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PeanutBase has transitioned to a new technology format. All updates are now at the new site still under development. Please visit the new site and give us your feedback. The legacy site is still available at legacy.peanutbase.org.
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New and improved assembly of Arachis ipaensis
A completely new PacBio and Hi-C sequence and assembly of the genome of Arachis ipaensis is now available (with some usage restrictions) at the PeanutBase Data Store as a result of a collaboration between USDA, University of Georgia and Hudson Alpha. Arachis ipaensis is the B subgenome donor of cultivated peanut (A. hypogaea) and its wild counterpart A. monticola. This remarkable accession, K 30076, is the only collection of this species ever made. Its location, far from that of other B genome Arachis species, is incompatible with natural dispersal, indicating past transport by humans. Its extraordinarily high DNA identity with peanut’s B subgenome and location, close to Villa Montes in Bolivia where the landraces of peanut that combine the most primitive, or wild-like, characteristics are grown indicate that it is descended from the very same population that gave rise to the tetraploid species. -
Peanut comparative expression data with other legumes
The peanut expression atlas data (Clevenger, et al. 2016) after remapping the reads to gnm2.ann1 is now in the CoNekT tool where the expression patterns can be compared with their orthologs in other legumes at LIS.
You can- Browse the list of peanut genes with expression profiles in this dataset; click on the gene to visualize the expression profile with links to other features.
- Visualization expression profile of a single peanut gene.
- Compare the profiles of a group of genes of interest. (Paste this list as an example after choosing peanut for species: arahy.Tifrunner.gnm2.ann1.0FWC6J arahy.Tifrunner.gnm2.ann1.5ZI49M arahy.Tifrunner.gnm2.ann1.61UWXT arahy.Tifrunner.gnm2.ann1.6T97B arahy.Tifrunner.gnm2.ann1.72B7PK)
- Look at the available legume orthologs (gene family members) and from there the comparative expression pattern (tabular view, tree view) in those genes.
- Search for a specific expression profile at Conekt.
- Coexpressed profile neighbors of a gene presented as a limited network (accessible from the profile page ).
- An example of a peanut gene arahy.Tifrunner.gnm2.ann1.T0173K specifically expressed in roots like its orthologs in Glycine but showing divergence in function (expression pattern in non-root tissues) as a result of speciation in Phaseolus and Vigna.
