Dr. S.A.J.R. Aparicio saparici at med.cam.ac.uk
Sun Jan 30 12:23:25 EST 1994

In article <robison1.759864272 at husc10.harvard.edu>, robison1 at husc10.harvard.edu (Keith Robison) writes:
> Readers of this thread should note the recent paper from 
> Sydney Brenner's group on the fugu (pufferfish) genome --
> less than 1/2 a gigabase and apparently relatively free of
> repetitive sequences.  The paper was in Nature in November
> (366:265 + a News&Views I think).  Brenner thinks that fugu
> represents an unexpanded, ancestral genome type but it's not
> obvious that it is not a reduced genome which ejected the 'junk'.

I have been follwing this thread with some interest, especially as I work
on Fugu in Sydney Brenners group.

I think most people would agree that gain and loss of DNA occurs vertebrate
genomes, however we propose that in Fugu the gain process is severely attenuated.
This is difficult to prove, but seems more likely than loss of information. Most
vertebrates (allowing for ploidy effects) show an increase genome size
in line with increasing specialisation but most of this expansion seems to be due to
non-coding DNA. I can find plausible reasons for this process giving rise to selective
advantages but I find it hard to imagine the converse - one would  expect a loss
mechanism to be active and I'm ignorant of any such process having been described in vertebrates (of
course this doesn't mean it doesn't exist!). Referring to the genome as ancestral may
be misleading - the hypothesis is that the complexity (ratio of intron size to exon size,
put crudely) is ancestral, but clearly the Fugu genome will have changed in the last 400My
or so, and in that sense it is not ancestral.

I hope that this argument will gain more weight in the next few months as we publish
the structures of genes and gene complexes, when it will be possible to compare what has
happened to intron sizes amongst genes with conserved coding sequences.

All the best

Sam Aparicio
saparici at med.cam.ac.uk

fax +44 223 210136
tel +44 223 402436

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