It is certainly possible to encode polycistrons in GFF3. In fact, this is discussed explicitly in the GFF3 specification.
This is the case in which a single (possibly spliced) transcript encodes multiple open reading frames that generate independent protein products.
Since the single transcript corresponds to multiple genes that can be identified by genetic analysis, the recommended solution here is to create four "gene" objects and make them the parent for a single transcript. The transcript will contain a single exon (in the unspliced case) and four separate CDSs:
chrX . gene XXXX YYYY . + . ID=gene01;name=resA
chrX . gene XXXX YYYY . + . ID=gene02;name=resB
chrX . gene XXXX YYYY . + . ID=gene03;name=resX
chrX . gene XXXX YYYY . + . ID=gene04;name=resZ
chrX . mRNA XXXX YYYY . + . ID=tran01;Parent=gene01,gene02,gene03,gene04
chrX . exon XXXX YYYY . + . ID=exon00001;Parent=tran01
chrX . CDS XXXX YYYY . + . Parent=tran01;Derives_from=gene01
chrX . CDS XXXX YYYY . + . Parent=tran01;Derives_from=gene02
chrX . CDS XXXX YYYY . + . Parent=tran01;Derives_from=gene03
chrX . CDS XXXX YYYY . + . Parent=tran01;Derives_from=gene04
To disambiguate the relationship between which genes encode which CDSs, you may use the
This example doesn't indicate what the coordinates of each feature should be, but I think it makes most sense to have the
CDS feature coordinates correspond to the region coding each protein product, and the
exon feature coordinates correspond to the entire span.
BIG CAVEAT: Polycistrons are not typically considered a normal feature of eukaryotic genomes—they're much more common in bacteria and archaea. However, there are some confirmed cases of eukaryotic polycistronic mRNAs. That said, if overlapping gene predictions are observed in a GFF3 file, one cannot immediately assume that these are polycistronic. One or both of the gene predictions might be technical artifacts, or real genes that are incorrectly annotated, or (more rarely) actual overlapping genes. A claim that multiple protein products are expressed from a single transcript would require some convincing experimental validation.