Contribution of gene gain vs gene loss?

[guillemmasfiol]

Hi Gerry,

thank you for this very useful tool that accounts for the different confounding factors and errors when dealing with the comparison of gene sets between species and lineages.
I understand that the main interest of PanStripe is to model and compare the gene flow between bacterial groups to better understand their evolution and diversification. In the model, gene flow accounts both for the theoretical acquisition of genes but also for their loss, giving the predicted rates of gene exchange.

My question is if PanStripe can help telling whether a species or lineage is significantly acquiring or rather losing more genes, on the overall dynamics. Could it be used to discriminate if a lineage is gaining more genes compared to another, or if it’s rather losing more genes compared to another? Similar to this, if a population may be losing more genes, will it be simple detected as a population showing reduced gene gain/loss rates in the model?

Many thanks!
Guillem

[gtonkinhill]

Hi Guillem,

Sorry for the slow response, I've just got back from holiday.

At the moment panstripe considers the overall rate of gene gain and loss. However, it should be possible to consider either gene gain or gene loss events separately. This would require modifying lines 72-93 of the main panstripe function.

I won't have a chance to add this functionality for a while, so will leave this as a feature request for now.

As an alternative in the meantime, you could look at the inferred rates (ignoring errors) by using the model of Zamani-Dahaj et al. We have implemented this in the Panaroo function panaroo-fmg.

[guillemmasfiol]

thank you for your kind reply, I will take a look at the FMG model you implemented in Panaroo ;)