When comparing two related species, the position of orthologous genes is often conserved. Positional conservation can be at the chromosomal level—e.g. when there are entire chromosomes or chromosomal segments that are orthologous between species; or it can be more local—e.g. neighboring genes in one genome are orthologous to neighboring genes in the other genome. Additionally, synteny between orthologs in extant genomes can be used to infer the ancestral gene order.
In OMA, we have several tools to help visualize and analyze synteny at different levels of resolution. The Synteny Dot Plot can be used to compare chromosomes (global synteny). The Local Synteny Viewer can be used to compare genes in a local gene neighborhood (microsynteny). Finally, the Ancestral Synteny View of Hierarchical Orthologous Groups can be used to deduce the likely order of ancestral genes at any taxonomic level. In this module, we will focus on using these three synteny viewers: how to use them and what types of useful biological information we can obtain from them.TODO: Where to find documentation For more information on OMA standalone, please see this blog post and the extensive documentation available here.
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How can you interpret the relationship between these genes?
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Let’s focus on the gene CANLF07749 in a dog and inspect its local synteny and the gene order conservation of its orthologous genes in other species. To go to the gene page you can either follow the instructions from question 4 in the “Synteny dot plot” section and click on CANFL07749 gene ID in the table below the dotplot. You can also select Explore->Local synteny on top of the OMA webpage and find the gene by inputting the ID into the search box. Your query gene will be in the center of the first row.
To understand the local synteny viewer, check out the documentation: Local Synteny Viewer
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Seeing the relationship between species, what would you infer about the evolutionary history of the olfactory genes CANFL007748 and CANFL007749 and their orthologs in the red fox and the ferret?
Consider the type of orthology between the genes (the colours of the boxes), the location of the genes and the number of genes in each of these 3 genomes.