Re: Largest animal genome 91 billion base-pairs.

On 9/4/24 11:02 PM, RonO wrote:

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
 

And it's nearly certain that none of this extra energy and material cost is significant, since the organism does just fine.