Largest animal genome 91 billion base-pairs.

[RonO]

https://www.nature.com/articles/s41586-024-07830-1

paywalled, but Science news article:

https://www.science.org/content/article/odd-fish-has-30-times-much-dna-humans-new-record-animals

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.

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.

Ron Okimoto

[John Harshman]

Post by RonO
https://www.nature.com/articles/s41586-024-07830-1
https://www.science.org/content/article/odd-fish-has-30-times-much-dna-humans-new-record-animals
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.
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.
Ron Okimoto

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.

Check out the animal genome size database:
http://www.genomesize.com/results.php?page=1

[John Harshman]

Post by John Harshman

Post by RonO
https://www.nature.com/articles/s41586-024-07830-1
https://www.science.org/content/article/odd-fish-has-30-times-much-dna-humans-new-record-animals
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.
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.
Ron Okimoto

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.
http://www.genomesize.com/results.php?page=1

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.

[RonO]

Post by John Harshman

Post by John Harshman

Post by RonO
https://www.nature.com/articles/s41586-024-07830-1
https://www.science.org/content/article/odd-fish-has-30-times-much-dna-humans-new-record-animals
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.
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.
Ron Okimoto

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.
http://www.genomesize.com/results.php?page=1

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.

Before this article I was not aware of any animal genome with such a
high C value was thought not to be polyploid.

Ron Okimoto

[x]

Post by John Harshman

Post by John Harshman

Post by RonO
https://www.nature.com/articles/s41586-024-07830-1
https://www.science.org/content/article/odd-fish-has-30-times-much-dna-humans-new-record-animals
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.
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.
Ron Okimoto

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.
http://www.genomesize.com/results.php?page=1

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?

[John Harshman]

Post by x

Post by John Harshman

Post by John Harshman

Post by RonO
https://www.nature.com/articles/s41586-024-07830-1
https://www.science.org/content/article/odd-fish-has-30-times-much-dna-humans-new-record-animals
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.
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.
Ron Okimoto

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.
http://www.genomesize.com/results.php?page=1

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?

Well, ferns are famous.

Post by x
What is the shortest frog genome?  Are there any frogs with
genomes shorter than humans or even chickens?  Which ones are
those?

You should check out the animal genome size database. Lots of answers
there. Check out the graph showing animal genome size ranges. I'd post
it here but images don't work.

Anyway, there are frogs with smaller genomes than any mammal and
crustaceans with longer genomes than some salamanders.

[Kerr-Mudd, John]

On Thu, 22 Aug 2024 12:36:27 -0700

Post by John Harshman

Post by x

Post by John Harshman

Post by John Harshman

Post by RonO
https://www.nature.com/articles/s41586-024-07830-1
https://www.science.org/content/article/odd-fish-has-30-times-much-dna-humans-new-record-animals
They have just identified the new largest animal genome, but unlike

[]

Post by John Harshman

Post by x

Post by John Harshman

Post by John Harshman
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.
http://www.genomesize.com/results.php?page=1

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?

Well, ferns are famous.

Post by x
What is the shortest frog genome?  Are there any frogs with
genomes shorter than humans or even chickens?  Which ones are
those?

You should check out the animal genome size database. Lots of answers
there. Check out the graph showing animal genome size ranges. I'd post
it here but images don't work.
Anyway, there are frogs with smaller genomes than any mammal and
crustaceans with longer genomes than some salamanders.

Size isn't everything.

"It ain't what you got, it's the way that you do it" </FBTwB>

[jillery]

On Thu, 22 Aug 2024 20:53:03 +0100, "Kerr-Mudd, John"

Post by Kerr-Mudd, John
Size isn't everything.
"It ain't what you got, it's the way that you do it" </FBTwB>

"It's not how long you make it, it's how you make it long."
(An old cigarette jingle)

--
To know less than we don't know is the nature of most knowledge

[RonO]

Post by jillery
On Thu, 22 Aug 2024 20:53:03 +0100, "Kerr-Mudd, John"

Post by Kerr-Mudd, John
Size isn't everything.
"It ain't what you got, it's the way that you do it" </FBTwB>

"It's not how long you make it, it's how you make it long."
(An old cigarette jingle)
--
To know less than we don't know is the nature of most knowledge

I remember the "silly millimeter longer" cigaratte commercials at around
that same time when they could still advertise on TV.

Ron Okimoto

[Ernest Major]

Post by John Harshman

Post by x
Are there some other organisms that have really long genomes
besides some lobe finned fish and some lungfish and some frogs?

Well, ferns are famous.

If science hasn't moved on the current record holder is a fern
(Tmesipteris oblanceolata). Paris japonica (a petaloid monocot) also
beats lungfish.

[John Harshman]

Post by Ernest Major

Post by John Harshman

Post by x
Are there some other organisms that have really long genomes
besides some lobe finned fish and some lungfish and some frogs?

Well, ferns are famous.

If science hasn't moved on the current record holder is a fern
(Tmesipteris oblanceolata). Paris japonica (a petaloid monocot) also
beats lungfish.

And there are protists that beat them all.

[Kestrel Clayton]

Post by John Harshman

Post by RonO
https://www.nature.com/articles/s41586-024-07830-1
https://www.science.org/content/article/odd-fish-has-30-times-much-
dna-humans-new-record-animals
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.
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.
Ron Okimoto

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.
Check out the animal genome size database: http://www.genomesize.com/
results.php?page=1

This is an interesting resource. Thank you very much!

[Richmond]

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?

[RonO]

Post by Richmond

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

[John Harshman]

Post by RonO

Post by Richmond

Post by RonO
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.