(a) In the Location tab of the FUM1 gene, configure the page to turn on the BLASTz/LASTz alignments (which will look like a pink block once it’s on in the Location tab).

The degree of conservation between Arabidopsis thaliana and A. lyrata is much higher than between A. thaliana and maize in the region of the FUM1 gene, which reflects the evolutionary relationships of these three species. Note there are no gaps in the alignment between the species of Arabidopsis. You may want to click on the pink block and select Alignments (text).

Alternatively, click on Alignments (text) in the left hand side menu in the Location tab.

(b) Zoom out until you get a ~30 kb window of this region to see that the regions where the alignments are the most conserved are where the genes have been annotated.

This is in accordance with our expectation: sequence of genes tend to be more conserved when comparing more distantly related genomes as they are likely to be under higher selection pressure than intergenic regions.

(c) Click on the Region Comparison link on the left hand side menu in the Location tab and add Arabidopsis lyrata, Brassica rapa and Sorghum bicolor by clicking on Select species or regions. Configure the page and under Comparative features turn on the Join genes option.

(d) The synteny view between chromosome 2 (where the FUM1 gene is) in A. thaliana shows synteny with chromosomes 3, 4 and 5 in A. lyrata.