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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

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  • $\begingroup$ I know what caused the difference. BUSCO uses more strict criterion to determine single-copy genes but manly of the result genes are identified as multicopy genes by OrthoFinder using less strict parameters. $\endgroup$
    – YP CHEN
    May 3 at 8:07
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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.

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  • $\begingroup$ Thanks for your reply. I run OrthoFinder with default parameters. The BUSCO identified 1000+ complete single-copy genes but only 387 identified by OrthoFinder. I am trying to confirm whether BUSCO single-copy genes are true single-copy. $\endgroup$
    – YP CHEN
    May 3 at 7:44

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