Example expression analysis

Analysing gene expression data for a gene or gene family of interest can be daunting, when using tools like the Lettuce Expression Browser (LEB). This guide walks you through a practical example, illustrating general steps that you can apply to any gene of interest.

Background

DRO1 (also known as LZY3) is a gene in A. thaliana that is known to be involved in the gravitropic growth of the plant. It is expressed in the root meristem, inflorenscence stems and in the hypocotyl (Taniguchi et al, 2017). Our goal is to investigate whether a lettuce homologue of DRO1 shows a similar expression pattern, which could suggest a conserved function.

Step 1: Retrieve a recognised gene identifier

Gene names like DRO1 are not always recognised as unique identifiers. In A. thaliana, standardised gene identifiers follow the format ATXGXXXXX. Searching for 'DRO1' on the TAIR website reveals its commonly recognised gene identifier: AT1G72490.

Step 2: Identify lettuce homologues

To find the homologue(s) in lettuce:

1. Visit the Gene Information page.
2. Select "Gene" from the dropdown menu.
3. Choose "Arabidopsis thaliana" as species.
4. Paste the gene identifier AT1G72490 into the search field and hit "Search".

The resulting table provides information about the DRO1 gene, including its homology group. Interestingly, this homology group contains two A. thaliana genes (DRO1 and DRO3), both with similar functions and expression patterns (Taniguchi et al, 2017). In the Lactuca genus, L. saligna has one homologue whereas L. virosa and L. sativa both have two homologues.

Step 3: Explore expression patterns in lettuce

Clicking on a lettuce homologue will open a new Gene Information page specific to that gene. Each page contains an Expression section. To view tissue-specific expression patterns: click the "Seedling tissue map" link for the desired homologue. A new tab will open, showing tissue-specific expression data in lettuce seedlings.

Step 4: Interpret the expression data

In A. thaliana, both homologues (DRO1 and DRO3) are expressed in root and shoot. In Lactuca species, the expression patterns of the homologues suggest divergence in expression patterns:

• In L. sativa, L. serriola and L. virosa, two homologues are present:
• One shows root-specific expression, mainly in the root tip.
• The other is expressed in both the root tip and the hypocotyl.
• In L. sativa (cv Salinas and Cobham Green), this homologue shows higher expression in the hypocotyl than in the root tip.
• In L. serriola and L. virosa, expression levels are comparable between the two tissues.
• L. saligna differs in having only one DRO1/3 homologue, which is expressed in both the root tip and the hypocotyl.

These patterns suggest that in L. sativa, L. serriola and L. virosa, the two homologues may have undergone expression divergence, possibly reflecting subfunctionalisation. In L. saligna, the absence of the root-specific homologue implies that this species may have lost one of the two ancestral copies (likely the root-specific one), retaining only the homologue with broader expression. Alternatively, it remains possible that the location of this lost copy in the genome assembly of L. saligna was not assembled well and therefore we cannot identify the gene.

Step 5: Explore other gene family members

You can also identify additional related genes by examining conserved protein domains. Both DRO1 and DRO3 are annotated with the "LAZY family" domain (as defined by InterPro). To explore this:

• Go to the Gene Information page of a DRO1/3 homologue.
• Locate the InterPro domain annotation.
• Click "See genes" to view all lettuce genes that are predicted to contain this domain.

This reveals another related gene: DRO2, which is also part of the LAZY family. In A. thaliana, DRO2(/LZY4) is expressed in root tissues (Yoshihara et al, 2017). In lettuce:

• DRO2 is a single-copy gene.
• It is root-expressed in all examined species:
• In L. sativa, L. serriola, L. saligna and L. virosa, expression is consistently found in root tissue.

This suggests a conserved root-associated role for DRO2 across both Arabidopsis and Lactuca species.