We now have new genomic data available for Arachis pangene set, Bailey II and Tifrunner genome2.

• Arachis Pangene set: Pangene set for Arachis species, based on A. hypogaea, A. duranensis, and A. ipaensis. This pangene set includes five annotation sets from A. hypogaea and one each from A. duranensis and A. ipaensis. More details and data at Data Store Arachis.pan1.4LN9.
• Bailey II genome: Arachis hypogaea accession Bailey II, genome assembly 1. More details for BaileyII.gnm1.1JTF.
• Tifrunner genome2: Genome assembly 2 for Arachis hypogaea, cultivar Tifrunner(Tifrunner.gnm2.J5K5). This version has structural changes relative to assembly 1.

Search Genes And Traits By Keywords

The ArachisMine Gene Keyword Search and Trait Keyword Search utilities are available from the Tools pannel. The search result lists the relevant features and are linked to the corresponding detailed display at ArachisMine.
Example: gene search with keyword 'photosystem II'.
Example: trait search with keyword 'pod'.

DSCensor for summary of genome assembly data & Gigwa2.5 multi-genotype comparison.

• DSCensor:
  Shows the summary statistics of assembly data.
• Gigwa2.5: Genotype comparison:
  Now it is possible to visualize variants between multiple lines within Gigwa(v2.5). This is achieved by selecting multiple individuals for display and then download and export as flapjack file format. The ‘keep files in server’ should be selected before export. Finaly, a click at ‘View in Flapjack-Bytes’ draws the visualization showing similarity and differences between the genetic lines at each of the SNPs.

• 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.

(April 2021) Arachis Phenotype server; PeanutMine update.

• Phenotype data server for PeanutBase is now operational at ArachisPheno. We now have the phenotype data for the peanut mini core collection: agronomic traits and seed biochemical traits. If you have phenotype data for peanut lines to share with the community, please contact us to house it at PeanutBase, or you may try a self submission too.
• PeanutMine updates:

The datasets are listed at the data sources page.

• Several genetic maps along with their derived QTLs are now loaded into the PeanutMIne.
• GWAS datasets in PeanutMine:

Gangurde_Wang_2020-NAMFlor7
Gangurde_Wang_2020-NAMTifr
Otyama_Kulkarni_2020

• New tool (ZZBrowse) for exploring marker-trait association from GWAS experiments – allowing comparisons with data from other species. Example showing pod/seed weight SNP in peanut that lands in one region of soybean associated with pod number.
• The GWAS data from the two Nested Association Mapping (NAM) populations reported in Gangurde SS, et al. (2020) is now at PeanutBase. Visualize using ZZBrowse (example), or download at the DataStore.
• New tool (MultiQC / DSCensor) for visualizing peanut genomic data in our Data Store. Example: Arachis annotation comparisons.
• New BLAST sequence-search interface (SequenceServer). Please try it and let us know your experience.

• Pathway data in gene pages at PeanutMine: Now Arachis hypogaea/duranensis/ipaensis reactome data is available in the gene pages at PeanutMine. Link: please scroll towards the bottom of the page to the section 'Pathways' to see if the gene function is related to a metabolic pathway. Not all genes have this feature, only genes that are listed in the reactome database have this special attribute.
• PeanutMine update: It has been updated to v2 with data coming from LIS Data Store.

• The PeanutBase team is working on new tools for interactively exploring phenotype data.
• Genotype data and phenotype data for the mini core are also available at the data store.
  

• African Breeding Lines data in PeanutBase gigwa instance: The PIL African Breeding Lines genotyping data are now in the PeanutBase GIGWA instance. The data files can be downloaded from our DataStore too.
• (New) Genotype Comparison Visualization Tool, GCViT: It is a tool for whole genome visualization of resequencing or SNP array data. GCViT allows a user to compare two or more accessions and visually identify regions of similarity and difference across the genome.
  It is capable of multiple chromosome visualisation for the comparison of multiple accessions from a single dataset. It extracts information from VCF file and does a parallel comparison between two or more lines within that VCF file plotting the location of these differences on the chromosome for visualization. One can, for example, plot the differences between progeny and its parents to identify which regions are inherited from which parents. (More information and a video tutorial about GCViT is at GitHub and SoyBase)

       We need your feedback on the usage of this tool and will appreciate it if you could let us know about your experience via Contact us.

• The genetic map and QTL data from Kolekar,Sujay, et al. 2016a has been loaded.

• Genotype data for the US peanut mini core (Otyama, et al., in press) is now available at PeanutBase via Gigwa (http://southgreen.fr/content/gigwa), a web-based tool for exploring genotype database. See instructions for filtering data and managing outputs.
• More information added regarding the Tifrunner genome assembly
• Some small bugs in the website and data have been fixed, particularly regarding germplasm records.

• The genetic map and QTL data from Leal-Bertioli, Moretzsohn, et al. 2016 has been loaded.

• Map and QTL for Rust and several morphological traits from Leal-Bertioli et al. 2018, "Identification of QTLs for Rust Resistance in the Peanut Wild Species Arachis magna and the Development of KASP Markers for Marker-Assisted Selection." have been loaded.
• Root transcriptome for A. hypogaea infected with Bradyrhizobium sp. SEMIA 6144 from Karmakar K., et al. (2018) "Transcriptomic analysis with the progress of symbiosis in 'crack-entry' legume Arachis hypogaea highlights its contrast with 'infected thread' adapted legumes. Mol Plant Microbe Interact."
• SNPs for the 2nd generation 48k Affymetrix SNP chip (Axiom_Arachis2) have been aligned on the A. hypogaea genome browser.

• Traits assessed between 1982 and 1988 for the 1977-1986 for the accessions collected in South America by Charles Simpson, Antonio Krapovickas, Walton Gregory, José Valls, Don Banks, and colleagues loaded and displayed on germplasm record pages. See an example.
• Above and below ground traits collected by Corley Holbrook in the late 1990s for the US Mini Core are loaded and displayed on germplasm record pages. See an example.
• The tissue expression atlas from Clevenger et al. 2016 is now available as a display of differential expression between tissues and showing expression levels on the peanut genome browser.
• The new Legume Federation gene model families are now available for BLASTing against a protein database (blastx or blastp). The older Phytozome gene families are also still available as a BLAST target, but deprecated. These are named "Gene Family Consensus - Legume Federation 1.0" and "Gene Family Consensus - Phytozome 10.2 (deprecated)" respectively.

Genes (coding sequence / CDS) can now be searched for the cultivated peanut genome, using BLAST. This extends the genome BLAST search which was enabled in December.

• The A. hypogaea gene models are now displayed on the genome browsers, both GBrowse and JBrowse
• The new gene models are also available for download.
• The 2017 report from the PeanutBase advisory committee is now online.

The cultivated peanut genome assembly is now available under the Ft. Lauderdale agreement. No group may publish whole-genome research until the IPGI has first published a formal description of the genome assembly. The genome assembly can be downloaded, browsed with GBrowse and searched with BLAST.

• Tripal, which provides most of the PeanutBase functionality, has been updated to version 1.2 so that PeanutBase can take advantage of the latest Tripal improvements. The update should be "invisible": all pages should look the same. Please let us know if anything stops working.
• Links to term definitions and protein domains have been added to gene model search results and record pages.
• Minor bug repairs to the gene model search and record pages.

• Now possible to search for markers by publication.
• Complete marker data for Liang et al.,2009 has been loaded.

• The Data Store is a new way to access bulk data at PeanutBase. Data sets (assemblies, annotation, repeats, synteny etc.) are now available in the Data Store, and via the mirrored CyVerse Legume Federation Data Commons. The Data Store is also available from a new button on the PeanutBase home page, and the data sets are still available via the older Download tab at PeanutBase.
• Marker data improvements: sequence and primers added for 7400 markers; an example marker page.

The 15,746 SNPs from the new Arachis SNP chip (Pandey et al., 2017) which were determined to by polymorphic in A. hypogaea (Clevenger et al., 2017) have been loaded into the A. duranensis and A. ipaensis genome browsers. Sequence and position details for each SNP can be found in the marker pages - search for markers starting with "AX-".

Genomic positions for an additional 3644 markers have been added to their marker records, for example Ah1TC06H03.

• Gene expression for 22 tissues (Clevenger et al., 2016) using the BAR eFP browser is available on the gene model pages.
• Whole genome visualization of hits added to the BLAST results page, for searches against the A. duranensis or A. ipaensis genomes (nucleotide-nucleotide search or protein-nucleotide search).

Trait data from GRIN has been imported into PeanutBase, permitting germplasm searching by trait.

About 15,000 new markers have been loaded. PeanutBase now holds germplasm data, which can be searched and viewed in detail.

• PeanutMine: A powerful new interface for querying peanut genetic and genomic data, and operating on lists of features. Developed in collaboration with the Legume Information System and Legume Federation projects.
• Improved search for peanut traits and QTL, to allow "broad" and "narrow" searches. For example, broad searches will expand a trait search for "oil" to return "seed linoleic" and other oil-related traits.
• Improved display of genetic markers in the genome browsers (now colored by by marker type).
• Report of a new "A" genome (Arachis duranensis) sequence report (for accession PI475845) adds information to complement the reference A genome at PeanutBase (accession V14167).

• A utility to scan the recent Arachis literature at Pubmed.

Expression views and atlases for nematode and drought responses, courtesy Patricia Guimaraes and Ana Cristina Miranda Brasileiro et al.

Access these via the Browse & Search menu, or directly:

• Tissue expression atlas (22 tissues from Arachis hypogaea)
• Nematode response experiment (treatment and control in A. stenosperma)
• Drought response experiment (treatment and control in A. duranensis)

• Nearly 500 additional markers (see the marker search page) have been added to the database from three publications: Cuc, Mace, et al. 2008; Ferguson, Burow, et al. 2004; and Moretzsohn, Hopkins, et al. 2004. Some examples: IPAHM023, pPGSseq9H8, Ah-736
• Improved gene family and synteny views (at partner site LegumeInfo): clearer legends, help, gene highlighting, and synteny features. An example gene tree with Arachis gene highlighted, and a corresponding synteny view.

• New germplasm search feature. The new feature, GRIN Connect, permits searching the GRIN global germplasm database directly from PeanutBase. (Or the direct link to the query page here.)
• 41 QTL reported by Sarvamangala C, Gowda MVC, Varshney RK. (2011) are now available: publication, map, and QTL features.

• InterPro domains: The Arachis gene models have now been annotated with protein domains searchable via InterPro domain IDs or a description word.
• New JBrowse feature: save sets of bookmarks (of tracksets and views) under Tools:"Quick Bookmarks"

• Now you can browse the genomes via the faster JBrowse:Aradu and Araip
• BLAST hit visualization: Now comes with a graphic presentation to help visualize the location of hits on the target
• Access the Arachis genetic maps via the Interactive CMap tool
• The Map Overview page has a new design that simplifies access to map sets and individual linkage groups. Also see the new RFLP-based tetraploid map published in Burow, Starr et al., 2014a.

• The A. duranensis and A. ipaensis genome assemblies were submitted to GenBank and now they have been published.
• The consensus genetic map for tetraploid Arachis published in Shirasawa, Bertioli et al., 2013a is now available for download.

• The PeanutBase team was recognized for its contribution towards facilitating the assembly of the diploid peanut genomes and the practical utility at the Seventh International Conference of the Peanut Research Community (Advances in Arachis through Genomics & Biotechnology), November, 2014, at Savannah GA USA.
• Our activity at AAGB included a tutorial on using PeanutBase, poster and powerpoint presentation, survey to get inputs from the user community and contacting the community for content contribution and further development.
• A practice tutorial for using PeanutBase is now available too.
• Now you can BLAST against both diploid genomes in one go: just select both species from the dropdown for 'Nucleotide BLAST Databases'.
• Outreach page: Please have a look at this page, our collection of outreach materials so far.

We have added the following three traits to our list in the Marker Assisted Selection page.

• Peanut root-knot nematode
• Seed oleic acid to linoleic acid ratio
• Rust, Puccinia

(Sep 2014) A prototype Marker Assisted Selection (MAS) page.

Here is a prototype MAS page for the trait Late leaf spot (Phaeoisariopsis personata infection) in peanut. We plan to add more Marker Assisted Selection (MAS) pages for various other traits relevant to peanut breeding to include, primarily information on the nearby markers used for MAS and lines carrying the various alleles of the trait. We welcome assistance from our user community having expertise on such traits to contribute information to these trait specific pages. Please contact us for this purpose if you would like to contribute or maintain a MAS page for a specific trait.

We have moved from the Tripal 1 / Drupal 6 web framework to Tripal 2.0a / Drupal 7. This shouldn't affect the content of the site, but will make it easier to add a number of important features - such as an integrated BLAST sequence search module - and to keep up with ongoing Tripal development. Please let us know if you like (or dislike) any aspects of the updated site. We will be adding a lot of features through the coming year, but are eager to hear about features that you would like to have.

Corresponding synteny regions with soybean, common bean, and the model species Medicago truncatela for both A. duranensis and A. ipaensis.

May 2014
We have made available the genome assemblies in a single 80 column multi-FASTA file, one for each diploid genome. These files contain the 10 pseudomolecule sequences in a 80 column format with the scaffold sequences concatenated (after ordering and orienting) and separated by spacer sequences of 10,000 "n"s. This format is compatible with some programs like IGV which requires the sequence lines be of equal width. They are availble via our Genomes (assembly) page and labeled in the corresponding dipoid pages as follows:

Aradu_v1.0.fa.gz       01-May-2014 14:26       251M       Pseudomolecules, one file

Araip_v1.0.fa.gz       01-May-2014 14:36       338M       Pseudomolecules, one file

April 2014
Genome Browser tracks are now available for the two diploid progenitor species, Arachis duranensis and Arachis ipaensis. In addition to the scaffold assembly, we have also provided a track with alignment of the Arachis hypogaea transcriptome data (Guo et al., BMC Genomics 2012, 13:608) on to each of the diploid genomes.

Nov-Dec, 2013
We have compiled and uploaded QTL data sets from 4 publications and now they are available at the 'Summary Table of All QTLs'. More details are available by clicking the QTL and wherever available we have also provided a cmap link to our collaborative site Legume Information System. You can also search the QTLs using this search page. Please explore this data and we encourage the community to give us feedback to make this resource more useful as we go along. As we keep compiling more QTL data sets, they will be available here through this summary page. All QTL related resources are accessible via our Qtls page.

Oct-Nov, 2013

• We have adopted a new theme for the site based on colors from a peanut. If you have suggestions for improvement or find errors, please don't hesitate to send us some feedback.
• The sidebar querying features have been temporarily removed while the database is being loaded.