Subgenomes separation in hybrid species

Question

[Matteo Schiavinato]

I am currently starting an analysis which is aimed at separating the two subgenomes in the genome of a hybrid species, i.e. originating from the hybridization of the genomes of two parental species, with subsequent genome downsizing / gene loss.

I have read some literature (few, so far) and I'll be on it for the whole week, but does anybody here have any experience in this field and analyses? Can anybody recommend me tools, papers, pipelines or approaches that have worked / are accepted? I have many ideas and the literature I find is scarce.

Among the ones I read, this is so far the most interesting: https://doi.org/10.1371/journal.pone.0036442

The resources I have are only DNA and RNA sequencing reads (Illumina paired-end).

Thanks!