I am aware that several genetic nomenclatures exist for specific groups of organisms. Unfortunatelly, such nomenclature is not available for my group (diatoms, microalgae, protists)and I did not find any general genetic nomenclature.

From what I read it seems there is a consensus among geneticists to distinguish between name formats of proteins (non-italicised) and corresponding genes (italicised; e.g. COI vs. COI). I have suspicion that this is often written incorrectly in taxonomy papers. Seems to me that most people write even protein-coding genes entirely non-italicised. Anyway, a letter coming for part of the gene/protein (lets call it sufix here for convenience) should be non-italicised (e.g. rbcL, psbA). Question is, shouldn’t „I“ sufix in „COI“ also be non-italicised because it also stays for the part of the gene/protein? Then when I refer to certain subregions of these genes and I define them as "COI-5P" and "rbcL-3P" (see postscript) then these „-5P“ and „-3P“ sufices should probably also be non-italicised, right? Following this logic it seems that these genes should be correctly written this way: COI-5P, rbcL-3P.

Yet another chapter are ribosomal genes which are written non-italicised as far as I have seen. It is true that it is easy to distinguish gene (LSU rDNA) and the product (LSU rRNA) if written in full. However, as short forms (just LSU or SSU) are often used in papers (also non-italicised) I guess it would be beneficial to distinguish product and the gene in the same way as in protein-coding genes. So I would prefer to write them this way to keep the same format as in protein-coding genes regardless of product type (protein vs. RNA): LSU rDNA and SSU rDNA, in short LSU and SSU (btw I would prefer to entirely avoid short forms here), and when speaking about products then LSU and SSU. I did not find anything in nomenclatures about genes encoding another product than proteins so I do not know. What is your opinion?

PS: Just to be sure what genes and their parts I am dealing with: COI = gene encoding Cytochrome c oxidase subunit I; COI-5P = 5' region of the mitochondrial gene encoding Cytochrome c oxidase subunit I (distinguished by specific primer pair in my manuscript); ITS rDNA, nuclear gene Internal Transcribed Spacer; LSU rDNA, nuclear gene encoding large-ribosomal subunit; psbA, plastid gene encoding Photosystem II protein D1; rbcL, plastid gene encoding large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase; rbcL-3P, 3' region of rbcL; SSU rDNA, nuclear gene encoding small-ribosomal subunit; UPA, Universal Plastid Amplicon; V4 SSU rDNA, subregion of SSU rDNA.