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.
1. Go to the Synteny Dot Plot by Tools -> Synteny dotplot on the omabrowser or by clicking here. The Synteny Dot Plot displays the pairwise orthologs (or homoeologs) between two chromosomes. Select the cat (genome 1) and dog (genome 2) to compare.
2. Which pair of chromosomes between cat and dog have the highest number of orthologs between them, and how many?
Select the chromosomes with the highest number of orthologs and click Launch Dotpot. Note that the synteny dot plot does not necessarily show the chromosome in its entirety. What is the general level of synteny conservation for the segments displayed for these two pairs of chromosomes?
Zoom in on the region of the chromosome with an abnormality: ~10.5-10.9 on FELCA A2 and ~47.2 - 47.7 on CANLF 20. It should look like a little nodule along the diagonal. What do you observe in this region in terms of chromosomal events?
Select the top “row” of duplicated genes using the Select tool, as indicated below:
TODO: add synteny_select_orthologs.png
How can you interpret the relationship between these genes?
Where are the physical locations of the duplicated cat genes from the previous question? (i.e. the locus coordinates along the chromosome)
Additionally, we can see that FELCA01637 has several orthologs in dog, thus meaning there have also been lineage-specific duplications in dog. What are the functions of these genes? Use the OMA browser to find the functions of these genes.
Let’s look at another pair of chromosomes. Go back to the Synteny Dot Plot home page and display cat chromosome E2 versus dog chromosome 1. What kinds of structural rearrangements do you observe?
TODO: insert synteny_rearrangements.png
Notice the region of the chromosomes which nonsyntenic genes (see answer to previous question). What can you say about these four pairs of orthologs, in terms of rate of evolution and duplication?
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
What are the first two most closely related species in OMA to the dog?
In the red fox (Vulpes vulpes) how many orthologs do we find to the gene CANLF07749 and how would you describe the relationship cardinality of these orthologs?
How much of local synteny around the CANLF07749 genes is conserved between the red fox and the dog? How many orthologous genes from this genomic fragment are co-localized in the two genomes? What evolutionary events can you infer happened in this area?
How many ferret genes are orthologous to CANFL07749?
What can we infer about the genomic location of the ferret genes orthologous to CANLF07749?
What can we infer about the genome assembly of the ferret?
Look at the phylogenetic relationship between the 3 species:
TODO: insert synteny_tree.png
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.