In one of the non-human organisms, GFF3 annotation file downloaded from NCBI genome FTP, there were some tRNA annotations (tRNA-Glu, tRNA-Ser, etc) in the mitochondrial genome that did not have a gene_id. They don't have any transcript features associated with them as well. Is it a usual annotation issue in the GFF3 format or by practice tRNA genes don't have either gene_id or transcripts associated with them?
The problem is that when the GFF3 is converted to GTF using gffread, no gene_id is present for those tRNAs and hence creating downstream issues. Should they be removed altogether if we are not exclusively interested in them?