(April 2024) More userguides and improvements

Comparing multiple genotypes in Flapjack format using Gigwa

  • We have taken advantage of the recent version of our Gigwa tool which provides a flapjack view of multiple genotypes using diversity data. All userguides are accessible from our Help page and the step by step instructions for
    multiple genotype comparison and
    – similarity and differences of one to many genotypes using Gigwa are here.
    Enhanced instructions for genome structure comparison
  • Other userguides are being enhanced with images(result after following the instructions).
(March 2024) More genome alignments

Genome alignments available to date are listed below and are accessible from our species page under each of the species resources as JBrowse links.

  • Against Tifrunner and BaileyII:
  • Against duranensis:
    JBrowse2 aradu.V14167.gnm2.x.araip.K30076.gnm2
    JBrowse2 aradu.V14167.gnm2.x.arast.V10309.gnm1
    JBrowse2 aradu.V14167.gnm2.x.araca.K10017.gnm1
  • Against ipaensis:
    JBrowse2 araip.K30076.gnm2.x.araca.K10017.gnm1
(February 2024) Stenosperma annotation at PeanutBase
  • Stenosperma annotation at PeanutBase GenBank RefSeq annotation for Genome assembly 1 for Arachis stenosperma, genotype V10309 is now available at PeanutBase. The primary source of this data is GenBank. The files are in our DataStore and you can look at other available resources at PeanutBase species resources page.
(December 2023) Quality metrics for expression data and userguide update.
  • Expression data quality metrics are now available: We have made available the quality metrics, MultiQC report with interactive graphics, for the expression dataset (Clevenger 2016) remapped to Tifrunner.gnm2.ann2. Links for expression related data have been compiled at the Gene Expression Resources page.

  • Userguide updated with gene family search: We have added instructions for finding gene family starting from a gene-id, phylogram or the tree view along with other members from legumes in our userguides collection.

(November 2023) BaileyII and Arachis pangenes in GCV.
  • BaileyII integrated into GCV: The BaileyII gene models have now been integrated with our Genome Context Viewer (GCV) tool enabling comparison with other Arachis and legume genomes. This gives a comparative view of the immediate neighborhood of the queried gene in the micro-syntenic region with added phylogenetic(gene family) information. Clicke here for a link to an example view.

  • Pangenes in GCV: The Genome Context Viewer has been linked to Arachis pangenes. The custom GCV instance. Clicking on the pangene takes to a link to the pangene report page in ArachisMine where all members are listed. Please note that the pangene view includes the NCBI annotation and helps lookup from the Genbank id to the corresponding annotations in other versions.

(October 2023) Tifrunner-gnm2(V2) in GenBank, expression data in ArachisMine and DataStore.
  • Tifrunner gnm2(assembly version 2) in GenBank: Genome sequence of Arachis hypogaea, cultivar Tifrunner - assembly version 2, accession number PIVG00000000 has been successfully released into GenBank.
  • Expression data in DataStore and in ArachisMine: The peanut expression data (Clevenger 2016) after remapping the reads to Tifrunner.gnm2.ann2 is now available at DataStore and has also been integrated into the ArachisMine gene report pages.
(September 2023) Synteny and expression tracks, Legumebot.
  • Tifrunner gnm2.ann2 synteny with other genomes: Synteny tracks for Tifrunner gnm2.ann2 with other genomes like diploids, gnm1, Bailley_II, etc. have been added in JBrowse.
  • Expression tracks: Expression tracks for various tissues have been added after reads were mapped to Tifrunner gnm2.ann2 (data from Clevenger 2016).
  • Legumebot: An experimental chatbot for answering questions about legume species, with content from PubMed and PubAg publication abstracts. More about it.
(June 2023) PeanutBase Migrated to new technology platform.

New Technology Platform: We have now moved to a new technology platform.

  • REQUEST: Please provide us your feedback when you find something is missing/fails/incomplete. We will try to provide that on a priority basis.
  • The legacy site is still available at but it won’t be updated anymore.
  • All further developments will now be at this new site.
  • The migration is not yet complete but some content still at the legacy site will be migrated over time.
(April 2023) New genomes at PeanutBase DataStore(Bailey, Tifrunner, Pangenes).

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.

(Januar 2023) Traits to associated markers using ArachisMine.

Traits to associated markers using ArachisMine
Now it is possible to select a trait from the dropdown and and generate a list of associated markers from QTL/GWAS studies. The markers can be further explored for details using the links in the page.
‘Try it at ArachisMine’ (Click the GENETICS tab for the preset query, ‘Trait –> GeneticMarkers’) OR
use the link directly to this ‘query page’.

(November 2022) Search genes and traits by keywords.

Search genes & 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’.

(October 2022) JBrowse2, a new genome browser with enhanced functionalities implented at PeanutBase.

JBrowse2, a new genome browser
JBrowse2: a new and genome browser with enhanced functionalities implented at PeanutBase.

  1. Aradu structural change, example.
  2. Multiple genome display, example.
  3. Details of features on the right panel, example.
  4. Display Variant data from VCF, example.
(September 2022) DSCensor:genome assembly stats; Gigwa2.5:Visualize variants in multiple lines.

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.

(May 2022) The peanut image catalog of the core collection is now available at PeanutBase.

Peanut core catalog

These images were taken to document unique traits of each accession during a large-scale project to comprehensively catalog the peanut core and mini core collection. Now the images of the accessions in the core collection are available as a catalog. (Contribution from Noelle Anglin, USDA-ARS and others)

(February 2022) A new and improved Arachis ipaensis genome; Peanut expression atlas mapped to genome2 assembly

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

(August 2021) The peanut mini core image catalog is now at PeanutBase.

Peanut mini core image catalog

These images were taken to document unique traits of each accession during a large-scale project to comprehensively catalog the peanut core and mini core collection. Now the images of the accessions in the mini core collection are available as a catalog. (Contributor: Noelle Anglin, USDA-ARS)

(April 2021) Arachis Phenotype server; PeanutMine update.

Arachis Phenotype server

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 update

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
(February 2021) New genome assembly for A. cardenasii, a diploid relative of peanut.

New genome assembly for A. cardenasii, a diploid relative of peanut.

The genome of Arachis cardenasii, a relative of cultivated peanut, has been sequenced and is available here (with some usage restrictions) at the PeanutBase Data Store. This diploid wild species has been used as an important source of disease resistance in cultivated tetraploid peanut. Genome sequencing was funded by the USDA (Dr. Brian Scheffler leading), under the scientific guidance of Drs. David and Soraya Bertioli and colleagues.

Older News

(November 2020) New trait association viewer (ZZBrowse); phenotype data from NAM project; data store visualizer.

  • 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 (NAM_Tifrunner, NAM_Florida-07).
  • 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.

(October 2020) Core genotype paper published, software update, minicore phenotype data.

  • Genotypic Characterization of the U.S. Peanut Core Collection: This publication is now out.
    Paul I. Otyama, Roshan Kulkarni, Kelly Chamberlin, Peggy Ozias-Akins, Ye Chu, Lori M. Lincoln, Gregory E. MacDonald, Noelle L. Anglin, Sudhansu Dash, David J. Bertioli, David Fernández-Baca, Michelle A. Graham, Steven B. Cannon and Ethalinda K. S. Cannon. Genotypic Characterization of the U.S. Peanut Core Collection
    G3: GENES, GENOMES, GENETICS November 1, 2020 vol. 10 no. 11 4013-4026.
  • Software update: A number of software packages have been updated to their latest versions to keep PeanutBase up to date and functional.
  • Initial instance of a new tool, ArachisPheno, for exploring peanut phenotype data. This includes data from the U.S. mini core collection. More data sets will be loaded as they become available.

(September 2020) Arachis pathway data, PeanutMine update.

  • 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.

(August 2020) Nematode resistance QTL dataset from Ballen-Taborda C, Chu, et al. 2019.

A new source of root-knot nematode resistance from Arachis stenosperma: The QTL dataset from the publication Ballen-Taborda C, Chu, et al. 2019 is now available at PeanutBase. QTLs, maps.

(May 2020) Ongoing work to provide access to phenotype data.

  • 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.

(February 2020) Instructions for GCViT, genotyping project and site improvement.

  • The genotype display tool Gigwa and comparison tool GCViT pages have been given a native PeanutBase look.
  • Instructions have been added to the GCViT page (Please click the ‘Instructions …’ bar).
  • There is a now a new information page for the genotyping projects.
  • Links have been corrected in the germplasm page.

(January 2020) African Lines genotyping data and new genotype comparison tool, GCViT for PeanutBase

  • 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.

(December 2019) AAGB Conference Abstracts now available in PeanutBase, 2018 & 2019.

The AAGB conference abstracts for October 21-25, 2019 (Jinan, CHINA) and November 12-16, 2018 (Saly, SENEGAL) along with their programs are now available at the AAGB page.

(October 2019) Map and QTL dataset from Kolekar, Sujay, et al. 2016a

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

(August 2019) Improvements to the A. hypogaea Tifrunner assembly released.

Corrections to the A. hypogaea var. Tifrunner genome assembly were made by the DNA Zoo, on the basis of Hi-C data produced by the Aiden lab. A summary of the changes is here, the genome data can be downloaded here, and the gene model annotations are available here. See also this DNA Zoo announcement.

(June 2019) US mini core genotype data available

(April 2019) New high-density genetic map from Hu, et al., 2018, CViTjs 1.0

(February 2019) Map and QTL dataset from Leal-Bertioli, Moretzsohn, et al. 2016

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

(November 2018) New comparative map viewer; map downloads in Legume Federation Data Store; new JBrowse tracks

(September 2018) Data from Leal-Bertioli et al., 2015 available; new root transcriptome expression atlas; more SNPs aligned to A. hypogaea.

(August 2018) SNP datasets aligned to genomes, new leaf spot and TSWV QTL, new high density SNP map, NCBI A. hypogaea annotation.

(June 2018) Two sets of germplasm traits (Simpson and Holbrook), tissue expression atlas on A. hypogaea, new gene family BLAST target.

  • 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.

(May 2018) Detailed data records and gene families for cultivated peanut (A. hypogaea) gene models are now available.

  • Gene models for cultivated peanut (A. hypogaea) have been added to the new Legume Federation gene families, which are searchable at More information about the gene families is here.
  • Detailed information about individual gene models can be found on the gene model pages.
  • Gene models are available for download and BLASTing, and can be browsed on the genome using GBrowse and JBrowse.
  • To learn more about the A. hypogaea Tifrunner genome assembly and gene models, see the peanut genome information page.

(April 2018) Sequence search (BLAST) for cultivated peanut genes is available.

  • 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.
  • Announcement: Breeders Workshop before APRES meeting
    A breeders workshop will be held July 9th, 2018 8:00AM-12:00PM in Williamsburg, VA, the day before the APRES meeting. The focus will be on Marker Assisted Selection. More information coming soon.

(March 2018) A. hypogaea gene models, PeanutBase advisory committee report available.

(February 2018) Gene atlas added to peanut browser

  • The tissue atlas from Clevenger et al. 2016 as been added to both the cultivated peanut (Arachis hypogaea) genome browsers. The new tracks can be viewed in GBrowse or JBrowse.
  • Cultivated peanut genome assembly available
    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.

(December 2017) Software updates, all downloads served from Legume Federation data store, page updates

  • PHP has been updated to the current version (7.1)
  • Database upgraded to to current version of Chado: 1.31. This change should be invisible, but please let us know if you find problems.
  • JBrowse has been updated to the current release (1.12.3)
  • All downloads have been moved to the Legume Federation data store, with a consistent naming scheme and directory structure, and mirrored at CyVerse (in the LegumeFederation folder inside “Community Data”).
  • Page updates: updated assembly information on several pages, improved gene model pages and added links to the LIS synteny browser, the Context Viewer, other bug fixes.

(November 2017) Tripal updated to version 1.2, repairs and improvements to gene model pages

  • 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.

(October 2017) NCBI annotations added to the A. duranensis and A. ipaensis genome browsers.

The NCBI annotations are now available in the A. duranensis and A. ipaensis genome browsers. These annotations are calculated by NCBI for the representative genomes of all eukaryotes. See more information about NCBI’s A. duranensis and A. ipaensis annotations.

(August 2017) Improvements to marker search and new marker data

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

(June 2017) PeanutBase now hosts Peanut Bioscience content

(May 2017) Peanut downloads in the data store, more marker data

  • 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.

(March 2017) Interactive tour for QTL data and new marker track

(February 2017) SNPs from the Arachis SNP chip now available

The 15,746 SNPs from the new Arachis SNP chip (Pandey et al., 2017) which were determined to be 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.

(January 2017) Improvements to whole genome view of BLAST results

CViTjs is now integrated into the BLAST utility to display BLAST hits locations on an entire genome. This view is only available when BLASTing against genome targets (with blastn or tblastn).

CViTjs provides an interactive hit viewer with these features:

  • Zoom in and out using the + and - buttons
  • Click the wrench button to get a tool palette for: panning, zooming to a selected region, drawing, erasing, and choosing colors
  • The reset button between the two zoom buttons will return the image to its original state

(December 2016) Gene expression with eFP browser, whole genome visualization of BLAST hits

(November 2016) Newsletter signup; transcript mappings, bug fixes.

(October 2016) Trait data attached to germplasm pages

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

(September 2016) New pedigree chart, transcriptome, genome summaries, and germplasm improvements

  • An interactive pedigree chart from ‘Use of Plant Introductions in Peanut Cultivar Development.’ 2001. T G Isleib, C C Holbrook, D W Gorbet.
  • Arachis hypogaea tissue transcriptome for A. hypogaea mapped to A. duranensis and A. ipaensis; also, atlas expression data has been imported into PeanutMine, where heatmaps of expression can be generated for arbitrary lists of transcripts (as in the templated query example Genes => GOTerms => mRNAs).
  • Pages describing the A. duranensis and A. ipaensis genome assemblies
  • Synonyms have been added to germplasm data and can be used to find stock records.
  • Instructions for finding promoters added the the FAQs and an interactive tour for the germplasm map.

(August 2016) New markers loaded and germplasm can be searched

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

(July 2016) New search page for peanut projects recorded at NCBI

A new search feature for peanut BioProjects at NCBI is now available.

(June 2016) New PeanutMine query tool, more intuitive trait search, improved marker display, new “A” genome report

(May 2016) Upload data to geographic map, improved QTL search

(April 2016) A utility for finding peanut/Arachis publications

A utility to scan the recent Arachis literature at Pubmed.

(March 2016) Arachis diploid genome paper published; interactive map of Arachis germplasm; new markers

  • The paper describing the A. ipaensis and A. duranensis genome, ‘The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut’, has been published in Nature Genetics. It is available here.
  • Interactive geographic map of Arachis germplasm, colored by species, and linking to GRIN records, with new functionality:
  • New microsatellite markers from Moretzsohn, Leoi et al. (2005), e.g. pPGSSeq17H10.

(February 2016) New gene expression atlases - for nematode and drought responses

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:

(December 2015) New metabolic pathway viewer; improved gene pages; markers loaded for germplasm diversity; improved gene pages

(November 2015) Genetic markers from three more map publications, and improvements to gene family and synteny views

  • 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.

(October 2015) New gene expression atlas; new marker search & reports; trait evaluation data; pollination & crossing technique video

  • New gene expression atlas. Comparison of RNA-Seq read counts from 22 Arachis hypogaea tissues against Arachis ipaensis and A. duranensis genomes combined, from Dr. Peggy Ozias-Akins and colleagues.
  • New marker search page and reports, e.g. Lec-1.
  • Trait evaluation data for peanut germplasm: PeanutBase has just started attempting serve the germplasm evaluation data (for traits or descriptors) for peanut. The evaluation data has been downloaded from the USDA GRIN website and are served here at PeanutBase. This utility is work in progress and would improve in future with better search capability and with more associated data. We request our user community to suggest improvements to make this utility more useful.
  • Pollination/Crossing technique in peanut: A video tutorial by Shyam Tallury, Ph.D. (Peanut Breeder, Advanced Plant Technology, Clemson Pee Dee Research & Education Center)

(September 2015) New feature to search germplasm; 41 QTL added

  • 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.

(July 2015) Peanut gene expression atlas; sequence viewer in JBrowse; new repeat/transposable sequences.

  • A gene expression atlas with 22 tissues from peanut is now available in the GBrowse genome browsers for A. duranensis and A. ipaensis. This pre-publication data is courtesy of Peggy Ozia-Akins lab in collaboration with Brian Scheffler. Transcript densities of these Arachis hypogaea tissues have been mapped onto the combined A. duranensis and A. ipaensis genomes here at PeanutBase by Wei Huang. Please contact the authors before using or citing this data.
  • The JBrowse genome viewers (e.g. Aradu.A01, Araip.B01) have a new sequence viewer plug-in, with the ability to grab up- and downstream sequence retrieval or reverse-complement sequence around features. Right-click or control-click on any feature (except for synteny), then choose “Sequence Viewer”. Also check the new fullscreen viewing capability of this browser (“Fullscreen” button at the top right corner of the JBrowse menu bar).
  • New repeat and transposable element sequences from the group of Drs. David and Soraya Bertioli: download repeats

(June 2015) InterPro domain descriptions for all proteins; new JBrowse bookmark feature

  • 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”

(May 2015) Phytozome 10.2 gene models, new and improved map and marker data experience; three new QTL datasets loaded.

(April 2015) View genomes via the faster JBowse; BLAST hit visualization; Interactive CMap; Enhanced Map Overview.

  • 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.

(March 2015) Many new peanut images (seeds, pods, plants; various species); New “gene basket” tool.

  • Peanut (Arachis) germplasm images can now be viewed at PeanutBase. Close to 2,000 images have been generously contributed by Noelle Barkley (USDA ARS, Griffin GA), to make them available to the peanut research community.
  • New “shopping cart” feature (or “basket”) for managing sets of genes (e.g. collect protein or CDS sequences and gene descriptions), under the gene search page.

(February 2015) Diploid assemblies now in GenBank; Peanut consensus genetic map available.

  • 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.

(January 2015) New BLAST targets (genes); New gene pages and descriptors; peanut at PAG

  • At the BLAST page, we have added A. duranensis and A. ipaensis gene targets, as peptides (blastp and blastx) and nucleotides (blastn and tblasn). These link to both alignment views and to the respective genome browsers.
  • New functional descriptions available at gene search page
  • [Peanut talks at 2015 PAG]( peanut%20groundnut%20Arachis method or pge 1)
  • Come visit us at PAG, for the LIS computer demo or stop by the Plant Databases Booth (#407).

(December 2014) PeanutBase was recognized at AAGB 2014, practice tutorial, BLAST against both diploid genomes

  • 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.

(November 2014) Diploid gene models in genome browser, new sequence search utility, reorganization of site and more QTL data

  • Gene models are now available, both as genome browser tracks for the sequenced wild peanut species A. duranensis and A. ipaenensis, and for download. Two gene model sets are available: predicted using the MAKER and GLEAN software, respectively. The Peanut Genome Consortium will be using the MAKER models as the primary set for analysis and description of the genes in these species.
  • Molecular markers from several mapping studies are available as genome browser tracks for A. duranensis and A. ipaenensis.
  • A new keyword search utility has been added to facilitate searching for sequence features, such as gene IDs/names, words in annotation, etc.
  • Many changes in the navigation and in the home page layout. Please let us know if you have questions or suggestions.
  • New QTL data sets have been added, covering a range of important traits: seed characteristics, and fungal and nematode resistance.
  • New data submission templates for QTL studies. We would love to work with you if you have such data, published or in process, that you would like to incorporate into PeanutBase!

(October 2014) Oil quality, nematode and rust resistance traits have been added to Marker Assisted Selection list.

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

(September 2014)

  • The BLAST sequence search tool has been refined at PeanutBase.
    The refined utility now includes both protein and nucleotide search against the A. duranensis and A. ipaensis genomes. We also have modified the user interface to look and feel like the most commonly used NCBI BLAST interface.

  • 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.

(August 2014)

  • New sequence-search tool, linking genomic hits to the genome browsers
    The BLAT sequence-search tool has been configured to search the A. duranensis and A. ipaensis genome sequences and link genomic hits to the genome browsers.

  • Updated web framework and graphical themes
    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.

  • Redesigned QTL/trait search system and feature report pages

  • Browser synteny between Arachis diploids and other sequenced legumes
    Corresponding synteny regions with soybean, common bean, and the model species Medicago truncatela for both A. duranensis and A. ipaensis.

(June 2014) Common bean and soybean gene models have been added to the PeanutBase Genome Browser

We have now enriched the PeanutBase Genome Browser with Glycine max (ver Glyma2.0) and Phaseolus vulgaris (build 1.0) gene models. Some of our users have found this comparison very useful along with the Arachis hypogaea transcripts (Guo et al.) track. Here is a view of the Genome Browser showing such a comparison.

(May 2014)

  • Pseudomolecule assemblies as 80 column multifasta files are now available for download
    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 available 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
  • BLAST and BLAT: Sequence search features are now available at PeanutBase
    Sequence search feature is now available at PeanutBase via BLAST and BLAT utilities. You can search your sequence against Arachis duranensis (assembly ver 1.0) or Arachis ipaensis (assembly ver 1.0) in the ARACHIS BLAST page (the general purpose NCBI BLAST sequence search utility appropriate for genomic sequences).
    you can use the BLAT alignment tool via the GBrowse pages for Arachis duranensis and Arachis ipaenensis. The BLAT alignment is recommended for aligning cDNA sequences against the corresponding assembly sequence.

    The steps for BLAT alignment are (at the GBrowse page):
    1. Select “Find Blat Alignment” in the drop-down menu for Configure.
    2. Click “Configure”
    3. In the “Find Blat Alignment” section that opens, enter your (single) sequence in the “Input Sequence to Align” box
    4. Click “Find”

    If a single hit is found, a new track called “BLAT” will be created in the genome browser with your aligned sequence. If multiple hits are found, you’ll have to select one from a list of locations.

    If you have questions or need further assistance please contact us.

(April 2014)

  • Genome Browser is now accessible for the two Arachis diploid progenitors.
    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.
  • Draft genome assemblies for the diploid progenitors of peanut are now available.
    Peanut Genome Consortium (PGC) has completed draft genome assemblies for the diploid progenitors of peanut, Arachis ipaensis and Arachis duranensis. These are available via our Download page.

(November-December 2013)

  • All available QTLs now accessible via a Summary Table
    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.

  • QTL terms with ontology compiled and available for download
    Ontologies will be an integral part at PeanutBase and we are trying to make them consistent with those for other legume species, with specialized terms for peanut where necessary, and with synonyms for existing terms in the literature and in use. This will help towards enabling searches that will integrate trait information for multiple legume species provided by, and will allow integration with other plant genetic databases. As of November, 2013, peanut QTL terms have been collected from published resources and are being aligned/integrated with the trait ontology developed at SoyBase. We have made this evolving resource, QTL terms with ontology, available for download as an excel spreadsheet. We also welcome and encourage comments and suggestions from the community about this resource.

(October-November 2013) A New Look for PeanutBase

  • 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.

(September 2013) Transcriptome assembly projects compiled and a few more QTL reports

  • A large number of peanut transcriptome sequencing projects are underway in 2013. We have compiled here these projects (as of September, 2013) and it is downloadable as an Excel file.
  • Seven new QTL reports are being reviewed and revised before before making them ready for uploading.

(July-August 2013) QTL and map resources downloadable from one place

A few QTL and map resources were compiled with the goal to make them available for download from a single location. These resources will be enhanced through the Tripal’s Chado database schema for convenient data sharing with other legume projects using the same schema.