Reference: 1 Gene Is Encoded By 1Kb Length Of Prokaryotic Genome

Question

[Pappu]

So 100kb length of prokaryotic genome encodes 100 genes. I noticed it recently but not aware of the reference. i also read about it in a paper but no reference was provides. Are you aware of the paper?

Answer 1

[Adrian Pelin]

you don't need a reference. It's the 1 gene per kb gene density for prokaryotes based on the E. coli genome.

[Neilfws]

We most certainly do need a reference, for this and any other "facts" that we state. Otherwise there is no difference between an evidence-based position and conjecture/opinion.

[Adrian Pelin]

You can't possibly reference everything you state. For example, would you reference the fact that E. coli is a prokaryote when you would write a sentence "E. coli being a prokaryote is intronless."? There are 2 statements there, it being a prokaryote, and intronless. Would you reference the fact that most eukaryotes have introns? mitochondria? Sometimes you may want to talk about something in a eukaryotes nucleous, do you first let people know that there is a reference that eukaryotes actually have a nucleous?

I can agree that for this case you might need to still reference it if you are really focusing on that subject, but if it's something that's sort of a "by the way"... You are limited to amount of references in some journals.

One gene per kb rule is very well known in the scientific community based on the fact that E coli has a genome of 4.6 Mb and 4400 genes, so roughly 1 gene per kb, which is not an opinion, but a mathematical expression.

[Neilfws]

I agree that referencing every known observation is not necessary - "any fact" was loose language on my part. I would not, for example, reference "the sky is blue."

I suppose the rule of thumb is: ask yourself whether the statement is considered "common knowledge" by a majority of the target audience. So: "E. coli is a prokaryote", written for a microbiology journal - yes (disregarding the fact that some dislike that term).

"One gene per kb" - I would not say that this observation is common knowledge in "the scientific community" unless you mean "the bacterial genomics community."

[Adrian Pelin]

We're on the same page.

Answer 2

[Neilfws]

Literature search is also an essential skill for bioinformaticians. To get you started:

• Average Gene Length Is Highly Conserved in Prokaryotes and Eukaryotes and Diverges Only Between the Two Kingdoms
• Trends between gene content and genome size in prokaryotic species with larger genomes