What does heterozygosity mean in a haploid genome?

Question

[brooklyn]

Hello,

I am doing a de novo algae genome assembly. I expect my genome to be haploid, however when I run GenomeScope I receive a heterozygosity value of 0.828%. I am also receiving results that indicate I have high duplication in the genome (GenomeScope dup:0.808%, BUSCO: C: 94.3%[S:19.8%, D:74.5%]). I am wondering if these two things are related and have a few questions.

1) What does heterozygosity mean in terms of a haploid organism? (i.e if not receiving two sets of chromosomes/alleles then why/how does heterozygosity exist in haploids ... is this plant specific?)

2) Is high heterozygosity concerning? Does it need to be removed/masked?

3) Does heterozygosity indicate the genome is diploid? is it connected to the duplication results?

Thank you for any clarification or references that cover this topic.

Answer 1

[Jean-Karim Heriche]

From the GenomeScope paper:

Finally, GenomeScope is only appropriate for diploid genomes because the heterozygosity model it uses only considers the possibility for two alleles.

So if you know the genome is not diploid, at face value, you seem to be using the wrong tool. At a minimum you should be careful about what assumptions are made in the process so that you know which results are reliable and which not. For example, GenomeScope statistical model used for assembly may not assume any ploidy so the assembled sequence could be fine but clearly there's a diploidy assumption somewhere.