this functionality, and now hope to deploy it to other JBrowses in the Legume Federation family- if it’s something you want to see sooner for your favorite genome let us know!

  • New peanut assembly:
    A new tetraploid peanut assembly (a structural update) along with the corresponding annotations can now be found at the Data Store. This version is essentially the same as Tifrunner version 1 (arahy.Tifrunner.gnm1.KYV3.genome_main.fna) at the base pair level, but has several large structural rearrangements, on the basis of HiC assessments, contributed by the Aiden lab at Baylor College of Medicine. See a summary of the changes here.