Interprteting the phylogenomic profiles plot
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Alexandros • 0
@cc06bc01
Last seen 6 days ago
Belgium

Hello,

I am trying to interpret the figure that is plotted by syntenet (https://github.com/almeidasilvaf/syntenet) that visualizes the phylogenomic profiles for the different species and groups; What exactly are the different colors corresponding to increasing numbers (e.g. red color -> +3)? In addition what does the clustering tree on top of the figure represent? Are these groups of clusters that are shared in different species? Some more infor in the documentation would help.

Best Alex

syntenet synteny Network • 163 views
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@fabricio_almeidasilva-14890
Last seen 3 hours ago
Ghent, Belgium

Hi, Alexandros,

The heatmap is based on a matrix mij that displays the number of genes in synteny cluster j that can be found in species i. That's what colors represent. Thus, if a synteny cluster (column) is red for a particular species (row), it means that this species contains 3 or more genes in this synteny cluster.

The clustering on the columns is a simple hierarchical clustering (Ward's clustering on a matrix of Euclidean distances) to group similar synteny clusters together.

You might want to read the manuscript describing syntenet (https://www.biorxiv.org/content/10.1101/2022.08.16.504079v2) and previous papers on synteny networks (for instance, see figure 5 of https://www.pnas.org/doi/full/10.1073/pnas.1801757116, and https://www.nature.com/articles/s41467-021-23665-0).

Best, Fabricio

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Thanks Fabricio,

It is then somewhat strange that my heatmap includes a lot of light blue areas (also in the vignette example) which according to your description include only 1 gene per synteny cluster for this specific species. How can a region be part of a synteny cluster based on only one gene? Or maybe I did not fully understand your description..

Best Alex

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Hi, Alex

I believe you have not fully understood the concept of synteny clusters. I think Figure 1 of https://www.nature.com/articles/s41467-021-23665-0 will be helpful.

Best, Fabricio

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Hi Fabricio,

Many thanks I think I got this now. Initially I thought that a cluster includes all the genes of a single synteny block across the analyzed genomes but as far as I understand it now each cluster is composed of separate gene anchor pairs of the defined blocks extended over several genomes. Am I correct?

What does it mean then if you have more than 1 gene per cluster? Could it be whole genome duplication or even uncollapsed haplotypes in the genome assembly? If tandem arrays are collapsed and are not part of the individual clusters I assume they cannot account for the pattern of multiple genes per cluster.

Thanks Alex

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Hi, Alex.

Your interpretation is correct. Multiple genes per cluster typically indicate polyploidization events (whole-genome duplication, triplication, etc.), but uncollapsed haplotypes are also a reasonable explanation.

As an example, in Figure 1B of the syntenet manuscript (https://www.biorxiv.org/content/10.1101/2022.08.16.504079v2), you can see some species with orange (2) and red (3+) for most of the synteny clusters, which is explained by the fact that these species are recent polyploids.

Best, Fabricio

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@f1c1bda2
Last seen 4 days ago
Vietnam

I would admit that the trimodality of the density plot of those data makes them appear strange, but I have not had much experience with Nimblegen data, so perhaps this is to be anticipated. gartic phone

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