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From: Ernest Major <{$to$}@meden.demon.co.uk>
Newsgroups: talk.origins
Subject: Re: Life: Turn it upside down!
Date: Sun, 14 Apr 2024 18:50:00 +0100
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On 13/04/2024 15:11, Arkalen wrote:
>> Based on the overlap in genome sizes and gene counts my provisional 
>> position is that the gap between viruses and cellular organisms is 
>> narrower than generally expected.
> 
> 
> I haven't finished reading the paper on Mimivirus but you seem to know 
> quite a bit about it - I saw something about part of its genome being 
> pretty stable and the other highly variable and apparently borrowed from 
> the host. Is that accurate to your understanding or did I misunderstand? 
> And if it's accurate, could it suggest that Mimivirus' genome is being 
> used in a different way from the "standard" way we think of (if such a 
> thing exists), and this might imply a different relationship between 
> genome size and complexity from that of cells or other viruses?

This is not just a feature of mimivirus and allies. I expect that gene 
content is fairly uniform with vertebrate families. But in plants there 
is turnover in membership of gene families - cycles of duplication 
followed by neofunctionalisation, subfunctionalisation or loss - so you 
end up with a core genome and genes found within some but not all 
species of a group. Places to look at this are Gossypium, where we have 
genomes for at least 25 species, including 6 species of subgenus Karpas 
which have a common allotetraploid ancestry and which may show 
differential loss during the ongoing process of diploidisation, and 
other agriculturally important groups such as Brassica and Triticum.

Generally as you go towards "simpler" organisms the magnitude of the 
contrast between the core genome and pangenome increases.

In E. coli strains have between 4,000 and 5,500 genes (4,288 in the 
first sequenced strain), with a soft core (found in the great majority, 
but not all strains) of around 3,000 genes, a core genome of 1,000 
genes, an a pangenome of 16,000 or more genes.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9205054/
https://en.wikipedia.org/wiki/Escherichia_coli

Wolbachia pipientis gene contents are strikingly variable between 
strains symbiotic with different hosts.

Mycoplasmas have a gene content of the order of 1,000 genes, a core 
genome of around 500 and a pangenome of well in excess of 30,000.

https://www.nature.com/articles/s42003-021-02105-1

Giant viruses (and pox viruses), with core genomes and substantial 
lineage specific genomes, don't seem out of line.

The question that needs to be asked is to what extent this a genuine 
phenomenon, and to what extent it is an artefact of greater taxonomic 
splitting in charismatic megabiota. Is it correct to treat Buchnera 
aphidicola, Wolbachia pipientis and Escherichia coli as single species, 
or are they equivalent to a vertebrate genus, family, order or class?
> 
> Like the prokaryotes thing it's not a claim, just an idea. I'd been 
> wanting to dig into it a bit but haven't yet so I thought I'd ask you 
> for thoughts anyway.

-- 
alias Ernest Major