I used BUSCO v.2 for finding the genome completeness and orthologus genes present in some Wolbachia genomes. The results show more number of orthologous genes present in the reference genomes as compared to the ones generated by us. Upon manually checking the presence of same genes using BLAST i could retrieve intact gene sequences in our own Wolbachia assemblies also.This happened for one of the reference genome assembly also. Why is BUSCO missing those genes when the exact same seqeunce is been annotated in case of reference genome assemblies.
(My assembly statistics are comparable with the reference genomes)