You would use paste in the same manner. The paste command can take any number of character arguments and will concatenate all of the strings separated by whatever is given in the sep argument (which defaults to " " in paste and "" in paste0). In this case, it would be:
system(paste("python BUSCO.py --in", example.fasta, "--out output_file -m genome --lineage bacteria_odb9/ --species=E_coli_K12"))
In addition, your code was not formatted correctly to make it easy to read for people trying to help you. Formatting code allows for people to more easily identify where issues may be occurring, and makes it easier to read, in general. I have edited you post to format the code properly.
In the future please put code that is inline (such as a function name, like mutate or filter) inside of backticks (`mutate`) and chunks of code (including error messages and code copied from the console) can be put between sets of three backticks:
```
example <- foo %>%
filter(a == 1)
```
This process can be done automatically by highlighting your code, either inline or in a chunk, and clicking the </> button on the toolbar of the reply window!
This will help keep our community tidy and help you get the help you are looking for!
For more information, please take a look at the community's FAQ on formating code