I have two fungal genomes that I blasted against the ITS, 18S, and 28S targeted loci database in NCBI. You would think that somewhere in the genome would have a hit against either of these databases, but for some reason, I am not finding any hits. If there is a hit, the query coverage is below 10%. NCBI recommended changing the expected threshold and the low complexity filtering, but this did not improve my matches.
Does anyone have any thoughts as to why this may be happening, considering my genomes are ~98% complete?