BUSCO producing different genome completeness

Question

[Mehmet]

Dear All,

I would like to have your idea on a topic.

I run Busco (the latest version) for genomes of six worm species using eukaryote and nematoda database separately, and received different completeness results in one species. the species had ~92 % completeness when I run eukaryote database and ~77 % completeness when I run nematoda database. Other five species had very close completeness in eukaryote and nematoda database.

Do you have any idea what may explain this difference?

I run same command except lineage (database).

[h.mon]

How are other metrics (N50, number of contigs / scaffolds, genome size, coverage, etc) for all six genomes? Is this particular genome more fragmented than the others? How many genes are included on the "Eukaryotes" and "Nematodes" sets?

First thing which springs to my mind is maybe it is not a nematode genome?

Answer 1

[Chris Fields]

This is expected; different taxonomic groups would have different single-copy orthologs (with more refined taxonomic groups having more SCOs compared to broader groups). Also, I know several nematode genomes have lower than expected BUSCO scores, which may be due to issues with assembly, etc.