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KamilSJaron / smudgeplot

Inference of ploidy and heterozygosity structure using whole genome sequencing data
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Interpreting a possible haploid #147

Closed jacquelinemattos closed 4 months ago

jacquelinemattos commented 4 months ago

Hi, I'm having trouble understanding my smudgeplot. We have some reasons to believe that our species' genome should be a haploid, but based on what you replied on another thread regarding the 1n coverage peak, we are no longer sure about the ploidy. Could you please help figure it out? It's a fungal species that was sequenced using PacBio HiFi.

Our plot looks like this:

pucciniasilphii_ploidy_smudgeplot

And this is the genomescope profile for the same genome:

transformed_linear_plot

If you could please help understanding this ploidy, it would be greatly appreciated. Thanks so much!

KamilSJaron commented 4 months ago

Hi Jacqueline, smudgeplot find all the k-mer pairs that are similar to each other (i.e. different by 1 nt) and generates this plot out of it while guessing the 1n coverage.

Basically what these two plots give you together, that there is no peak ~100x, all the k-mer pairs that are similar to each other have 200x coverage each - suggestion that that's the 1n peak. And given how big it is, it's quite possibly a haploid genome (obviously, there are some exceptions, very heterozygous genomes can occasionally look like this as well, but I don't think it's your case)

What's the species?

jacquelinemattos commented 4 months ago

Hi @KamilSJaron, Thanks so much for your response! This is really helpful. Yes, we're working with a Puccinia sp. isolate (a rust fungus). We also thought it would be a haploid, so I'm guessing we could conclude that afterwards? Thank you!

KamilSJaron commented 4 months ago

Oooh, a rust fungus! Cool!

Yeah, i would be comfortable thinking that. I would try to fit the haploid model in genomescope (-p 1) so you have a meaningful genome size estimate. Then keep an eye on the size of the assembled genome. if they would be a lot different you can post here again and we can give it a think again.

jacquelinemattos commented 4 months ago

Hi @KamilSJaron! Oh, for sure, I'll do that. But this has already been super helpful!! We really wanted to underestand the ploidy of this species and now it seems to be much more clear! Thank you so much for you help! I'll come back and post again if needed, for sure.

KamilSJaron commented 4 months ago

Great, I will close for now, feel free to reopen