Your set of PSG is probably enriched in non real genes or genes with very low selective constraints. This kind of genes typically lack functional annotations. Genes evolving under strong purifying selection are those that are most relevant and most studied.

Dear Federico,

Thank you very much for your answers.

Federico " probably enriched in non real genes or genes with very low selective constraints. This kind of genes typically lack functional annotations"

Chen: My plant is belong to the plant Lobelia genus, non-model plant. I BLASTX the transcriptome DNA sequences of the Lobelia to Arabidopsis protein database. So I annotated my PSGs to Arabidopsis protein database (BLASTX E value = 0.00001). Most of these PSGs have functional annotations, similar to the negatively selected genes. So, I suspect these PSGs are real genes.

'Genes evolving under strong purifying selection are those that are most relevant and most studied'

Thank you for this valuable answers. I will read more papers on your topic.

Best regards.

Chen Lingyun

I agree with Federico. Why don't you use the Panther and Plant MetGenMAP?