Very satisfying annotations ... Except for one species

[vpymerel]

Hello !

I have a question more than an issue, but maybe you can help me,

I am annotating a dozen of arthropods assemblies from a same genus with braker3 (arthropoda prot + RNAseq data),

For all assemblies, the BUSCO genes are predicted satisfactorily (no compleasm):

• braker3: ~4% BUSCO missing,
• Augustus: ~ 1% BUSCO missing,
• GeneMark: ~1.5% BUSCO missing

Except for one assembly:

• braker3: 29.99% BUSCO missing,
• Augustus: 6.00% BUSCO missing;
• GeneMark: 6.07% BUSCO missing

I would like to understand the discrepancy, but I don't have any clue of what may be happening,

RNAseq data is similar for each species (tissues, replicates, libraries ...), assembly quality also (chromosomal level, no huge duplication or missing parts),

Have you ever seen anything similar ? Or could you pinpoint me some statistics to get the beginning of an answer ?

Thank you, V