BUSCO attempts to provide a quantitative assessment of the completeness in terms of the expected gene content of a genome assembly, transcriptome, or annotated gene set. The results are simplified into categories of Complete and single-copy, Complete and duplicated, Fragmented, or Missing BUSCOs.
BUSCO completeness results make sense only in the context of the biology of your organism. You have to understand whether missing or duplicated genes are of biological or technical origin. For instance, a high level of duplication may be explained by a recent whole duplication event (biological) or a chimeric assembly of haplotypes (technical). Transcriptomes and protein sets that are not filtered for isoforms will lead to a high proportion of duplicates. Therefore you should filter them before a BUSCO analysis. Finally, focusing on specific tissues or specific life stages and conditions in a transcriptomic experiment is unlikely to produce a BUSCO-complete transcriptome. In this case, consistency across your samples is what you will be aiming for.
For more information please refer to the Busco user guide .