two species share a feature of great conve-
nience for genomics: their cells possess less
DNA than those of any other group of back-
boned animals — about eight or nine times
less than human cells.
Although the Tetraodon genome is small
compared with that of other vertebrates,
sequencing it was still a hugely formidable
task.The research reported in this issue2was
performed in a collaboration between Geno-
scope in France and the Broad Institute of
the Massachusetts Institute of Technology
and Harvard University in the United States.
Together they have generated a genome
sequence of impressive accuracy and cover-
age,with 64% ofthe DNA sequence mapped
to specific chromosomes3.
By comparing the Tetraodon genome
sequence with that of humans, Jaillon et al.
even allow us to peer into the genome of
the last common ancestor of pufferfish and
humans — a primitive bony fish that lived
hundreds of millions of years ago. The
descendants of this long-extinct ancestor
split into two distinct evolutionary lineages:
the actinopterygians (ray-finned fish),
which include teleosts such as pufferfish and
zebrafish, and the sarcopterygians (lobe-
fins), which include lungfish, coelacanths
and ourselves (Fig. 1). By matching up the
genes on each pufferfish chromosome to the
related genes on human chromosomes,Jail-
lon et al.deduce that the extinct ancestor had
12 pairs of chromosomes.Work on partially
completed genome sequences had suggested
this number4,5,but the new analyses add fas-
cinating detail to the picture.For example,it
is now possible to say which genes were on
which chromosomes, despite this unknown
animal having been extinct for more than
400 million years.
One puzzling observation concerns the
apparent stability of the genomes of ray-
finned fish. It seems that the ancestral
genome underwent as few as ten large inter-
chromosomal rearrangements (exchanges,
fissions or fusions) to give rise to the present-
day Tetraodongenome.Indeed,11 Tetraodon
chromosomes have not experienced any
such rearrangements. Only one human
chromosome (14) can make the same claim,
despite the timescale being identical.
Although the genomes of ray-finned fish
may have been slowly evolving in terms of
chromosome breakages and fusions, they
have experienced a cataclysmic event in their
history.Jaillon and colleagues’analyses ofthe
complete Tetraodon genome sequence show
clearly that a duplication of the whole
genome occurred sometime within the ray-
finned-fish lineage. This inference is not
new,having been previously suggested from
analyses of the Hox-gene clusters and other
gene families in zebrafish,Takifuguand other
teleosts4–7, but the conclusion has remained
Two new analyses should now settle the
issue, however. First, Jaillon and colleagues
plotted the chromosome positions for about
750 pairs of‘ancient’duplicated genes within
the Tetraodon genome, revealing related
pairs of chromosomes or chromosomal
regions. Every chromosome is involved,
consistent with an ancient whole-genome
duplication.In the second test,chromosome
positions for more than 6,000 pufferfish
genes were compared with the positions
of related genes in the human genome.
This revealed a striking pattern of ‘double
conserved synteny’, meaning that one
chromosomal region in humans matches
two in pufferfish, across the entire genome.
This is a clear echo of whole-genome dupli-
cation in the ray-finned-fish lineage. Every
gene,on every chromosome,was duplicated,
although there has since been a massive
degree ofgene loss and local gene shuffling.
When did this whole-genome duplica-
tion occur? Analysis of zebrafish genetic
maps strongly suggests that this species also
underwent such an event in its history4.
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NATURE|VOL 431|21 OCTOBER 2004|www.nature.com/nature
papers from the IHGSC1and She et al.4
argue for a hybrid strategy in which WGS is
supplemented by a modest amount of BAC
cloning and mapping. This would protect
draft WGS sequences from some of the
‘simplification’ reported by She et al. and
provide the clones needed for finishing
selected regions ofspecial interest.
What is next for the human genome pro-
ject? Even with a finished sequence in hand
there is much still to do. Surprisingly, one
task is to develop the definitive catalogue of
protein-coding genes.In the current paper1,
the number is estimated to be between
20,000 and 25,000. This wide range reflects
limitations to state-of-the-art gene-predic-
tion software that leave doubts about the
validity of many predicted genes. One
promising approach is to use comparative
genomics to align the human genome with
the genomes of other animals. Because
natural selection ensures that functional
regions are more highly conserved than
non-functional ones, this approach high-
lights candidate protein-coding regions.The
same approach shows promise for finding
other functional elements such as gene pro-
moters,which control the timing and level of
expression ofgenes,and micro-RNAs,which
have been implicated as regulatory agents of
many developmental processes.
Much farther in the future is the task of
sequencing the remaining 20% of the
genome that lies within heterochromatin,
the gene-poor, highly repetitive sequence
that is implicated in the processes of chro-
mosome replication and maintenance. The
repetitiveness of heterochromatin means
that it cannot be tackled using current
sequencing methods, and new technologies
will have to be developed to attack it.So don’t
be shocked to see another paper announcing
the ‘finishing’of the human genome in 2010
— it will describe how the heterochromatin
problem has been cracked.
In sequencing the human genome,
researchers have already climbed mountains
and travelled a long and winding road.But we
are only at the end ofthe beginning:ahead lies
another mountain range that we will need to
map out and explore as we seek to understand
how all the parts revealed by the genome
sequence work together to make life.
Lincoln D. Stein is at Cold Spring Harbor
Laboratory, 1 Bungtown Road,
Cold Spring Harbor, New York 11724, USA.
1. International Human Genome Sequencing Consortium Nature
2. International Human Genome Sequencing Consortium Nature
3. Venter, J. C.et al. Science 291,1304–1351 (2001).
4. She,X. et al. Nature 431,927–930 (2004).
complete DNA sequence determined, even
to draft coverage. These are predominantly
the widely studied model species, such as
mice, fruitflies and nematode worms, or
species ofparticular interest to humans,such
as the malaria-carrying mosquito.
It may come as a surprise, therefore, to
find that the list now includes not one, but
two species ofTetraodontiformes,a relatively
obscure group of fish also known as puffers.
Following on from the publication two
years ago of the genome sequence of
the Japanese pufferfish Takifugu rubripes1,
Jaillon and colleagues2report, on page 946
of this issue, the near-complete sequence
of the spotted green pufferfish Tetraodon
nigroviridis. Takifugu is a poisonous marine
fish best known to connoisseurs of sushi
restaurants, whereas Tetraodon is a small,
brackish-water pufferfish commonly kept in
aquaria. But, like all Tetraodontiformes, the
t is still early days for the field of com-
parative genomics. Only around a dozen
species of animal have so far had their
Small genome, big insights
John Mulley and Peter Holland
The genome of a second pufferfish species has been sequenced. Why
is this important? Because comparing this genome with that of other
animals yields a wealth of information on genome evolution.
© 2004 Nature PublishingGroup
Pufferfish and zebrafish belong to distinct Download full-text
taxonomic orders of fish,so the duplication
must have occurred early in teleost evolu-
tion.As previously pointed out7,this implies
that traces of the ancient whole-genome
duplication should be found in more than
20,000 species of living teleost fish. But
teleosts do not make up the whole of the
ray-finned fish. Significantly, a study of
one of the Hox-gene clusters of an earlier
(more ‘basally’) branching ray-finned fish,
Polypterus (Fig. 1), found no evidence of a
genome duplication9. Together with data
from other basal actinopterygians10,this sug-
gests that the genome duplication occurred
close to the origin of the teleost fish them-
selves,perhaps 230 million years ago.
Less clear are the biological conse-
quences. It is tempting to suggest that the
species richness of the teleosts is somehow
related to the whole-genome duplication,
either because natural selection has ‘exploit-
ed’ the extra genes, or because differential
mutation of duplicate genes caused repro-
ductive isolation, facilitating speciation11.
However, much of teleost diversity is found
in just one group, the acanthopterygians
(‘spiny fins’), which underwent a massive
increase in diversity only around 55 million
years ago. So if the whole-genome duplica-
tion did affect species richness, it was not
immediate, and further studies of morpho-
logical and genetic evolution in teleosts will
be needed to resolve the mechanisms
news and views
NATURE|VOL 431|21 OCTOBER 2004|www.nature.com/nature
Figure 1 Evolutionary relationships between humans,pufferfish and other vertebrates.Jaillon et al.2
have sequenced the genome of the pufferfish Tetraodon nigroviridis.By comparing this genome
sequence with that of humans,the authors deduce that the extinct ancestor of actinopterygians
(ray-finned fish,including pufferfish) and sarcopterygians (lobe-finned fish,the lineage that gave
rise to humans) had 12 pairs of chromosomes (n?12).They also show that a whole-genome
duplication (WGD) occurred during the evolution of ray-finned fish.
A final lesson from the Tetraodon study2
concerns the power of
genomics, both for gaining insights into
mechanisms of genome evolution and for
deducing genome organization in extinct
species.But we have a long lineage of extinct
ancestors,which means that a wide range of
genomes will need to be compared ifwe want
to look at each node in our evolutionary
history (Fig. 1). Particularly useful will be
complete genome sequences for a shark, a
lamprey and amphioxus,as each will provide
insight into yet more ancient ancestral states.
We may not have long to wait: this year the
Joint Genome Institute in California began
sequencing the amphioxus genome, while
the National Human Genome Research
Institute has announced plans to sequence
that ofthe sea lamprey.
John Mulley and Peter Holland are in the
Department of Zoology, University of Oxford,
South Parks Road, Oxford OX1 3PS, UK.
1. Aparicio,S. et al. Science 297, 1301–1310 (2002).
2. Jaillon, O.et al. Nature 431, 946–957 (2004).
4. Postlethwait, J. et al. Genome Res. 10, 1890–1902 (2000).
5. Naruse,K. et al. Genome Res. 14, 820–828 (2004).
6. Amores,A. et al. Science 282, 1711–1714 (1998).
7. Taylor, J., Braasch, I., Frickley, T., Meyer,A. & Van de Peer,Y.
Genome Res. 13, 382–390 (2003).
8. Robinson-Rechavi,M.,Marachand,O.,Escriva,H.& Laudet,V.
Curr. Biol. 11, R458–R459 (2001).
9. Chiu, C.-H.et al. Genome Res. 14, 11–17 (2004).
10.Hoegg, S., Brinkmann, H., Taylor, J. & Meyer,A. J. Mol. Evol. 59,
11.Lynch,M.& Force,A.G. Am. Nat. 156, 590–605
100 YEARS AGO
The Cultivation of Man. The author of this
book is very much in earnest. He condemns
modern civilisation in strong terms for its
many vices, especially for its worship of
money and the mammonite marriages that
result from it, and urges that men should
apply to their own species the methods
of the breeder of cattle. He recommends
polygamy, apparently in all seriousness,
and not as a mere counsel of perfection.
It would, of course, destroy the family,
but to this Mr. Witchell has no objection…
Certainly he speaks out fearlessly, and that
is no small merit. But it is to be regretted
that he did not study his subject more before
writing.“Natural selection,” he says,“is
sometimes operative, chiefly among the
poor.” Considering that in England nearly
fifty per cent. of the population die before
the average age of marriage, this is a
wonderful understatement. If we bear
the facts in mind, we can hardly agree
with Mr. Witchell that the business man is
“the surviving type,” i.e. apparently the type
that is to survive to the exclusion of others.
Business men are not a separate species.
There is a continual upward movement of
able men from the great underlying social
stratum, and from this stratum directly or
indirectly our successful men, as we call
them, have emerged.
From Nature20 October 1904.
50 YEARS AGO
Anatomist, pathologist, epidemiologist,
sanitarian and clinician, and one of the
most advanced thinkers in the history of
the medical sciences, Giovanni Maria Lancisi
was born in Rome three hundred years ago,
on October 26, 1654… It was at [Pope]
Clement’s request that in 1707 he wrote
his monumental treatise “De subitaneis
mortibus”, in which he carefully records
the pathological lesions of the brain and
heart observed at autopsy, gives the first
description of syphilis of the heart and of
growths on the valves, and lists hypertrophy
and dilatation of the heart as a cause of
sudden death. Lancisi’s book,“De motu
cordis et aneurysmatibus” (1728), is another
landmark in the history of heart disease,
for it stresses the significance of heredity,
syphilis and violent emotions as causes
of aneurysm… In the tercentennial year of
his birth he is gratefully remembered chiefly
for having laid the foundation for a true
understanding of the pathology of the heart.
From Nature23 October 1954.
© 2004 Nature PublishingGroup