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Finding orthologous genes for a root transporter in rice

Search Ensembl Plants for the gene LOW SILICON RICE 1 (Lsi1) in Rice (Oryza sativa Japonica). This gene is known to code for an aquaporin transporter that facilitates the uptake of silicon and arsenic through the roots. Silicon concentration is highest in grass species, and is associated with defence.

(a) From the gene tab, click on the Plant Compara > Orthologues page. Which plant group has the highest number of 1-to-1 orthologues? Is it the same group that has the highest number of 1-to-many orthologues?

(b) Reduce the orthologues table to look only at wheat (Triticum aestivum) orthologues. Why are there three results for a 1-to-1 orthologue?

(c) Click on the Compare regions link for chromosome 6B region in wheat to go to the Location tab, Region comparison page.

Scroll to the bottom image. How do the gene models compare between the species? Do they have the same number of exons?

(d) Click back to the Gene tab and click on the Gene gain/loss tree page. Which species has the highest number of members of this gene family? Is it a grass? Can you change the view to see a radial tree?

Go to plants.ensembl.org. Look for the main search box highlighted in green. Select Oryza sativa Japonica Group from the drop down box and type in LOW SILICON RICE 1. Click Go and click the first link to go to the gene page.

(a) Find and click the link for the Plant compara > Orthologues page.

The Liliopsida group has 24 1-to-1 orthologues, the only group with 1-to-1 orthologues. This group is synonymous with monocotyledon, so the group that contains the grasses. The Eudicotyledons has the highest number of 1-to-many orthologues, indicating that this gene has been duplicated in the eudicots.

(b) Use the search box at the top right of the Selected orthologues table and start to type in Triticum aestivum, the table should automatically filter.

There are three results, one for each component (A,B,D). Note that these are considered 1-to-1 orthologues, rather than 1-to-many. This is because these genes arose in wheat by hybridisation (allopolyploidy), rather than duplication (autopolyploidy).

(c) Click on Compare regions (found in the 3rd column below the gene identifier) from the 2nd result for component 6B. This takes us to the Location tab. Scroll down to the bottom of the page.

Both genes have five exons and the same structure. This looks unusual because the gene in rice is on the forward strand, while the gene in wheat is on the reverse strand. This is reflected in the crossing green links between the pink alignment blocks.

(d) Click on the Gene: LOW SILICON RICE 1 tab at the top of the page and click on the Gene gain/loss tree link.

Significant expansions are shown with red branches, and the number of genes in the family shown in the count next to the image and species name. We can see that Brassica napus has 22 members in this group.

We can change the tree to radial view by clicking on the icon with two arrows at the top left of the image.