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Whole genome alignments

(a) Find the HORVU5Hr1G033980 gene for barley and go to the Region in detail page.

(b) Turn on the LASTZ-net alignment tracks for Aegilops tauschii, Brachypodium distachyon, Oryza sativa Japonica and Triticum turgidum. Are there any regions where you can see gaps in in some of the species alignments?

(c) Go to the Region comparison view and compare to Brachypodium distachyon. What occurs at this gap in the alignment?

(d) Is there evidence of any duplicated regions in Brachypodium distachyon compared to barley?

(a) Go to the Ensembl homepage (http://www.ensembl.org/). Select Search: Hordeum vulgare and type HORVU5Hr1G033980 in the search box. Click Go. Click on chr5H:229682099-229689352.

You may want to turn off all tracks that you added to the display in the previous exercises as follows: Click Configure this page in the side menu. Click Reset configuration green button. SAVE and close.

(b) Click Configure this page in the side menu

Click on Comparative genomics in the menu on the left. Select Aegilops tauschii - LASTz net, Brachypodium distachyon - LASTz net, Oryza sativa Japonica - LASTz net and Triticum turgidum - LASTz net. SAVE and close.

There is alignment across most of the region, with some gaps occurring in all four species.

(c) Click on Region comparison in the left-hand menu. Go to the Select species or regions button and add Brachypodium distachyon. Save and close the menu.

The gap in the alignment in barley translates to an even larger gap in Brachypodium distachyon.

(d) On the right-hand side of the alignment there is a region with three pink bars in Hordeum vulgare, indicating that this region maps to three different locations in Brachypodium distachyon, which might indicate a duplication event. This region is around chr5H:229686000-229688000.

To confirm this, go to the Alignments (text) view and select Brachypodium distachyon again.

The blocks show that the region around chr5H:229686000-229688000 matches to neighbouring regions in Brachypodium distachyon, suggesting a duplication.