Getting higher duplicated BUSCO for a genome assembly

Question

[u.nakandala]

Hi, I have done an assembly for a few plant species using hifiasm. Complete and duplicated BUSCO values for one of the species is too high (91.4%) and complete and single copy BUSCO is very low which is 8.6% for this species. Can it be a polyploid species? But no previous records of polyploidy have been reported for this particular species previously. So we are doubtful of this result. If it is not a polyploid, what would be the other possible reasons to get this much higher duplicated BUSCOs?

Answer 1

[h.mon]

I don't have experience with hifiasm (and if there are settings you could tweak here), but if the species is highly polymorphic, the assembler could keep contigs from both chromosomes separated, instead of collapsing them into haplotigs.