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Exploring whole-genome alignments for Triticum aestivum (wheat)

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Exploring whole-genome alignments for Triticum aestivum (wheat)

Go to Ensembl Plants and answer the following questions:

  1. Find the TraesCS2D02G080000 gene in Triticum aestivum (wheat). What is the function for this gene and what are its coordinates?

  2. Go to the Location tab. Turn on the LASTZ-net alignment tracks for Arabidopsis thaliana, Zea mays (corn) and Sorghum bicolor (great millet). Are there any regions where you can see gaps in in some of the species alignments?

  3. Go to the Region comparison view and compare to A. thaliana. What occurs at this gap in the alignment?

  4. Export the Block 2 alignment between T. aestivum and A. thaliana in ClustalW format.

  1. Go to the Ensembl Plants homepage. Select Triticum aestivum from the Species drop-down, enter TraesCS2D02G080000 in the search box and click Go. Open the Gene tab.

    The gene description is as follows: Ascorbate peroxidase, ROS homeostasis, Chloroplast protection, Carbohydrate metabolism, Plant architecture, Fertility maintenance. This was projected from Oryza sativa (Os07g0694700).

  2. Go the Location tab in the top left-hand corner. Click on CConfigure this page in the side menu. Open Comparative genomics: BLASTz/LASTz alignments in the pop-up menu. Turn on the tracks for Arabidopsis thaliana, Zea mays (corn) and Sorghum bicolor (great millet) in the Normal style. Save and close the pop-up menu

    There is alignment across most of the coding regions, with some gaps occurring in all 3 species. These gaps map with the intronic regions of the T. aestivum gene.

  3. Click on Comparative Genomics: Region Comparison in the left-hand menu. Go to the Select species or regions button and add A. thaliana. Save and close the menu.

    The gap in the alignment translates to the intronic regions of the T. aestivum gene.

  4. Go to Comparative Genomics: Alignments (text) and select A. thaliana from the Alignment drop-down. Click on the green Download alignment button and select ClustalW. Download the file to your local machine either in a compressed format, or as it is by clicking the green Download button above the file format preview.