Homologues and gene trees for the Triticum aestivum (wheat) RHT1 gene

Go to Ensembl Plants and answer the following questions:

How many orthologues are predicted for the Triticum aestivum (wheat) gene RHT1 (gene ID TraesCS4D02G040400) gene in Liliopsida?
How much sequence identity does the Secale cereale (rye) protein have to the maize one?
Download the alignment in Nexus format.
Open the gene tree for the wheat RHT1 gene. What is the gene tree ID?
How many speciation and duplication nodes does the phylogeny have?

Go to the Ensembl Plants homepage, select Triticum aestivum from the Species drop-down and search for TraesCS4D02G040400. Click through to the Gene tab. On the Gene tab, click on Plant Compara: Orthologues at the left-hand side of the page to see all the orthologous genes.

These are the orthologues in the Liliopsida:
- 24 1-to-1
- 9 1-to-many
- 0 many-to-many
Filter the table by entering Secale cereale in the filter box on the top right-hand corner of the table.

The percentage of identical amino acids in the rye protein (the orthologue) compared with the gene of interest (i.e. wheat RHT1; the target species/gene) is 98.71%. This is known as the Target %ID. The identity of the gene of interest (wheat RHT1) when compared with the orthologue (the rye gene, i.e. the query species/gene) is 97.91% (the query %ID).
Note the differences in the values of the Target and Query % ID reflects the different protein lengths for the genes.
Click on View Sequence Alignments in the Orthologue column. Select View Protein Alignment from the pop-up menu. Click on the green Download homology button above the table and select Nexus. Click on Download or Download Compressed to save the alignment on your local machine.
Go to Plant Compara: Gene tree in the left-hand menu. You can find the gene tree ID above the phylogeny.

The gene tree ID is EPlGT00940000163877.
You can find some summary statistics below the gene ID.

There are 418 speciation nodes and 149 duplication nodes.