I want to download the annotation file in gff3 format for the corresponding genome. As this fairly easy on the ncbi-webpage I don't find a possibility to do the same with efetch or the kind.

I hoped I could use something like this:

    esearch -db nuccore -query "$genome_id" | efetch -format gff3  > "$path_data/$genome_id.gff"
I don't think NBCI offers GFF formatted files through efetch (yet).
Probably the best you can do is either indeed do it manually on the website (if you don't have many to do) or efetch genbank format and convert that to gff.

Otherwise, depending on the organism(s) you look for, there might be 'dedicated' databases that offer direct gff download.
