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From: RonO <rokimoto557@gmail.com>
Newsgroups: talk.origins
Subject: Re: Largest animal genome 91 billion base-pairs.
Date: Wed, 4 Sep 2024 10:02:39 -0500
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On 8/24/2024 5:58 PM, Richmond wrote:
> RonO <rokimoto557@gmail.com> writes:
> 
>> transposon sequence.  About 90% of the genome seems to be transposon
>> sequence at this time, but my guess is that most of the remaining 90%
>> is just old transposon sequence that has been mutated to the extent
> 
> If 90% is transposon, that only leaves 10%. Or do they mean 90% of the
> remaining 10%?
> 
> Anyway, do these parasitic bits of DNA speed up evolution by creating
> more replication errors?
> 

I missed this post.

90% of the genome can be identified as being transposon sequence.  The 
remaining 10% (9 billion base-pairs) is an amount 3 times the size of 
the human genome.  Most of that 10% is likely highly repetitive 
heterochromatic DNA or old transposon sequences that have accumulated so 
many mutations, insertions, and deletions that it can't be identified as 
once being transposon sequence.  Only a small fraction of that 10% codes 
for genes, probably less than 0.1% of the total 91 billion base-pair genome.

For most organisms transposons affect their evolution by the insertion 
and deletion mutations that they are associated with.  Since they 
produce short bits of identical sequence along the chromosomes they have 
been associated with deletions involving recombination between two 
transposon sequence found as direct repeats (in the same orientation) 
and inversions caused by recombination between transposon sequences 
inverted in relation to each other.  They often carry their own 
transcription regulatory sequences so they cause aberrant transcription 
where they insert.  If they insert into a coding sequence then can knock 
out that gene.  Insertion into introns has been known to alter exon 
splicing so that the coding sequences are no longer put together 
correctly.  So they can regulate genes differently, knock out genes, and 
create new protein sequences by altered exon splicing.

For this extreme example you have excessive energy demands placed on the 
organism to replicate all the parasitic DNA and it requires the same 
ratio of maintenance and support machinery (just think of all the extra 
histones needed to condense all that DNA into chromatin so that it fits 
into a nucleus.  3 billion base-pairs of DNA is about 1 meter in length, 
so this animal has to condense around 61 meters of DNA into each of it's 
cellular nuclei (2 times 91 billion base-pairs).  It takes one ATP just 
to charge a nucleotide so that it can be added to a replicating strand, 
and much more energy to make the nucleotides, and support and 
maintenance proteins.  You can see that having a genome 30 times larger 
than a human genome is a huge energy drain on the animal especially 
during embryogenesis and growing to adult body weight.  The ENCODE 
project determined that transposons are responsible for a huge amount of 
spurious transcription.  The energy wasted making parasitic RNA is 
probably many times greater than the cost of replicating the parasitic DNA.

Ron Okimoto