Re: Largest animal genome 91 billion base-pairs.

On 8/21/24 20:22, John Harshman wrote:

On 8/21/24 7:43 PM, John Harshman wrote:

On 8/21/24 12:51 PM, RonO wrote:

https://www.nature.com/articles/s41586-024-07830-1
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paywalled, but Science news article:
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https://www.science.org/content/article/odd-fish-has-30-times-much-dna-humans-new-record-animals
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They have just identified the new largest animal genome, but unlike amphibians that duplicated their whole genomes over and over to create their large genomes this lobe-finned fish (a species of lungfish) enlarged it's genome by failing to regulate the multiplication of transposons.  It has a 91 billion  base-pair genome, but still only as many genes as related lobe-finned fish (lobe-finned fish gave rise to tetrapods).  It has roughly the same number of genes that humans have, but it's genome is 30 times larger.  Allowing transposons to run rampant has increased it's genome size with copies of transposons by about 3 billion base-pairs every 10 million years.
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Transposons are parasitic bits of DNA that can replicate and move from place to place in the genome.  Because of their parasitic nature they have been lumped into junk DNA, but they often do have functional genes, and take their own transcription regulatory sequences with them when the hop around the genome, so they have some function, but it isn't geared to helping out the host.  They just use the host cells to keep replicating more copies of themselves.  Jumping into genes causes genetic diseases and jumping around genes can cause differential regulation of the surrounding genes, so they cause insertion mutations that do affect the organism, but like other mutations, most of the mutations are benign, some of them are bad, and a few of them may do some interesting things.  At this time for this lungfish probably nearly all new transposition events are likely messing up existing 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 that they can't recognize the fragments as once being transposons.
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Ron Okimoto
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That's Lepidosiren paradoxa. It's been known for a long time that it has a huge genome, and that the other lungfish also have huge genomes. In fact, it appears that Protopterus aethyopicus has an even bigger one. So no huge surprise here, just greater detail on *why* it has a huge genome.
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Check out the animal genome size database: http://www.genomesize.com/results.php?page=1
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Ah, I see it's actually the largest animal genome *sequenced so far*. It may be the 4th or 5th largest, and possibly the second-largest to get that way without polyploidy.

So it is interesting how you can look at a macroscopic organism
and not really tell very well - this has a long (base pairs)
genome and this one does not.
So exclude the slime molds and do not call them something like
ultra-polyploidal.
Are there some other organisms that have really long genomes
besides some lobe finned fish and some lungfish and some frogs?
What is the shortest frog genome?  Are there any frogs with
genomes shorter than humans or even chickens?  Which ones are
those?