Fig. 1

Benchmarking of BUSCO using reference genomes. a We downloaded eukaryotic RefSeq genomes excluding bilateria and vascular plants and ran BUSCO in ‘genome mode’ using the ‘eukaryota_odb9’ set. For each clade, we summarised the number of BUSCO markers matched. For fungal clades, such as Ascomycota, Mucoromycota and Basidiomycota, most BUSCOs matched a single target—suggesting 100% completeness of the reference genomes. However, in other clades, a substantial fraction of BUSCOs were frequently not matched (Apicomplexa, for example). b For species not belonging to fungal clades, we created a matrix using the detailed BUSCO results. Genomes are sorted taxonomically (using the assigned NCBI taxonomy) in columns and the result for each BUSCO in rows. The matrix is coloured according to the BUSCO result, which reports complete, duplicated, fragmented and missing marker genes. Fragmented hits are reported if only part of the BUSCO was detected. Above is shown the percentage of duplicated BUSCOs, the number of the RefSeq transcripts for each genome, the genome size and the GC content. In some clades, there is a clear relationship between the genome taxonomy and missing BUSCOs. In the case of Microsporidia and Apicomplexa, but also for Euglenozoa, this relationship is especially strong