Plukenetia volubilis attacks again: Allopolyploid or Autopolyploid? about smudgeplot HOT 3 CLOSED

Thank you so much for using our tools and taking a look at our preprint!

To answer your question, the results from genomescope 2.0 for aaab and aabb are nucleotide level values while the results for AAAB and AABB from smudgeplots are k-mer level values. More specifically, the value of 12.6% for your data for aabb means that 12.6% of the nucleotides across the monoploid genome are of the form aabb. The value of 70% for AABB means that 70% of the k-mer sibling pairs are of the form AABB. So, the higher value of AABB makes sense because we are taking a proportion only of k-mer sibling pairs (one SNP different), not of all k-mer pairs.

In terms of allotetraploid versus autotetraploid, it seems quite clear from both genomescope and smudgeplot that your sample is allotetraploid. I believe you can also infer allo vs auto using smudgeplots with a high proportion of AAAB giving evidence for autotetraploid and a high proportion of AABB giving evidence for allotetraploid.

Finally, the reason the website with the results doesn't load is because we forgot to update the link for the results for the new 2.0 version of the website. To see your results, please go to genomescope.org/genomescope2.0/analysis.php?code=XU4ieWwELZjptFnWUpUe. Thanks for pointing this out and we will fix it shortly.

from smudgeplot.

Thanks for your thoughts and quick reply Timothy, all this analysis will definitively improve the development of our projects.

I wish you the very best!

from smudgeplot.

Dear @tbenavi1, I would like to ask you a fast question regarding genomescope2. I was not sure where to put it, because the genomecscope2, and didn't seem appropiate in the original genomescope repo.

Anyway, what does exactly the "dup" estimate mean? I did not find any explicit mention to it in the preprint (I apologize if I missed it). I did notice that it has a broad range along the genomes you evaluated: from less than 1 to ~6.

In the case of Plukenetia volubilis this value is 3.5. Does this say something about the genome?

Thanks in advance.

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