Difference between revisions of "MaizeGDB and CoGe"

Latest revision as of 18:35, 11 February 2010

Overview

MaizeGDB's genome bowers can now to used to quickly view the same region in CoGe. A link to CoGe is shown at the top of the browser when viewing a genomic region from the maize genome assembly (i.e. pseudomolecules) called "View This Region in CoGe. This link will take you to the same region in CoGe's GenomeView (in a new window so you won't lose your region at MaizeGDB). When accessed from MaizeGDB GenomeView will, by default, display the working gene set models from MaizeSequence.org release 4a.53 on B73 version 1 reference sequence. GenomeView will also display special icons to draw your attention to maize genes that have been identified as having a sorghum ortholog. Clicking on either these icons (currently a series of overlapping blue ovals) or the gene models themselves will display detailed information on the gene including the name of its sorghum ortholog and whether we've identified another maize gene as a retained homeolog from the maize whole genome duplication. The annotation window also has a link to automatically compare the orthologous genes and the syntenic regions surrounding them in another CoGe tool called GEvo.

MaizeGDB's genome browser link to CoGe's genome broswer, GenomeView

Screen-shot of MaizeGDB with link to CoGe. View can be regenerated at: http://gbrowse.maizegdb.org/cgi-bin/gbrowse/maize/?name=chr1:1000000..1200000

MaizeGDB is one of the leading web resources for maize genomic information and provides tools for finding genes, loci, and genomic regions of interest to scientists. Individual genes have specific web-pages for displaying their annotations and associated information, including links to their genome browser for visualizing genomic regions. Their browser is powered by GBrowse of the GMOD project. To facilitate sending information from MaizeGDB to other genomic resources, there are links at the top of MaizeGDB's genome browser. One of these is a link to CoGe's genome browser, GenomeView, and is labeled "See this region at CoGe". If you click this link, GenomeView will open in a new window displaying the same genomic region.

GenomeView showing icons marking genes with identified sorghum orthologs

Screen-shot of GenomeView showing GEvo link glyphs. View can be regenerated at: http://synteny.cnr.berkeley.edu/CoGe/GenomeView.pl?z=5&x=1100000&dsgid=8054&chr=1&sl=1

GenomeView can display a variety of genomic information. With the current default settings, show above, the background is colored green in GC rich regions and white for AT rich regions. The dashed line in the middle separates the top and bottoms strands of the DNA sequence being displayed. Gene models and other sequence features on the forward stand are drawn above the line and while gene models on the reserve strand are drawn facing the opposite direction below the line. For information about gene models and various visualizations available GenomeView, please see this page. Genes with annotations that link to GEvo are marked with special icons, currently a series of overlapping blue ovals. The current annotation information for any gene can be accessed by simply clicking on the gene model which with bring up the dialog box with annotation information and, in the case of genes marked as having sorghum orthologs, a GEvo link to compare the genes and their surrounding regions.

Getting a link to GEvo

GenomeView with annotation dialog box shown for a GEvo link glyph. View can be regenerated at: http://synteny.cnr.berkeley.edu/CoGe/GenomeView.pl?z=5&x=1100000&dsgid=8054&chr=1&sl=1

The dialog box for genes annotated has having a sorghum ortholog have a line called "GEvo link" that also lists the name of the sorghum ortholog and, when we find one, the maize homeolog generated by the maize whole genome duplication. Just click on the link to launch GEvo which will automatically compare these genes and their surroundings.

Automatically running GEvo with syntenic maize-sorghum regions pre-loaded

GEvo running a maize-sorghum syntenic analysis automatically. Genomic regions (400kb) have been preloaded in the sequence submission boxes. Analysis can be run at: http://tinyurl.com/yhgnu8a

When GEvo is launched using the custom links now included in maize and sorghum gene annotations, it will default to comparing 400 kb regions centered on the orthologous genes and masking all noncoding sequences. Non-coding sequences are masked by default to avoid problems with all the transposons in the maize genome. You can turn the masking off, but running GEvo will take much longer and noise from transposons will make results harder to interpret. If you do need to look at non-coding sequences, the best solution is to use the masked sequence to narrow down the region you wish to compare, and then run GEvo again on that smaller region without any masking. GEvo also defaults to comparing sequences using the blastz which is good at identifying large regions of similar sequence, as are usually found between maize and sorghum. If blastz is not suited to your particular analysis GEvo can use a number of other alignment tools, including lagan, a global alignment tool, and blastn, which takes longer to run than blastz but will identify small regions of similar sequence.

• More information on the different alignment algorithms that can be used by GEvo.
• More information on how to link to GEvo and set various parameters from the URL.

GEvo's results

GEvo results from a maize-sorghum sytnenic analysis. Lines have been drawn connecting regions of sequence similarity showing ~5 collinear pairs of genes. This is evidence that the regions are syntenic. Results can be regenerated at: http://tinyurl.com/yhgnu8a

When GEvo finishes running, you will be presented with panel for each of the genomic regions that have been compared. These images can be interpreted similarly to GenomeView, however in the default analysis you will notice that the background has a lot of purple. Purple marks the areas of the sequence masked from the analysis (in this case, everything that isn't a coding sequence). The heart of the GEvo analysis is represented by the colored blocks located above and below the gene models. These colored blocks mark sequences that have been identified as similar to a sequence in one of the other regions being compared. Clicking on these blocks will bring up a window describing the details of the hit and draw a transparent wedge to the location of the similar sequence (also marked with a colored box). By clicking on many of these (or holding the 'shift' key then click on one to connect all of the hits between two compared regions), various patterns of genome evolution can be observed.

• This page has more information on GEvo's interactive results viewer.

More help and examples

If you are interested in:

• Whole genome comparisons of maize and sorghum
• Identifying syntenic regions
• Differentiating syntenic regions derived from the:
  • maize-specific whole genome duplication event
  • the divergence of the maize and sorghum lineages
  • the pre-grass whole genome duplication event
• Identifying patterns of genome fractionation
• Identifying conserved non-coding sequences

Please see this page.

Thanks

Thanks to:

• James Schnable in Michael Freeling's lab at UC Berkeley for generating maize-sorghum syntenic gene sets.
• Taner Sen at the USDA-ARS, Iowa State University for linking MaizeGDB to CoGe and other MaizeGDB specific activities.
• Michael Freeling at UC Berkeley
• Carolyn Lawrence at USAD-ARS and Iowa State Univerity