Sturgeon genome with different ploidies
VictorHerp opened this issue · comments
Hi @clwgg,
I used nQuire to estimate the ploidy of each chromosome (60) of a sturgeon, running nQuire separately for each chromosome. This species has had at least two duplications of the entire genome, so evolutionarily it is believed that it has reached a level of octaploidy. However, a diploidization process is taking place and is in an intermediate state, so it is considered functionally tetraploid (most loci have this ploidy). Although, in theory, some chromosomes could still be octaploid and some already diploid. According to the delta log values and the SSR values of nQuire 6 chromosomes adjust to the diploid model and 54 to the tetraploid model. I was wondering if there is any way to identify loci that are octaploids that maybe have been adjusted to the tetraploid model for example. I mainly have three doubts:
- For example, in these results of the estmodel's histogram of chromosome 60 (the smallest), could it be said that it is tetraploid? Even if the R^2 of the diploid is higher and even if it has the higher std.Err? Many of my chromosomes that adjust to the tetra model have the highest std.Err.
Diploid:
Norm SSR: 0.0831641
y-y slope: -0.308615, with std.Err: 0.0786867
r^2: 0.206805
Triploid:
Norm SSR: 0.0389892
y-y slope: -0.0439825, with std.Err: 0.128467
r^2: 0.00198273
Tetraploid:
Norm SSR: 0.0175127
y-y slope: 0.559049, with std.Err: 0.186463
r^2: 0.132214
- If there were some octaploid locus how would nQuire behave?
- Could there be a bias for the length of each chromosome? the largest is 122 Mb and the smallest is 488 Kb (Fig.1 attached), although the percentage of non-repeated regions does not vary as much in each chromosome (Fig.2 attached). *I am using a reference genome from another species
If you want to see some files with the results do not hesitate to ask me.
Thanks for your help!
Víctor
