Site Overview and Guide

Browse & Search Tools | Germplasm | Submit & Download Data | Website Tours | FAQ | About PeanutBase | Contact

PeanutBase is organized around these features and tools:

• Genome browsers: currently including A. duranensis and A. ipaensis. From the browsers, you can do key-word searches (enter text under "Landmark or Region" in the browser), or go to regions that you know are of interest (for example, around genetic markers that you know about; edit the chromosome and coordinates under "Landmark or Region," or just scroll and zoom).
• Traits and Maps: PeanutBase maintains a relatively large (and growing) collection of published genetic maps. We are working to add QTL features to these when possible - and also to link from sequence-based genetic markers to the genome browsers. This allows a breeder to identify markers close to a trait of interest (the QTL) - and ultimately, will allow researchers to identify causative genes and perfect markers for some traits.
  • Traits overview: A major effort at PeanutBase is to collect published peanut QTL information and integrate it into a common genetic framework. The QTL data is loaded into PeanutBase and integrated with other genetic and genomic data. This data can be searched and viewed on genetic maps.
  • Maps overview: Arachis maps can be viewed as interactive maps, can be searched, and downloaded in CMap format below.
  • Marker Assisted Selection (MAS): These are custom-compiled pages that summarize what is known about markers and breeding lines relevant to important traits such as rust, nematode resistance, and oil quality. These pages require expert knowledge. If you have knowledge to contribute about existing MAS pages or new ones (for traits not yet covered), please contact us. We are looking for new information to help flesh out these pages, and we would love to credit anyone who can provide important information about high-value traits.
• Browsing Data:
  • Browse A. duranensis genome: Gbrowse | JBrowse
  • Browse A. ipaensis genome: Gbrowse | JBrowse
  • Browse Gene expression Resources: Microarray and high throughput sequencing data for peanut. We currently have three gene expression atlases: Tissue expression atlas, Nematode expression atlas and Drought expression atlas.


• Searching Tools:
  • BLAT: You can conduct a BLAT ("Blast-Like Alignment Tool") search using either DNA or RNA as the query sequence against the Arachis genomes. BLAT is a tool for aligning gene/transcript sequences, or highly-similar DNA sequences, to a genome. May be better than BLAST for genic sequences that require spliced alignments around introns. Alignments will be displayed in the genome browser.
  • BLAST: You can conduct a BLAST search for your sequences (nucleotide or protein query sequence) against the Arachis genomes, coding sequences, or peptides. Hits link to alignments or genes in the genome browsers. This tool is useful if there is a gene (or other sequence) that you know about - perhaps from lab work or from reports from another species - and you want to know where similar sequences exist in the Arachis genomes.
  • Gene & gene family search: Search for genes with gene name (i.e. [Contains]: Aradu.00EZV) and/or gene description (i.e. [Contains any word]: proteasome) and/or Phytozome (link is external) gene families (i.e. [is equal to]: phytozome_10_2.59192412) NOTE: The gene family links will direct you to our sister site LegumeInfo.org.
    • Gene Basket/Bulk download: Click Add to Basket or Add all genes to Basket button. To view genes in the basket, click on Go to basket page. From this page you can bulk download polypeptide or mRNA sequences.
    • Detailed gene family search info: This link will direct you to our sister site LegumeInfo.org.
  • Keyword Search: Search genome browser by entering terms to search for features (gene or marker names, functional descriptions, etc.) on the indicated genome. You will see the results displayed on a karyotype view of chromosomes and in a list report. You can go from there to a detailed view of the features on the genome browser.
  • Map Search: Enter text for the name and/or description for a map and click "Search". Leave both fields empty and click search to see a list of all maps.
  • Marker Search: Enter marker name (can be partial) and click "Search". Columns in the result table can be sorted by clicking on column headers.
  • Protein Domain Search: Search for protein domains by using protein domain ID (i.e. [is equal to]: PF00139) and/or protein domain name (i.e. [Contains]: Zinc finger) and/or Interpro term (i.e. [is equal to]: IPR027278) and/or protein domain description search (i.e. [Contains all words]: disease resistance). You can also search by using the "count" filters to protein domains by size or species composition.
  • Arachis QTL Search: You can search PeanutBase QTL collection by trait class (i.e. yield or root) and/or by QTL symbol used in the experiment and/or by QTL symbol in the publication (i.e. Pod harvest or Seed weight). The narrow search feature (when checked) will only return traits containing the text within the trait text box.
  • Publication search:
    • Search PeanutBase data collections for QTL publications
    • Search recent Arachis publications from Pubmed
• PeanutBase Germplasm Resources:
  • GRIN Connect: Search for germplasm at USDA GRIN (NPGS) database. Use this utility if you want to search the entire USDA GRIN germplasm database from within PeanutBase. You will be able to see and search the GRIN website within a LIS page with a GRIN accession number. You can also check, if it exists, the evaluation data for the germplasm accession from the 'Detailed Accession Observation Page' link in the GRIN webpage.
  • Trait Evaluation Data: Search for germplasm evaluation data. Germplasm evaluation data (for common crop traits or descriptors) for Arachis are available via PeanutBase from GRIN. The evaluation data sets have been downloaded from the GRIN website and are served here by PeanutBase.
  • Geographic distribution of Arachis germplasm: Locate germplasm accession in a map. Arachis germplasm accessions can be located on a map using a Geographical Information System (GIS) utility . You can search the distribution of germplasm accessions in a given geographic area, can map multiple species or restrict it to a single Arachis taxon, look at the accession details and evaluation data if available, and overlay trait evaluation data on the map.
  • Arachis germplasm image collection: Image collection contains ~2000 images from the USDA-ARS germplasm collection in Griffin, GA.
• Community resources and external links: meetings, other peanut or relevant plant research websites, etc. If you are aware of resources that we have missed, please let us know.
• Download: we are maintaining major data sets that you can analyze on your own computing hardware.
• Data submission: there is a spreadsheet form available for describing QTL experiments, maps, and their publication. Data submissions we have received directly from researchers are extremely valuable, since a researcher knows the information intimately and is the expert on their work. If you are working on phenotyping or mapping, please feel free to download the form, and contact us with questions.
• External tools: Some tools at other sites have important capabilities for peanut research. For example, gene family pages at the Legume Information System include Arachis gene models. These families show the genetic relationships to genes from soybean, common bean, and other species for which the functions are known for many genes (e.g. Arabidopsis).

Website Tours:

• Germplasm Map

• QTL search to GBrowse

• More are in the works!

FAQ

GBrowse FAQ | Traits & Maps FAQ

Where can I download Arachis gene sequences?

Gene sequences from the diploid ancestors of peanut, A. ipaensis and A. duranensis, are available on the PeanutBase download page.

The transcriptome assembly for tetraploid peanut, A. hypogaea, from the PeanutBase Gene Expression Resources page.

How can I view my data Gbrowse?

Gbrowse allows you to add your own data as a 'Custom Tracks' in a variety of file formats including SAM or BAM, GFF and GFF3.

Adding Custom Tracks

To upload your data, click on the 'Custom Tracks' tab and click on the link on the bottom for the source of the data you wish to add to Gbrowse. All tracks can be edited in the browser by clicking the '[edit]' link to the right of the file you wish to modify. A text box will appear where you can make changes, then click 'submit' to save your edits.

Uploaded Tracks

Click '[From a file]' to the right of the phrase Add custom tracks:. Click 'Choose File' to browse for the file you want to upload to Gbrowse. Click on 'Upload' to start the upload or 'Remove' to remove the upload box or cancel the upload process. The file will upload to the server and the screen will refresh once the upload is finished. If you want to overwrite the file you already uploaded, check the box beside 'If this file exists, overwrite it'.

Remove Tracks and URLs

Click '[From a URL]' to the right of the phrase Add custom tracks:. Paste the URL into the text box and click 'Import' to start the upload. If you know that the file has changed at the URL, click the '[reload]' link beside the source file and it will be updated.

Create Tracks

Click '[From text]' to the right of the phrase Add custom tracks:. Start typing the track information in the text box that appears, using one of the supported file formats. Once you are done, click 'Upload', Gbrowse will determine which file format you created and upload it.

Can I download track data from Gbrowse?

It is possible to download the track information from Gbrowse. All Gbrowse files available for download on LIS are in GFF3 file format. Recommendation: Do not open a gff3 file using Microsoft word or Microsoft excel. Recommend programs: Windows: Notepad++, Apple: TextWrangler

Information about the Gbrowse track

To view more information about the Gbrowse track and/or download the track information, click on the red question mark shown in the red circle in the figure above.

Download all data from Gbrowse track

After clicking the red question mark associated with the Gbrowse track of interest a box will appear. This box contains information about the track and a link to download the track data. Click on 'Download ALL DATA for this track' to download the data. To close the box click on the 'X' on the top right corner of the box.

Is there citation information about tracks in Gbrowse?

Citation information about the Gbrowse track

To view citation information about the Gbrowse track, click on the red question mark shown in the red circle in the figure above.

After clicking the red question mark associated with the Gbrowse track of interest a box will appear. This box contains information about the track, including the citation information. To close the box click on the 'X' on the top right corner of the box.

Can I find the coordinates of synteny features in Gbrowse, or navigate to the corresponding regions?

Information about how the synteny tracks were calculated

To view information about how the syntey track was calculated and what programs were used, click on the red question mark shown in the red circle in the figure above.

After clicking the red question mark associated with the synteny Gbrowse track of interest an information box will appear. This box contains information about the track, including a link to download the data associated with the track (red arrow) and it shows the methods used to calculate the synteny, and which species genome version was used (green box) . To close the box click on the 'X' on the top right corner of the box.

Coordinates of synteny features

After clicking on the interested synteny feature (example circled in red above) a GBrowse information box will appear. This box will contain the coordinates of the synteny feature chosen, the corresponding target genomic location, and median Ks. The box also contains a link that will direct you to the corresponding target genomic location, shown in the green box in the image above.

More information about the synteny features is available here.

How do I find the promotor for my gene of interest using GBrowse?

View the gene in GBrowse

Using your computer mouse, drag and select the region upstream your gene of interest under the lower GBrowse ruler.

Choose "Dump selection as FASTA" (red arrow). The upstream region can be downloaded for analysis on your local computer.

How do I find the promotor for my gene of interest using the PeanutMine?

Use the search utility at the top left for your gene of interest and the result would have a link in the Details column.

The Details link would take you to a gene page which has a number of details about this gene including JBrowse, Legume Gene Family, GO Annotation, Exon Features and Upstream/Downsteam Intergenic Region.

The 'Upstream Intergenic Region' (red arrow) can be found near the bottom of the page and the FASTA is available for download (red box). Multiple sections within the gene detail page have FASTA available for various features.

How to search the traits/QTLs available on PeanutBase?

You can search the PeanutBase QTL collection by:

• Species/Organism
• Trait Class (i.e. yield or root) See image below
• Trait
• QTL symbol used in the publication
• Trait name used in the publication (i.e. Pod harvest or Seed weight).

All fields are optional and partial names are accepted. See the two images below.



The QTL/trait search has a broad and narrow search approach. The default is a the board approach. The broad approach uses relationships between trait terms to return the all traits that might relate to the requested search term.

By checking the box next to "Use narrow search", a fewer number of QTLs may be returned because only those traits that contain text in the "Trait" text box will be returned. In the example shown below, narrow search has been selected and the word 'pod' is entered into the Trait text box. All trait class and QTL name that are returned contained the word 'pod'.

How to browse the traits/QTLs available on PeanutBase?

Browse traits available

There are multiple columns to browse within the Traits feature. Each of these columns can be re-organized in alphabetical order or descending alphabetical order. To re-organize a column place your mouse over the column title and the column title will become underlined. The red box around the underlined words "Trait Class" indicates that the mouse curser is over these words and by right clicking the table will reappear with "Trait Class" column in alphabetical order. This is shown in the image below.

The small arrow next the column title "QTL Symbol in Publication" (in small red square) in the image above indicates that the column is organized in descending alphabetical order. In contrast in the image below the small arrow next the column title "Trait Class" indicates that the column is organized in alphabetical order.

About The PeanutBase Project

This web portal is designed to provide convenient access to peanut genetic and genomic data deriving from U.S. and international research, and particularly from the Peanut Genomics Initiative: The U.S. industry has embarked on an ambitious plan to map the peanut genome over the next six years to provide our breeders with gene markers for positive traits already found in peanuts to accelerate traditional cross breeding to bring more sustainable and productive peanut seed varieties to the farmer sooner. This non-GMO approach to improving peanuts will provide benefits to farmers and consumers alike by the development of peanuts les susceptible to plant diseases and drought stress. Moreover, this technology will allow for peanuts with enhanced vitamins and minerals --- all naturally found in current peanut plants. This genomics effort (and this website) have been made possible by many industry supporters. This web site is being built by the USDA-ARS SoyBase and Crop Legume Database group in Ames, IA, with assistance from many researchers, and by the LIS team at NCGR.

Contact Us

If you have any questions about how to use features at PeanutBase, or if you have requests for new features, or have data or information that you would be willing to contribute, please contact us! Thanks! We would like your help to make the site as useful as possible.