Test for recombination in a clonal tetraploid?

[AdrianP]

I have been searching this subject and trying to find a technique that fits my needs and so far I have been having no success.

I am looking to test try and find crossover events in my HiSeq datasets. I have 9 strains of the same non-model clonal species that are very similar to each other in that sense that a lot of genomic variation due to ploidy is shared. I am now interested if despite clonal propagation, there is still recombination occurring.

All I have is 9 HiSeq 100bp x 2 PE reads with a fragment size of ~300bp for my 9 strains.

Any recommendations?

[SNPsaurus]

It doesn't sound as though you have a dataset that would give you an answer if I understand the situation properly. You want to find haplotypes that bridge a recombination breakpoint, so you need to find an allele from parental chromosome 'M' with one read and an allele from parental chromosome 'P' with the paired read. You could write a script to sort through and try to find examples of this.

If the polymorphism rate is high, then you have a better chance of finding SNPs in both reads. Then, what is the chance of the PE fragment covering the recombination event? Are you hoping that you will see the event in 1 strain compared to the others, or events within a strain? If within, then you need very high coverage to see it and it would be hard to not ascribe the allele change to a sequencing error.

[AdrianP]

I am more interested in events between strains. The data shows the organism is clonal, so the strain can be treated as an individual, most variation is due to ploidy. My coverages range from 120x to 17x. I can certainly use the top coverage strains as a start.

Any ideas?

[SNPsaurus]

Are you asking about available tools? I don't think there are any to do exactly that. If you wanted to do it yourself, you'd want to take every region and inspect the reads aligning to it to develop 4 haplotypes as a reference, then see if the haplotypes differ between strains. There are some haplotype/phasing prediction programs out there, but I'm not familiar with them enough to know if they are good enough to help.

One other issue I forgot to mention--I think many recombination hotspots are in repeat DNA, so you may not have a PE read that spans the breakpoint.