Download Reconstruction of a 450-My-old ancestral vertebrate protokaryotype

ARTICLE IN PRESS
Opinion
TRENDS in Genetics Vol.xx No.xx Monthxxxx
Reconstruction of a 450-My-old
ancestral vertebrate protokaryotype
Matthias Kohn1,*, Josef Högel1,*, Walther Vogel1, Peter Minich1,
Hildegard Kehrer-Sawatzki1, Jennifer A.M. Graves2 and Horst Hameister1
1
Department of Human Genetics, University of Ulm, D-89070 Ulm, Germany
Comparative Genomics Research Group, Research School of Biological Sciences,
Australian National University, Canberra ACT 2601, Australia
2
From recent work the putative eutherian karyotype from
100 Mya has been derived. Here, we have applied a new
in silico technique, electronic chromosome painting (Epainting), on a large data set of genes whose positions
are known in human, chicken, zebrafish and pufferfish.
E-painting identifies conserved syntenies in the data set,
and it enables a stepwise reconstruction of the ancestral
vertebrate protokaryotype comprising 11 protochromosomes. During karyotype evolution in land vertebrates
interchromosomal rearrangements by translocation are
relatively frequent, whereas the karyotypes of birds and
fish are much more conserved. Although the human
karyotype is one of the most conserved in eutherians, it
can no longer be considered highly conserved from a
vertebrate-wide perspective.
Introduction
The genomes of different mammalian species are far more
similar than has been expected from their karyotypic
diversity. Overall these genomes share a similar number
of w24 500–26 000 genes [1]. Mapping of orthologous
genes and comparative painting techniques using DNA
probes from single chromosomes has enabled the reconstruction of an ancestral eutherian founder karyotype
from w100 million years ago (Mya) [2–6]. These reconstructions are based on ancestral chromosome characteristics shared between extant mammalian species. Most
informative for these reconstructions are genomes from
species with highly conserved karyotypes [4]. It was
surprising to realize that the human karyotype is similar
to this ancestral karyotype, implying that no major
karyotype change occurred during the evolution of
humans in the past 100 My.
Similar comparisons have also been performed between
the karyotypes of different fish species and human [7–11].
With the availability of the chicken genome [12] as a
connecting link between mammals and fish, it is now
possible to reconstruct the protokaryotype of a common
vertebrate ancestor that lived 450 Mya. Because of the
greater DNA divergence rate, chromosomal painting
techniques are not applicable when comparing different
Corresponding author: Hameister, H. ([email protected]).
* These authors contributed equally to this article.
vertebrate genomes. For karyotype reconstructions one
has to switch to in silico analysis and search for shared
ancestral syntenies of genes across multiple species. To do
this, we established a gene orthology database containing
w3300 genes at a density of one gene per Mb along all
human (Homo sapiens, HSA) chromosomes. This database
contains human genes and their orthologous genes
together with their chromosomal assignment from
chicken (Gallus gallus, GGA), green spotted pufferfish
(Tetraodon nigrovirides, TNI) and zebrafish (Danio rerio,
DRE). This database is an extension of the one we used
previously to reconstruct the ancestor of the mammalian X
chromosome [13]. Genes from chicken and fish were
considered to be orthologous to the respective human
gene if reciprocal BLAST best-hit searches identified them
as such in the Ensembl database (Table S1 in supplementary online material). Another 801 genes were added from
a third fish species, medaka (Oryzias latipes, OLA) [9].
Table 1 shows the numbers of orthologous genes that could
be unequivocally identified in each genome. Because the
chicken [12], pufferfish [10] and zebrafish genome
analyses are still incomplete, the number of orthologous
genes retrieved for each species differs. This database,
which is described in more detail in Box 1, can be used for
electronic chromosome painting (E-painting), which is
highly informative. By E-painting conserved syntenies
(for a definition, see Box 1) are identified and used to
reconstruct the ancestral vertebrate protokaryotype. For
the comparison only synteny groups with three or more
genes in the sample were considered. First, the karyotype
of the early tetrapod (TET), which is ancestral to both
birds and mammals, was reconstructed. Second, a
reconstruction was performed of the karyotype of an
ancestral teleost fish (TEL), which lived before the extra
whole-genome duplication that is characteristic for the
teleost fish genomes [10,14]. Finally, a common early
vertebrate (VER) protokaryotype from 450 Mya
was established.
Reconstruction of the ancestral tetrapod protokaryotype
The reconstruction of the tetrapod karyotype was based on
chicken and human genome data including the conserved
chromosome characteristics that had already guided the
reconstruction of the ancestral eutherian karyotype (e.g.
Refs [2,6]). The following syntenic associations of
www.sciencedirect.com 0168-9525/$ - see front matter Q 2006 Elsevier Ltd. All rights reserved. doi:10.1016/j.tig.2006.02.008
ARTICLE IN PRESS
Opinion
2
TRENDS in Genetics Vol.xx No.xx Monthxxxx
Table 1. The number of orthologous genes compared in
different species
Human
Chicken
Pufferfish
Zebrafish
Human
3283
Chicken
2751
Pufferfish
2149
1915
Zebrafish
2085
1825
1499
Medaka
801
667
543
550
neighboring chromosomal segments of the ancestral
eutherian karyotype are also present in the chicken
genome: 1/19p, 3/21, 4/8p, 7/16p, 12/22 (2 chromosomes),
14/15, 16q/19q (Table 2). Therefore, these associations and
the well-established chromosomal fusion making up HSA
chromosome 2 were integrated into the reconstruction of
the tetrapod karyotype from 310 Mya. The genome data
from pufferfish served as outgroup information.
As an example, the reconstructions for the tetrapod
chromosomes TET 6 and TET 18 are described. Comparative mapping studies in mammals have confirmed the
association of segments from HSA 12p/q and 22q on two
different chromosomes in the ancestral eutherian protokaryotype. Yang et al. [4], using chromosome paints,
proposed that these associations represent the eutherian
chromosomes EUT 7 and 21. The respective genes of the
first and larger association of segments from HSA 12p/q
and 22q map on the duplicated pair of pufferfish
chromosomes TNI 13 and 19, as does a further segment
from HSA 7 (Table 2). All these segments together are
included in the large chicken chromosome GGA 1 and are
derived from TET 6 (Figure 1). The second and smaller
association, which represents the eutherian chromosome
EUT 21 [4], is found on TNI 12. It makes up the whole
GGA 15 and is derived from TET 18 (Table 2).
In a similar manner all other tetrapod protochromosomes were reconstructed according to the parsimony
principle and having in mind the whole-genome duplication in the teleost fish (Table 2). Reconstruction of the
Box 1. The study of karyotype evolution in vertebrates
Chromosomal banding techniques
In silico whole-genome database comparisons
The study of karyotype evolution in vertebrates was boosted when
chromosomal banding techniques became available. The astounding
similarity of the chromosome banding pattern between human and
the other primates enabled Dutrillaux [22] to put forward a
phylogenetic reconstruction of the primates based on karyotype
similarity. But when species from different mammalian orders were
compared, banding similarity was found to be restricted to a few
chromosomal regions (e.g. human versus cat [23,24] and human
versus mouse [25]).
When whole genomes from evolutionarily distantly related species
are compared one has to concentrate on the most conserved singlecopy sequences, which are the coding sequences of the genes.
Pevzner and Tesler [18] have provided the GRIMM software, which
enables the researcher to extract the minimal number of rearrangements that separate two genomes. The advantage of this tool is that
intrachromosomal inversions are also counted. Both segments of
conserved synteny and conserved gene order are taken into
consideration. A highly dynamic picture of genome evolution is
revealed, which could be biased because in the current applications
the data from the greatly rearranged genomes from mouse and rat are
integrated [16,17].
Gene mapping data
The long and informative history of the human–mouse comparative
gene-mapping initiative has dominated this area. In an early and
highly influential article, Nadeau and Taylor [26] predicted on the
basis of only w83 orthologous loci a total number of segments
with conserved synteny and gene order of 178G39 between
both species. The accuracy of this calculation remained unchallenged over the next 20 years. Similar comparative studies with
human as the reference genome are reported for zebrafish [7,8],
which is the other vertebrate species favored by developmental
biologists. Again, a greatly rearranged genome is observed. A
crude estimate arrived at 260 to 420 segments of conserved
synteny [8].
Chromosomal painting techniques (Zoo–FISH analysis)
This technique relies on DNA sequence similarity, which is revealed
by fluorescence in situ hybridization (FISH) techniques. Preferably,
DNA probes from single chromosomes are used, which under
prolonged hybridization indicate the orthologous chromosome
segments in other species [27]. This technique reveals segments
with conserved synteny, but is not informative about gene order.
With human DNA probes this technique works with all species of
mammals. Outside of eutherians the technique has been successfully
applied only with an X chromosome probe in marsupials [28]. It was
immediately evident that most mammalian species show a much
greater degree of karyotype conservation than expected from the
human–mouse comparison [29]. Shared ancestral chromosome
characteristics in the form of associations and fissions were observed
as soon as more species were analyzed [30]. There are species with a
relatively high rate of rearrangements (mouse, dog and gibbon) and
other species with few rearrangements (aardvark, harbor seal and
cat) [31]. These species bear a highly conserved karyotype and
therefore are informative for karyotype reconstructions [4]. Several
studies arrived at a eutherian protokaryotype with 21–22 chromosomes [2–6], which proves to be similar to the present-day
human karyotype.
www.sciencedirect.com
In silico search for conserved syntenies
In the studies that integrate fish genome data, orthologous gene pairs
are registered in the databases together with their chromosomal
assignment [9–11]. Conserved synteny is present when two or more
orthologous loci map to a single chromosome in each of two or more
different species, irrespective of conserved gene order [32]. Conserved
synteny defines characteristics of ancestral chromosomes. This
approach has been shown to be especially informative when
integrating fish genome data, which show a high frequency of
lineage-specific intrachromosomal inversions.
In the present study we have developed the in silico analysis of
orthologous gene pairs in the form of a universal E-painting tool (Table
S1 in supplementary online material). For the four species to be
compared in this study the genes and their chromosomal assignment
were listed in an Excel spreadsheet. This enables us to order the genes
according to different principles. An ordering preference can be given to
the position of these genes on human chromosomes, or a preference can
be given to their order on pufferfish, chicken or zebrafish chromosomes
(Figure S1 in supplementary online material). This procedure reveals at
once the segments of conserved synteny in all the other species. When
ordered according to pufferfish chromosomes the respective segments
of common synteny in zebrafish, chicken and human are revealed.
Synteny can be assigned according to the species of choice, and the
segments of common synteny in the other species are indicated.
Therefore, this Excel database is highly informative and will be even
more informative if further genes and more species are included. As has
been successfully applied in the reconstructions of Naruse et al. [9] and
Woods et al. [11], only synteny conservation was considered, that is, the
positions of the respective genes on the same chromosome. Linkage
conservation, or conserved gene order, was neglected. In this way the
numerous and mostly lineage-specific intrachromosomal rearrangements by inversion are circumvented and the scenario of karyotype
evolution is made much clearer.
ARTICLE IN PRESS
Opinion
TRENDS in Genetics Vol.xx No.xx Monthxxxx
Table 2. Reconstruction of the tetrapod protokaryotype (TET)
Tetrapod
protochromosome
1
Chicken
chromosome
2, 9, 16
2
1, 24
3
3, 14
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
5, 10
4q, 22
1
17, Z
7
8, 28
6
18, 19, 27
4p
12
11
21, 23, 26, 32
13
20
15
Eutherian
chromosome [4]
3, 4, 5, 7, 8,
13, 17
3, 6, 9, 12,
15, X
1, 2, 5, 12,
19, 20
6, 9
2
7, 8
4, 11, 17
10
1
14
16
Xq
1, 3, X
18
1
4
19
21
Human
chromosome
3, 5, 6, 7, 8q,
10, 18
2p, 3, 21,
11, 13, 15, X
1, 2p, 6, 8, 7,
16p, 20
11, 14, 15
4, 8p
7, 12pq, 22
5, 9, 18
2q
1, 19p
10q
17
Xq
1, 3, X
16q, 19q
1
5
20
12q, 22q
Pufferfish
chromosome
6, 15, 8, 21
7, 16, 2, 3
2, 3, 10,
14, 17
5, 13, 10, 14
12, 18
13, 19
4, 12, 18
2, 3
1, 15
2, 17, 18
2, 3, 7, 16
1, 7
9, 11
5, 13
8, 21, 9, 11
1, 7
9, 11
12
large chromosomes TET 1–3, which are all found spread
on several human chromosomes remains questionable.
However, when the reconstruction is seen from the
perspective of the chicken genome, it only needs one
fusion of a microchromosome to a macrochromosome to
form both TET 2 and 3 (Table 2). (For the reconstruction of
TET 1, see Figure 3.)
The reconstruction reduces the TET protokaryotype to
nZ18 chromosomes. This protokaryotype includes large
chromosomes, such as TET 9 (HSA 1 and 19p), and small
chromosomes, for example, TET 18, which is made up of
the small segments from HSA 12q and 22q (EUT 21).
Reconstruction of the teleost protokaryotype
Next we deduced the protokaryotype of an ancestral
teleost fish that lived before the third and extra round of
whole-genome duplication [10,14]. Again, only synteny
Chicken
(GGA)
Pufferfish
(TNI)
Tetrapod
(TET)
1
Eutheria
(EUT)
13
19
6
7
8
Human
(HSA)
12
22
7
TRENDS in Genetics
Figure 1. Reconstruction of the tetrapod protochromosome TET 6. The association
of segments from HSA 12p/q and 22q is known from the eutherian protokaryotype
[2–6] and found in chicken on GGA 1. In pufferfish these associations are on the
paralogous chromosome pair TNI 13 and 19, which bears also a conserved segment
from HSA 7 as does chicken chromosome GGA 1. All three segments form the
protochromosome TET 6.
www.sciencedirect.com
3
segments with three or more genes in the sample were
considered. Genome data from pufferfish [10] and medaka
[9] provided most of the information.
The principle used to reconstruct the teleost protokaryotype is illustrated in Figure 2 (Table 2, and Table S2 in
supplementary online material). For simplicity, chromosomes are presented as boxes of the same size. Although
genes from a single pufferfish chromosome are usually
found spread on several zebrafish chromosomes, a
pairwise homology is evident. For instance, TNI 5 and
TNI 13 genes are each localized on DRE 7, 13, 18 and 25,
and TNI 6 and TNI 15 genes are each localized on DRE 2, 7
and 24. This organization is easily explained by the
independent evolution of the two chromosome duplicates
that followed after the extra round of whole-genome
duplication in pufferfish and zebrafish. The mapping
data from medaka confirm these reconstructions, which
lead to an ancestral teleost protokaryotype with nZ12
chromosomes. The ancestral teleost chromosomes were
numbered according to the size relations known from the
pufferfish genome; for example, protochromosome TEL 1
consists of the large TNI 2 and 3 chromosomes, which are
included in chromosomes TET 2, 3, 8 and 11 (Table 2),
implying that TEL 1 is a large chromosome. By contrast,
protochromosome TEL 12 consists of segments of TNI 6
and 15 and corresponds to the small chromosome OLA 20.
Similar reconstructions of the ancestral teleost protokaryotype with human included as outgroup species have
been put forward [9–11]. There is extensive overlap
between these different approaches. Jaillon et al. [10]
also arrived at a karyotype of nZ12 chromosomes in the
haploid state, but did not describe the smallest chromosome TEL 12, which is made up of TNI 6 and 15. Instead of
this, these authors divided the largest chromosome, our
TEL 1 made up of TNI 2 and 3, into two chromosomes.
Woods et al. [11] arrived at a karyotype of nZ11
chromosomes. They did not describe TEL 5, which is
made up of TNI 1 and 7 and corresponds to chromosome H
of Jaillon et al. [10]. Naruse et al. [9] compared medaka
with zebrafish and described our protochromosomes TEL
1, 2, 3, 7, 8 and 9. But the much smaller sample size of
genes and markers used in this comparison is responsible
for more discrepancies between the data of Naruse et al.
[9] and the other studies [10,11].
Reconstruction of the vertebrate protokaryotype
For the final reconstruction of the 450-My-old ancestral
vertebrate protokaryotype (VER) no outgroup species is
available to date. Two slightly different procedures, not
independent of each other, were followed.
To begin we went back to the original mapping data in
human, chicken, pufferfish and zebrafish as given in Table
S1 in supplementary online material. The map positions of
w1500 genes were available in all four species and the
reconstruction is based on this data set. The genes and
their chromosomal assignment were listed in an Excel
spreadsheet as described in detail in Box 1. By ordering
these genes by E-painting according to their chromosomal
assignment, it became evident that when the first
preference is given to the chromosome position in
pufferfish, and a second minor preference is given to
ARTICLE IN PRESS
Opinion
4
7
13
18
25
7
13
18
25
3
6
4
6
5
6
13
13
7
4
13
17
20
23
22
24
19
11
2
10
TRENDS in Genetics Vol.xx No.xx Monthxxxx
17
20
1
13
17
1
3
5
13
14
22
24
15
19
1
8
10
21
14
17
2
18
20
4
1
5
10
21
5
8
21
1
3
9
12
1
3
6
9
12
6
8
11
23
6
8
11
23
5
14
21
5
14
21
16
19
16
19
5
10
15
24
2
5
10
15
2
6
8
20
22
2
6
8
20
22
2
7
24
2
7
24
Zebrafish
(DRE)
12
9
12
19
21
2
8
19
21
5
7
5
7
4
10
10
14
11
16
11
16
13
14
13
14
4
4
17
20
20
Medaka
(OLA)
15
Green
spotted
pufferfish
(TNI)
4
12
2
6
3
3
1
11
4
9
11
1
7
8
21
7
16
1
15
6
3
5
8
9
10
12
Teleost
protokaryotype
(TEL)
5
6
7
8
9
10
Vertebrate
protokaryotype
(VER)
TRENDS in Genetics
Figure 2. The reconstruction of the teleost and ancestral vertebrate protokaryotype from the combined genome data of Danio rerio (DRE), Oryzias latipes (OLA) and Tetraodon
nigrovirides (TNI). From teleosts to the extant fish species a whole-genome duplication has taken place [10,14]. Therefore, each ancestral teleost chromosome is represented
by a pair of paralogous pufferfish chromosomes. Genes from a pair of pufferfish chromosomes are found spread on defined pairs of medaka and zebrafish chromosome sets
(the respective chromosomes are indicated by their numbering).
chicken, the genome conservation between these four
genomes is most apparent, that is, the largest segments
with shared synteny are revealed (Figure S1 in supplementary online material). This observation is crucial
for the reconstructions proposed here. One has to be aware
that this procedure introduced a bias towards the fish
genomes. This is justified, because from the genome data
of the four species compared in this study the pufferfish
genome is the most conserved. In some way the pufferfish
genome served as an ‘index fossil genome’, as did the
aardvark karyotype for the reconstruction of the ancestral
eutherian protokaryotype [4]. Therefore, the paralogous
pairs of duplicated pufferfish chromosomes, which correspond to single TEL protochromosomes (Figure 2), are key
to reconstructing the vertebrate protokaryotype.
The other slightly different but not independent
procedure is shown here for the reconstruction of the
protochromosome VER 7 (Figure 3). The respective genes
reside on the duplicated pair of pufferfish chromosomes
TNI 8 and 21 and zebrafish chromosomes DRE 16 and 19.
In human these genes are spread on five different
chromosomes, HSA 1, 3, 6, 7 and 8, but in chicken these
genes are concentrated mostly on chromosome GGA 2
with one further syntenic segment on microchromosome
23. For this example the VER protochromosome reconwww.sciencedirect.com
struction is evident at once, when the intermediate states
of the teleost and tetrapod protochromosomes are
combined into a common scheme (Figure 3). This example
is informative, because it illustrates the advantage of the
stepwise procedure during the reconstruction described
here. Both the teleost and tetrapod protokaryotypes were
assembled with the help of information from an outgroup
species. These intermediate protokaryotypes from O
300 Mya each prove to be already so similar that the
reconstruction of the common vertebrate genome is
possible in spite of the lack of information from an
outgroup species.
One or the other reconstruction could be questionable.
Two alternative reconstructions are possible for VER 6. In
the first, the two TET chromosomes 12 and 16 are not
fused in the VER protokaryotype (Table 3f and Figure S2
in supplementary online material) but remain as separate
VER protochromosomes. Accordingly, fusion of these
chromosomes occurred only in the teleost lineage. Consequently this VER protokaryotype would consist of 12
chromosomes. In the second scenario, TET 12 and 16 arise
by fission of VER 6, as is favored in the version proposed
here. There is independent evidence for the second
scenario because the Xenopus tropicalis scaffold_105
contains genes from HSA Xq and 5 (Table S3l in
ARTICLE IN PRESS
Opinion
TRENDS in Genetics Vol.xx No.xx Monthxxxx
5
Chicken
Pufferfish
23
Tetrapod
8
21
Vertebrate
Teleost
2
15
Zebrafish
Human
8
7
Pufferfish
8
16
19
1
Zebrafish Chicken
16
2
Human
7
21
16
2
7
21
16
2
8
8
8
19
2
8
19
2
7
8
19
2
6
21
19
2
3
21
19
2
8
21
19
23
1
1
3
6
7
8
TRENDS in Genetics
Figure 3. Reconstruction of the protochromosome VER 7. Two slightly different procedures were followed. In the first, the original mapping data (from Table S1 in
supplementary online material) were evaluated by E-painting (long black arrows). In the second, the reconstruction is at once evident by pure inspection, when the teleost
and tetrapod protochromosomes, TEL 8 and TET 1, are apposed (small gray arrows). These intermediate protochromosomes were each reconstructed with information from
an outgroup species and already represent states from O300 Mya. The segments of conserved synteny that are informative for this reconstruction are color-coded as
indicated in the table.
supplementary online material). This can be taken as
independent evidence that TET 12 and 16 are fused in the
ancestral vertebrate genome.
Overall, only three segments containing 12 genes (from
a total of 1500 genes compared in this study) could not be
directly assigned (Table S4 in supplementary online
material). A vertebrate protokaryotype with 11 chromosome pairs is therefore proposed.
Comparison of the vertebrate protokaryotype with the
teleost and tetrapod karyotypes
In most cases the teleost protochromosomes were shown to
represent ancestral vertebrate protochromosomes
(Figures 2 and 4). However, some fissions and fusions
must have occurred. The largest chromosome, TEL 1, is
composed of genes from TNI 2 and 3 and is the fusion
product of the protochromosomes VER 4 and 11 (Figure 2).
In zebrafish, chicken and human the genes of these two
protochromosomes are separated on different sets of
chromosomes (Table S3d,k in supplementary online
material). In the proposal of Jaillon et al. [10] these
genes were assigned to the two different protochromosomes C and D.
Another complication brings in VER 2, which is
separated into TEL 7 and 11, as is evident from their
distribution on two different sets of chromosomes in
www.sciencedirect.com
zebrafish (Figure 2, and Table S3b in supplementary
online material). This time in pufferfish the separation is
not as evident, because genes from TNI 13 are found on
both TEL 7 and 11. A more complicated situation is seen
for the fission of VER 1 and 3, resulting in three teleost
protochromosomes, TEL 2, 4 and 6 (Figure 2; and Table
S3a,c in supplementary online material). Most parts of
VER 1 are identical with TEL 2 and consist of genes from
TNI 10 and 14. A smaller segment made up of TNI 17
genes and some TNI 18 genes is split away from VER 1
and fused with another small segment from VER 3, which
also contains TNI 18 genes and some TNI 20 genes. The
fusion product of both these small segments results in
TEL 4. The remaining larger segment of VER 3 is made up
of TNI 4 and 12 genes, which are found in the teleost
karyotype as TEL 6. TEL 2, 4 and 6 correspond to the
protochromosomes J, B and A in the proposal of Jaillon et
al. [10].
Concluding remarks
There are several initiatives underway to use the genome
data from mammalian and vertebrate species to reconstruct by in silico analysis an ancestral founder genome
[10,11,15–17]. An approach similar to that proposed here
was taken by Jaillon et al. [10]. Data from 6684 genes with
proven orthology in pufferfish and human were combined
ARTICLE IN PRESS
Opinion
6
TRENDS in Genetics Vol.xx No.xx Monthxxxx
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
X
100 My
Eutheria
1
2
4
3
5
6
180 My
Human
(Homo sapiens, HSA)
Theria
7
9
8
10
11
12
Marsupialia
210 My
13
14
15
16
17
Mammalia
18
310 My
Synapsidia
Tetrapod
protokaryotype
(TET)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
26
27
28
32
Z
Protheria
Tetrapoda
3
Diapsidia
2
Sarcopterygians
1
4
Aves
450 My
6
7
8
9
10
Chicken
(Gallus gallus, GGA)
Actinopterygians
5
11
Vertebrate
protokaryotype
(VER)
Zebrafish
(Danio rerio, DRE)
Medaka
(Oryzias latipes, OLA)
3R
Atherinomorpha
Teleostei
280–160 My
1
2
3
4
5
6
7
8
9
10
11
Teleost
protokaryotype
(TEL)
12
Percomorpha
80–60 My
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
Pufferfish
(Tetraodon nigrovirides, TNI)
TRENDS in Genetics
www.sciencedirect.com
ARTICLE IN PRESS
Opinion
4
92
TRENDS in Genetics Vol.xx No.xx Monthxxxx
VER
18
47
41
65
TET
TEL
90
DRE
15
15
TNI
GGA
40
HSA
TRENDS in Genetics
Figure 5. An analysis of the number of interchromosomal rearrangements using
GRIMM. To use GRIMM [18], synteny blocks were formed for each pair of genomes
considered in this study. The synteny blocks were numbered consecutively and
entered into the online version of GRIMM. In the source genome (which is always
the ancestral genome), numbers were in ascending order, separated by
chromosome delimiters. In the destination genome, within each chromosome
synteny blocks were also in ascending order. In the specific proposal of an optimal
rearrangement scenario, we subtracted the number of reversals (inversions) from
the total number of operations, thus only counting the number of fissions, fusions
and translocations between chromosomes. The numbers are given next to the
arrows.
to reconstruct a protokaryotype with 12 chromosome
pairs. Similar to the procedure used here, the genes
were assembled in synteny segments, and only 110
segments with the most complete conserved synteny
were used for the reconstruction. However, 20 of these
110 segments were left unassigned in this study.
Because of the availability of the chicken genome the
reconstruction presented here could be performed in a
stepwise manner. In a first step the ancestral tetrapod and
teleost protokaryotypes were reconstructed. They served
as intermediates for the subsequent reconstruction of a
more plausible ancestral vertebrate protokaryotype with
11 protochromosomes (Figures 2 and 4). We must
emphasize that currently it is not possible to determine
where this putative vertebrate protokaryotype is positioned exactly between teleosts and tetrapods. As is
evident from Figure 5 it seems to be biased towards the
fish genomes. On the basis of the conserved segments
considered in our data set the number of interchromosomal rearrangements (fusions, fissions and translocations)
was analyzed with the GRIMM software (http://www.cse.
ucsd.edu/groups/bioinformatics/GRIMM/) [18]. The transition from the ancestral vertebrate to the tetrapod
protokaryotype requires far more rearrangements than
the transition to the teleost protokaryotype. Furthermore,
the similarity between the chicken and teleost proteogenome is apparent, which proved to be highly informative for
the reconstructions proposed during this study. Many
more rearrangements are necessary for the transition
from the tetrapod to the human karyotype. Thus the
human karyotype can no longer be considered to be the
most conserved, as was assumed when the eutherian
founder karyotype was reconstructed [2–6]. Indeed, from
the karyotypes of the three species shown in Figure 4
(pufferfish, chicken, human) the human karyotype is the
7
most rearranged one. This is apparent, for instance, for
the sex chromosomes. The avian Z chromosome is made up
of a single syntenic segment of one protochromosome
(VER 3), whereas the mammalian X chromosome is a
conglomeration of segments from three protochromosomes
[13]. Nevertheless, four human chromosomes (9, 11, 14
and 18) each represent a single segment of a vertebrate
protochromosome (Figure 4). These syntenies have been
conserved for O450 My. The consequences and significance of the conservation of these syntenic relationships
are currently unknown.
The summary of the comparative mapping data in
Figure 4 also shows that in fish and in birds the ancestral
syntenies are best conserved and least interrupted by
interchromosomal translocations. Following the extra
round of whole-genome duplication in teleost fish a process
of deletion, subfunctionalization and neofunctionalization of
complements of the duplicated genes took place – a process
termed divergent resolution [11] – which facilitated
speciation. Today, the teleost fish have diverged into
w20 000 different species, making them the most speciesrich order of vertebrates. However, they show a highly
conserved karyotype with a uniform haploid chromosome
number of nZ24–25. In birds, there have been many fissions
into smaller segments, known as microchromosomes. But
the bird karyotype turns out to be highly conserved, with
proven homology down to turtle [19], the respective lines
separating from each other 210 Mya. From their karyotypes
the green spotted pufferfish and chicken are indeed ‘living
fossils’ [6], and this has been enormously helpful for the
karyotype reconstruction presented here (Figure 3). Typical
karyotype evolution is shown in the land vertebrates, where
diploid chromosome numbers vary from six in the Indian
muntjac [20] to 102 in the red viscacha rat [21] and there
have been many interchromosomal exchanges by translocation. Only land vertebrates can be effectively isolated, when
living on different continents or separated by geographic
barriers (e.g. the Indian and Chinese muntjacs, with six and
42 chromosomes, respectively, are separated by the Himalayan mountain range). It is suggested that karyotype
evolution is more prominent during allopatric speciation
events, when species diverge with local isolation.
Supplementary data
Supplementary data associated with this article can be
found at doi:10.1016/j.tig.2006.02.008
References
1 Hedges, S.B. and Kumar, S. (2002) Vertebrate genomes compared.
Science 297, 1283–1285
2 Chowdhary, B.P. et al. (1998) Emerging patterns of comparative
genome organization in some mammalian species as revealed by ZooFISH. Genome Res. 8, 577–589
3 Murphy, W.J. et al. (2001) Evolution of mammalian genome
organization inferred from comparative gene mapping. Genome Biol.
DOI:10.1186/gb-2001-2-6-reviews0005 (http://genomebiology.com/
2001/2/6/reviews/0005)
Figure 4. A phylogenetic tree of the extant species compared during this study and the protokaryotypes reconstructed during this study are shown. The color code for the
chromosomes is the same as in Figure 2. The third and extra round of whole-genome duplication in euteleost fish (3R) is indicated.
www.sciencedirect.com
ARTICLE IN PRESS
8
Opinion
TRENDS in Genetics Vol.xx No.xx Monthxxxx
4 Yang, F. et al. (2003) Reciprocal chromosome painting among human,
aardvark and elephant (superorder Afrotheria) reveals the likely
eutherian ancestral karyotype. Proc. Natl. Acad. Sci. U. S. A. 100,
1062–1066
5 Richard, F. et al. (2003) Reconstruction of the ancestral karyotype of
eutherian mammals. Chromosome Res. 11, 605–618
6 Froenicke, L. (2005) Origins of primate chromosomes as delineated by
Zoo-FISH and alignments of human and mouse draft sequences.
Cytogenet. Genome Res. 108, 122–138
7 Amores, A. et al. (1998) Zebrafish hox clusters and vertebrate genome
evolution. Science 282, 1711–1714
8 Woods, I.G. et al. (2000) A comparative map of the zebrafish genome.
Genome Res. 10, 1903–1914
9 Naruse, K. et al. (2004) A medaka gene map: The trace of ancestral
vertebrate proto-chromosomes revealed by comparative gene mapping. Genome Res. 14, 820–828
10 Jaillon, O. et al. (2004) Genome duplication in the teleost fish
Tetraodon nigrovirides reveals the early vertebrate proto-karyotype.
Nature 431, 946–957
11 Woods, I.G. et al. (2005) The zebrafish gene map defines ancestral
vertebrate chromosomes. Genome Res. 15, 1307–1314
12 International Chicken Genome Sequencing Consortium. (2004)
Sequence and comparative analysis of the chicken genome provide
unique perspectives on vertebrate evolution. Nature 432, 695–716
13 Kohn, M. et al. (2004) Wide genome comparisons reveal the origins of
the human X chromosome. Trends Genet. 20, 598–603
14 Vandepoele, K. et al. (2004) Major events in the genome evolution of
vertebrates: Paranome age and size differ considerably between rayfinned fishes and land vertebrates. Proc. Natl. Acad. Sci. U. S. A. 101,
1638–1643
15 Blanchette, M. et al. (2004) Reconstructing large regions of an
ancestral mammalian genome in silico. Genome Res. 14, 2412–2423
16 Bourque, G. et al. (2004) Reconstructing the genomic architecture of
ancestral mammals: Lessons from human, mouse and rat genomes.
Genome Res. 14, 507–514
17 Bourque, G. et al. (2005) Comparative architectures of mammalian
and chicken genomes reveal highly variable rates of genomic
rearrangements across different lineages. Genome Res. 15, 98–110
18 Pevzner, P. and Tesler, G. (2003) Genome rearrangements in
mammalian evolution: Lessons from human and mouse genomes.
Genome Res. 13, 37–45
www.sciencedirect.com
19 Matsuda, Y. et al. (2005) Highly conserved linkage homology between
birds and turtles: Bird and turtle chromosomes are precise counterparts of each other. Chromosome Res. 13, 601–615
20 Wurster, D.H. and Benirschke, K. (1970) Indian muntjac, Muntiacus
muntjak: A deer with a low diploid chromosome number. Science 168,
1364–1366
21 Contreras, L.C. et al. (1990) The largest known chromosome number
for a mammal, in a South American desert rodent. Experientia 46,
506–508
22 Dutrillaux, B. (1979) Chromosomal evolution in primates: Tentative
phylogeny from Microcebus murinus (Prosimian) to man. Hum. Genet.
48, 251–314
23 O’Brien, St.J. and Nash, W.G. (1982) Genetic mapping in mammals:
Chromosome map of domestic cat. Science 216, 257–265
24 von Kiel, K. et al. (1985) Early replication banding reveals a strongly
conserved functional pattern in mammalian chromosomes. Chromosoma 93, 69–76
25 Sawyer, J.R. and Hozier, J.C. (1986) High resolution of mouse
chromosomes: Banding conservation between mouse and man.
Science 232, 1632–1635
26 Nadeau, J.H. and Taylor, A.T. (1984) Lengths of chromosomal
segments conserved since divergence of man and mouse. Proc. Natl.
Acad. Sci. U. S. A. 81, 814–818
27 Scherthan, H. et al. (1994) Comparative chromosome painting
discloses homologous segments in distantly related mammals. Nat.
Genet. 6, 342–347
28 Glas, R. et al. (1999) Cross-species chromosome painting between
human and marsupial directly demonstrates the ancient region of the
mammalian X. Mamm Genome 10, 1115–1116
29 Rettenberger, G. et al. (1995) Visualization of the conservation of
synteny between humans and pigs by heterologous chromosomal
painting. Genomics 26, 372–378
30 Rettenberger, G. et al. (1995) ZOO-FISH analysis: Cat and human
karyotypes closely resemble the putative ancestral mammalian
karyotype. Chromosome Res. 3, 479–486
31 Wienberg, J. (2004) The evolution of eutherian chromosomes. Curr.
Opin. Genet. Dev. 14, 657–666
32 Ehrlich et al. (1997) Synteny conservation and chromosome
rearrangements during mammalian evolution. Genetics 147,
189–296