Community Outreach Workshop
A physical map and sample sequencing of the homoeologous
group-3 chromosomes of wheat
Funding: USDA-NRI
Project Director:
Bikram S. Gill, Kansas State University, USA
Co-Project Directors:
Katrien M. Devos, University of Georgia, USA
Justin D. Faris, USDA–ARS, USA
Piotr Gornicki, University of Chicago, USA
Wanlong Li, Kansas State University
Ming-Cheng Luo, University of California Davis, USA
Pablo Rabinowicz, Institute for Genome Sciences, U. of Maryland, USA
Agnes Chan, J. Craig Venter Institute, USA
Collaborators:
Rudi Appels, Murdoch University, Australia
Jaroslav Dolezel, Institute of Botany, Czech Republic
Jan Dvorak, University of California, USA
Catherine Feuillet, INRA-UBP, Clermont-Ferrand, France
C. Robin Buell, Michigan State University, USA
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IGS / JCVI Wheat Genome Annotation And Web Tools
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The project tools described in this tutorial are found under the URL http://wheat.tigr.org
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The website contains data generated by this project as well as other wheat genomics data
downloaded from GenBank
One of the tools available in the website is a BLAST server. The link to the BLAST
server as well as other tools can be found in the links on the left side of the page
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Different BLAST programs can be used to search any nucleotide or amino acid sequecne
against several wheat sequence databases
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Other types of searching tools are found in the links to the left of the page to, for
example, text-search the wheat gene annotation using key words.
Any word can be typed in the text box
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All the annotations that contain that key word will be listed.
Each entry has links to GenBank (right column) and to the genome browser (left column)
as we will see later.
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The genome annotation can be browsed using the Generic Genome Browser implemented
for this project. The link to the genome browser is at the top and under the “Annotation”
link on the left of the page
In the “Landmark or Region” box, a BAC clone name or selected sequence coordinates
result in the display of the annotation of the selected BAC or region.
At the bottom of the page multiple layers (tracks) of annotation can be selected for
display.
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Doing a mouse-over of the gene model shows annotation information
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Clicking on the “Locus” leads to the Manatee annotation page
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The genomic, coding and protein sequence can be displayed using the “Download
sequence” function in the Manatee page.
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The “wheat BAC” in the genome browser links to the corresponding GenBank entry
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The navigation bar at the top allows to zoom in and out, browse the adjacent sequence,
and clicking in the coordinates of the “overview” box centers the sequence in the region
chosen.
After zooming in, more detailed annotation is shown
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Clicking in the different gene predictions, the sequence and intron/exon structure
predicted by each gene finder is shown
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The “Landmark or Region” search box can also be used for a keyword search.
Clicking each gene model displays it in the genome browser context
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The community can request the team to perform automatic annotation of BAC sequences
generated by users. There is a link on the left of the page that brings up a BAC sequence
upload form.
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The team can be contacted using a web-based email page or sending an email directly to
wheat@jcvi.org
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