Are pseudogene counted as a subtype of long non-coding RNA genes?

Question

Are pseudogenes regarded as a subtype of the genes for long non-coding RNAs?

I could not find the answer to this question in an internet search.

Answer 1

A note on nomenclature in modern biology

As it stands, this question seems to assume there is some legal commission, Académie française, or the like that is devoted to continually determining scientific nomenclature, and that those in the field obediently follow it. While organizations like IUPAC — The International Union of Pure and Applied Chemistry — do exist for standardization, they move very slowly, and only come out when the dust has settled (so to speak). So if I write an article about genes I can classify them as suits my purpose. I may wish to distinguish just between coding or non-coding; or between structural, informational, regulatory and junk etc. etc. Nobody is going to throw me in gaol if they disagree.

Is it scientific to classify pseudogenes in this way?

By this, I mean do the genes (for that is what we can compare) for long non-coding RNAs (ncRNAs or lncRNAs) have enough general features shared by pseudogenes that it would be useful to sub-type pseudogenes in this way. In my opinion, No. Pseudogenes are generally regarded as non-functional — remnants of unsuccessful or uncompleted gene duplication, or of reverse transcription of mature mRNAs into the germ-line DNA. In many cases they are not even transcribed. There may not be a single function for those gene-products termed lncRNAs but in general they are transcribed and thought to have functions concerned with gene regulation. There are no structural similarities with pseudogenes, so that all the genes have in common is that they are, well, long, so to that idea I would say “So long!”

How do the genome annotators regard this?

The people that make the rules, de facto — and revise them as science advances — are the ones with the job of annotating sequenced genomes. I haven’t made a general survey of genomes, and am restricting myself to the genome of the fruit fly, Drosophila melanogaster, with which I am familiar. The distinct Biotypes for genes in the data at FlyBase are currently (2019) as follows:

• ncRNA (aka lncRNA)
• protein coding
• pseudogene
• snRNA
• tRNA
• rRNA
• snoRNA
• pre miRNA

I suspect that this is standard among the large genome databases, and it can be seen that pseudogene and ncRNA are regarded as distinct categories.

Of course, one can argue with this classification — where are the SINES and LINES and Drosophila-specific mobile elements, for example? But that just illustrates what I have written above.