How to perform GO enrichment in non-model organisms?

Question

[CaERu]

Hello

I am a beginner using RNA-seq data for analysis. I would like to use GO enrichment analysis to infer the functions of genes that are upregulated by DEG analysis. However, since my analysis target is a non-model plant, there are no annotation files available, so I have to create them myself. Fortunately, I obtained the whole genome sequence and the GFF file describing the positions of the gene sequences. If I were to annotate all genes myself, what tools would be optimal? I personally plan to use eggNOG-mapper.