Q: what does high BUSCO duplication results in a green algae genome assembly mean

Question

[brooklyn]

Hello, I used BUSCO to assess the quality of a de novo green algae genome assembly and I received this result: C: 94.3%[S:19.8%, D:74.5%], F:1.8%, M:3.9%,n:1519 C:1433 [S:301, D:1132], F:28, M:58, n:1519

I am wondering what a normal level of duplication would be to expect for a plant/algal genome and reasonings why this might be so high for mine?

Should I be considering removing some of this duplication? How can I detect where it is and how can I remove it?

My genome is larger than expected so that is why I am concerned about the duplication level. Any advice is appreciated. Thank you!

Answer 1

[Mensur Dlakic]

It is normal to have some gene duplication, but I would not expect 75%. It could mean several things:

• polyploidy
• contamination with a related genome
• artificial contamination due to sequencing errors stemming from very deep sequencing

How identical are your duplicated regions at nucleotide and protein levels? That may help answer why they are there in the first place.