Number of sing-copy genes identified by orthofinder is far less than BUSCO assessment? Dear Orthofinder users and BUSCO users,
Recently, I have assessed 30 genome annotataions using BUSCO with lineage dataset ascomycota_odb10, I got 1100+ complete and single-copy genes. But the orthofinder  only identified 300+ single-copy genes. Aneone else have encountered this similar problem?
Thanks,
Yanpeng
It's hard to say for sure without seeing the exact commands you used. However, Orthofinder identifies/defines single-copy orthologues as those genes present in a single copy in all species being compared in the analysis. If a BUSCO orthologue is present in more than one copy in one of the species being compared (could be multi-copy, could be fragmented etc.), then it won't be recovered as single copy by Orthofinder.