Low number of collinear genes

[DustinSokolowski]

Hey!

Thank you for the excellent tool. I am attempting to identify syntenic blocks and tandem duplications between the mouse (mm10) and naked mole-rat genome that I assembled and I am finding some surprisingly low collinearity.

When using the parameters on the github page, I found 26.8% gene collinearity, which I thought was fairly low.

Here are a handful of chromosomes (with X as a highly syntenic reference)

I was hoping to look at a linear plot (or dot plot) of some tandem duplicated genes, but a lot of the genes didn't exist.

One is a cytochrome P450 gene(s), which in the blastp file has a very strong set of very consistent hits (all other CYP genes), see below. Strangely, these hits did not make it into the collinearity file.

My initial guess was that the BLAST hits were other CYP genes on other chromosomes and therefore couldn't chain the regions together, so I allowed for up to 15 hits in blastp. Once completed, I ended up with a slightly lower collinearity overall, which I'm not sure how to interpret.

Have you come across this type of issue before and do you have any suggestions?

Best, Dustin