Custom Arachis Genome Context Viewer
A custom version of GCV(Genome Context Version) for Arachis is now available at PeanutBase. It shows micro-syntenic view of the genomic region with adjacent genes and the gene families they belong to. Start with a full query gene ID like, arahy.Tifrunner.gnm2.ann2.Ah02g344500,arahy.Tifrunner.gnm2.ann1.H916D0, arahy.BaileyII.gnm1.ann1.mikado.chr02G4069,aradu.V14167.gnm1.ann1.Aradu.32WCY in the search box to get their genomic context.
Pangene set version-3 has been integrated into GCV(Genome Context Viewer)
The updated pangene version pan3 has also been integrated into the custom GCV version.
An example with
i. a pangene: https://www.peanutbase.org/tools/gcv_pangenes/gene;arachis_pangenes=Arachis.pan3.pan18851
ii. a Tifrunner gene: https://www.peanutbase.org/tools/gcv_pangenes/gene;arachis_pangenes=arahy.Tifrunner.gnm2.ann2.Ah02g344500
Now Gene Report Page shows gene expression view
The ArachisMine gene report page now shows the expression chart below the gene structure.
An example link with a starch synthase gene
Pangene set version has been updated to ver-3
Re-computed pangene-sets for Arachis, the pan3 version is now available at the DataStore for the community as Arachis.pan3.BYQ9 that includes Arachis stenosperma in this update. With this our pangene work involves four species (A. hypogaea, A. duranensis, A. ipaensis and A. stenosperma) consisting of seven annotation sets (four annotation sets from A. hypogaea and one each from A. duranensis, A. ipaensis and A. stenosperma). We will soon start integrating this version in other tools at PeanutBase.
Two new Arachis duranensis genomes, K30060 and K30065
K30060: This accession is one of the closest identified to A. hypogaea. The genome assembly is avaialable at our DataStore.
K30065: The assembly files for this accession are also available at the dataStore here.
Genome alignments with K30060 and K30065 strains of dueanensis
Available alignments to date are listed below and are accessible from our
Comparing multiple genotypes in Flapjack format using Gigwa
Genome alignments available to date are listed below and are accessible from our species page under each of the species resources as JBrowse links.
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.
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(Tifrunner.gnm1.ann2) and helps lookup from the Genbank id to the corresponding annotations in other versions.
New Technology Platform: We have now moved to a new technology platform.
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.
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’.
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’.
JBrowse2, a new genome browser
JBrowse2: a new and genome browser with enhanced functionalities implented at PeanutBase.
Examples:
DSCensor
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.
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)
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
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)
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.
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.
(November 2020) New trait association viewer (ZZBrowse); phenotype data from NAM project; data store visualizer.
(October 2020) Core genotype paper published, software update, minicore phenotype data.
(September 2020) Arachis pathway data, PeanutMine update.
(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.
(February 2020) Instructions for GCViT, genotyping project and site improvement.
(January 2020) African Lines genotyping data and new genotype comparison tool, GCViT for PeanutBase
(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.
(May 2018) Detailed data records and gene families for cultivated peanut (A. hypogaea) gene models are now available.
(April 2018) Sequence search (BLAST) for cultivated peanut genes is available.
(March 2018) A. hypogaea gene models, PeanutBase advisory committee report available.
(February 2018) Gene atlas added to peanut browser
(December 2017) Software updates, all downloads served from Legume Federation data store, page updates
(November 2017) Tripal updated to version 1.2, repairs and improvements to gene model 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
(June 2017) PeanutBase now hosts Peanut Bioscience content
(May 2017) Peanut downloads in the data store, more marker data
(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:
(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
(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
(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
(October 2015) New gene expression atlas; new marker search & reports; trait evaluation data; pollination & crossing technique video
(September 2015) New feature to search germplasm; 41 QTL added
(July 2015) Peanut gene expression atlas; sequence viewer in JBrowse; new repeat/transposable sequences.
(June 2015) InterPro domain descriptions for all proteins; new JBrowse bookmark feature
(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.
(March 2015) Many new peanut images (seeds, pods, plants; various species); New “gene basket” tool.
(February 2015) Diploid assemblies now in GenBank; Peanut consensus genetic map available.
(January 2015) New BLAST targets (genes); New gene pages and descriptors; peanut at PAG
| [Peanut talks at 2015 PAG](https://pag.confex.com/pag/xxiii/webprogram/#srch=words | peanut%20groundnut%20Arachis | method | or | pge | 1) |
(December 2014) PeanutBase was recognized at AAGB 2014, practice tutorial, BLAST against both diploid genomes
(November 2014) Diploid gene models in genome browser, new sequence search utility, reorganization of site and more QTL data
(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)
| 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 |
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)
(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 LegumeInfo.org, 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
(September 2013) Transcriptome assembly projects compiled and a few more QTL reports
(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.