Vol.2, No.10, 1104-1112 (2010) Natural Science
http://dx.doi.org/10.4236/ns.2010.210137
Evolution based on genome structure: the “diagonal
genome universe”
Kenji Sorimachi
Educational Support Center, Dokkyo Medical University, Mibu, Japan;
Received 13 July 2010; revised 16 August 2010; accepted 20 August 2010.
ABSTRACT
The ratios of amino acid to the total amino acids
and those of nucleotides to the total nucleotides
in genes or genomes are suitable indexes to
compare whole gene or genome characteristics
based on the large number of nucleotides rather
than their sequences. As these ratios are strictly
calculated from nucleotide sequences, the val-
ues are independent of experimental errors. In
the present mini-review, the following themes
are approached according to the ratios of amino
acids and nucleotides to their total numbers in
the genome: prebiotic evolution, the chrono-
logical precedence of protein and codon forma-
tions, genome evolution, Chargaff’s second pa-
rity rule, and the origins of life. Amino acid for-
mation might have initially occurred during pre-
biotic evolution, the “amino acid world”, and
amino acid polymerization might chronologically
precede codon formation at the end of prebiotic
evolution. All nucleotide alterations occurred
synchronously over the genome during biolo-
gical evolution. After establishing primitive lives,
all nucleotide alterations have been governed
by linear formulae in nuclear and organelle ge-
nomes consisting of the double-stranded DNA.
When the four nucleotide contents against each
individual nucleotide content in organelles are
expressed by four linear regression lines rep-
resenting the diagonal lines of a 0.5 square—the
“Diagonal Genome Universe”, evolution obeys
Chargaff’s second parity rule. The fact that linear
regression lines intersect at a single point su-
ggests that all species originated from a single
life source.
Keywords: Evolution (Prebiotic and Biological);
Genome; Origin of Life; Chargaff’s Parity Rules;
Organelle; Double- and Single-Strand DNA; Amino
Acid; Nucleotide; Linear Formula
1. INTRODUCTION
“The Origin of Species”, written from the observa-
tions Charles Darwin made during his voyage on the
HMS Beagle, was published in 1859. According to Dar-
win’s theory, all species have a common ancestor and a
single origin. During the same period when Darwin
wrote, Gregor Mendel reported “Mendel’s laws” that
accorded with his observations of the inheritance of cer-
tain traits in pea plants. The former and latter are based
on inter- and intra-species phenotypic expression simi-
larities, respectively, and based on long and compara-
tively short lifespans, respectively. In general, interspe-
cies changes are thought of as “evolution”, while intras-
pecies changes are “genetics”. These two great concepts
were established by two scientists without any knowl-
edge of DNA; although nowadays it is well known that
almost all traits of organisms are based on gene charac-
teristics. After almost a century, Oswald Avery and co-
workers reported in 1944 that DNA is the material of
genes and chromosomes [1].
Although it was clarified by Avery’s group that DNA
is important material for the inheritance of certain traits
in organisms, the structure of DNA, which has an ex-
tremely large molecular weight, was completely un-
known and, therefore, the mechanisms of trait inheri-
tance were also unknown. On the other hand, Ervin
Chargaff reported in 1950 that nuclear DNA consists of
four nucleotides, and that the nucleotide content rela-
tionships are: G = C, A = T, and [(G + A) = (C + T)].
This rule is well known as Chargaff’s first parity rule [2].
He and his colleagues later discovered that these rela-
tionships are applicable to the single DNA strand, and
this is Chargaff’s second parity rule [3]. After Chargaff’s
first parity rule, another great scientific discovery was
reported in 1953 by Watson and Crick [4]. Namely, that
the DNA structure is double-stranded, and C vs. G and T
vs. A pairs are formed between two DNA strands. These
two base-pair formations can consistently explain the
inheritance of genetic traits from generation to genera-
tion. Even though this DNA structure can explain Char-

K. Sorimachi / Natural Science 2 (2010) 1104-1112
1105
gaff’s first parity rule, the second parity rule based on
the single DNA strand cannot be explained by the dou-
ble-stranded DNA model. Chargaff’s parity rules were
originally discovered from a single species and recently
it was shown that Chargaff’s second parity rule is appli-
cable to interspecies evolution [5]. Nuclear nucleotide
relationships were clearly expressed by linear regression
lines with extremely high regression coefficients among
various species. The single DNA strand which forms the
double-stranded DNA has been shown, based on the
huge amount of genomic data, to obey Chargaff’s second
parity rule [5]. Furthermore, as nucleotide relationships
in the coding region are also expressed by linear formu-
lae, 64 codons can be correctly estimated from just one
nucleotide content [6].
Molecular clock research—using amino acid or nu-
cleotide replacement rates [7] has enabled scientists to
create a phylogenetic tree representing biological evolu-
tion [8-12]. However, as this method is based on se-
quences of certain genes among various organisms, we
cannot investigate organisms without these genes. Fur-
thermore, this method does not fit the research on whole
genomes consisting of an extremely large number of nu-
cleotides. On the other hand, by using the ratios of nu-
cleotides to the total nucleotides or amino acids to the
total amino acids after normalization, it is possible to
compare certain characteristics among different genes or
genomes. As this method is independent not only of sam-
ple size but also of species, the method can be recom-
mended for comparative studies on genomes consisting
of extremely large and different numbers of nucleotides.
Using normalized values, each organism can be repre-
sented by simple indexes that represent whole genome
characteristics. In fact, this method has been applied to
genome research and its usefulness proven by using
graphic representation or a diagram approach [13]. Visu-
alization to study complicated biological systems can
provide an intuitive picture and provide useful insights
[14-16].
2. PREBIOTIC EVOLUTION
We have no evidence of “the origin of life”, although
there are two distinct ideas: one being that the origin of
life was on the primitive Earth and the other that it was
derived from another planet (extraterrestrial universe).
Based on either idea, “the origin of life” did indeed oc-
cur somewhere after the “Big Bang”. Many physical and
chemical reactions occurred during prebiotic evolution
and substantial materials for the formation of primitive
life may have accumulated during this period. For ex-
ample, Miller’s experiment showed that amino acids
could be formed by electric discharges in the atmosphere
on the primitive Earth [17]. Furthermore, amino acids
have been detected in meteorites [18,19]. Accumulation
of amino acids might lead to the appearance of amino
acid polymers or peptides without the codon system. As
well, certain polymers or peptides might have enzyme
activity that accelerates amino acid polymerization,
which is reported as being able to occur in soil via heat
without either enzyme or codon system [20]. The pro-
duction of enzymes led to the accumulation of substan-
tial materials for “the origin of life”.
Amino acid polymers formed chemically might reflect
the amino acid concentrations on the primitive Earth.
Sueoka initially investigated the cellular amino acid com-
position of bacteria [21] and then we independently ex-
amined, not only bacterial but also plant and animal cells
[22,23]. Based on amino acid composition patterns, it is
clearly shown that cellular amino acid composition is
very similar among organisms from bacteria to Homo
sapiens [22], as shown in Figure 1. This fact led us to
conclude that primitive life forms might have similar
amino acid composition presumed from present organ-
isms [24]. Based on an amino acid pattern (Figure 1),
the ratios of the amino acids that have ultraviolet (UV)
absorbance (i.e., phenylalanine, tyrosine and tryptophan)
to the total cellular amino acids are very low. To explain
this fact, the strong irradiation of UV light might have
induced their decomposition and reduced their concen-
tration on the primitive Earth. However, the contents of
glycine and alanine, which were formed easily in Miller’s
experiment, are relatively high [22]. In addition, the
contents of hydrophobic amino acids such as leucine,
isoleucine, alanine and valine are comparatively high.
These amino acids might contribute to self-aggregation
of amino acid polymers to form the “coacervate” pro-
posed by Aleksandr Oparin through their hydrophobicity
under low polymer concentrations.
The basic pattern of cellular amino acid compositions,
E. coli
H
. sapiens
Figure 1. Cellular amino acid compositions of Escherichia coli
and Homo sapiens on radar charts. Amino acid compositions
are expressed as the percentage of total amino acids. Gln and
Asn are combined with Glu and Asp, respectively, because the
former two are converted to the latter two during hydrolysis
[22].

K. Sorimachi / Natural Science 2 (2010) 1104-1112
1106
the “star-shape”, is formed with characteristic differen-
ces in amino acid contents. The fact that the basic pattern
is conserved from bacteria to Homo sapiens, suggests
that the pattern is extremely important for organisms on
earth. It would be quite interesting to evaluate whether
this “star-shape” is conserved on other planets with life
in the future, if any is found.
3. CHRONOLOGICAL PRECEDENCE OF
PROTEIN AND CODON FORMATION
Evolutionarily, it remains unclear whether protein
formation preceded codon formation or codon formation
preceded that of protein. However, it should be possible
to judge which theory is better at explaining this theme,
though it might be impossible to design a complete ex-
periment. Amino acids, which are monomers of proteins
or peptides, were easily formed by electric discharges in
an atmosphere presumed from the primitive Earth [17].
In addition, their polymerizations took place in clay
without the codon system [20] and certain products, pro-
tein or peptides, might possess an enzymatic activity
which accelerates amino acid polymerizations. Eventu-
ally, these processes might produce various biomaterials,
such as amino acids and their polymers, whereas the
production of nucleic acids whose formation requires
nitrogenous base and sugar synthesis, their coupling and
condensation, might be difficult in the primitive Earth.
Although the so-called “RNA world” has been proposed
[25], the possibility of the accumulation of RNA, which
has UV absorbance at around 250 nm, might be very low
under the strong UV irradiation present on the primitive
Earth. In general, the composition of polymerization
products depends on monomer concentrations and re-
flects their free concentration on the primitive Earth, as
mentioned above.
Simulation analysis based on random choice of amino
acids showed consistent results in which amino acids
were polymerized randomly without the codon system
[26]. The amino acid composition obtained by a random
choice of amino acids from the amino acid pool reflects
each amino acid concentration in the pool. After estab-
lishing the codon system, the sequence information has
been conserved until now. On the other hand, polymeri-
zation of nucleotides based on the random choice of nu-
cleotides does not yield functional proteins [26]. Even
when the codon table is considered for nucleotide poly-
mer formation, the amino acid composition depends on
the original four nucleotide contents. The nucleotide
compositions differ between the coding and non-coding
regions, while they are quite similar among the coding or
non-coding regions [6,27,28]. Thus, the coding frag-
ments that possessed the same characteristics might be
combined through the non-coding fragments with each
other like a “patchwork” in the whole genome. This
structural model fits the proposed model that the forma-
tion of proteins might have preceded codon formation.
At present, even though there is no experimental evi-
dence for the process of how sequence information of
amino acid polymers transfers to codon formation during
a codon establishing period, protein formation might
precede codon formation based on the present genome
structure [26].
4. HOMOGENEITY OF GENOME
STRUCTURE
The amino acid sequences of proteins differ, not only
among different genes, but also among different species,
and naturally, their nucleotide sequences also differ. As
these differences relate to evolutionary time [7], this con-
cept has been applied to draw phylogenetic trees [8-12].
Using the ratios of each amino acid to the total amino
acids, or those of each nucleotide to the total nucleotides,
it is possible to compare samples independently regard-
ing size, kind and species, even though DNA has an ex-
tremely large number of nucleotides.
The method to analyze nucleotide sequences was es-
tablished by Frederic Sanger [29], and Allan Maxam and
Walter Gilbert [30], and the first complete genome ana-
lysis was carried out on Haemophilus influenzae in 1995
[31]. Then the complete genome analyses of species such
as human (Homo sapiens) [32,33], mouse (Mus muscu-
lus) [34], rat (Rattus norvegicus) [35] and sea urchin
(Strongylocentrotus purpuratus) [36] were carried out
within the last two decades. Several species of Archaea
were also examined and their complete genomes were
determined. Based on these intriguing results, the amino
acid compositions were presumed from the complete
genomes. Surprisingly, the cellular amino acid composi-
tions obtained from the whole cell lysates resemble those
presumed from the complete genome [24], although the
former is based on a different protein mixture and the
latter is based on a different gene mixture. The coinci-
dence of these two results in our study was not explain-
able until the genomic structure was fully understood
[37].
The full sequence of mouse cDNA was determined in
2001 [38]. The total number of mouse cDNAs includes
10,465 genes and was divided into two equal parts and
the amino acid compositions presumed from the first 5,
10, 50, 100, 500, 1,000 and 5,232 genes, according to
the order listed in the data table, were compared between
the two parts and within the same parts (Figure 2). The
amino acid compositions of gene assemblies resembled
those presumed from the complete genome. Of course,

K. Sorimachi / Natural Science 2 (2010) 1104-1112
1107
Asp Glu
Ser
Gly
His
Arg
Thr
Val
Met
Phe
Lys
Tyr Pro
Complete
Ala
Leu
Cys
Ile
Figure 2. Amino acid compositions. Computational amino acid
sequences (10,465) of FANTOM clones were divided into two
equal parts; first (red) and latter (green) halves. In both parts,
the first 5, 10, 50, 100, 500 and 1,000 genes were used for
analyses of amino acid compositions for the units. The num-
bers of genes were 5,232 and 5, 233 in the first and second
halves, respectively. The left side graph shows the amino acid
composition based on 10,465 genes [38].
the amino acid compositions presumed from genes differ
among various genes. Therefore, the genome structure is
constructed homogeneously with certain similar units that
encode similar amino acid compositions. The consistent
result was obtained from the complete Archaeal genome
(Methanobacterium thermoautotrophicum) [39], as shown
in Figure 3.
When the amino acid composition presumed from the
complete genome is expressed by the radar chart, the
amino acid composition patterns based on a small seg-
ment, encoding 3,000-7,000 amino acid residues, repre-
sent the pattern based on the complete genome, as shown
in Figures 2 and 3. The consistent result was obtained
using the nucleotide composition [40] as well as amino
acid composition of the Saccharomyces cerevisiae ge-
nome [37]. Additionally, the genome structure resembles
the appearance of a “pearl necklace” (Figure 4). Based
on this model, the genome is constructed with almost the
same putative small units, encoding 3,000-7,000 amino
acid residues, over the entire genome. This fact indicates
that all nucleotide alterations occurred synchronously
over the genome. In addition, based on this fact, the co-
incidence between the cellular amino acid composition
Figure 3. Radar charts of amino acid compositions calculated
from various units of the complete genome of Methanobacte-
rium thermoautotrophicum. A, the complete M. thermoauto-
trophicum genome consisting of 1,869 protein genes [39] was
divided into 10 or 20 units. Ten units (1-10); based on 186 and
195 genes, half size units (1-H- 9-H); based on 93 genes, single
genes (1-F-9-F); based on the first single gene of each unit.
Glutamine and asparagine were calculated as glutamic acid and
aspartic acid, respectively, and tryptophan (< 1%) was omitted
in the radar charts [22].
Figure 4. Model for homogeneous genome structure: a “pearl
necklace” model.
obtained from cell lysates and that presumed from the
complete genomes can be explained because each gene
characteristics are cancelled in certain units in both dif-
ferent analytical systems. The genome homogeneity makes
it possible to characterize the genome by the ratios of
nucleotide to the total nucleotides and/or those of amino
acid values. In fact, bacteria [41] and other organisms
such as Archaea and eukaryotes [42] were classified based
on these values. Organisms were classified into “GC-type
equal to E-type” and “AT-type equal to S-type” repre-
sented by high G or C (low T or A), and high A or T (low
G or C) contents, respectively, at every third codon posi-
tion [42]. Similar conclusion was obtained from research
that examined the content of G + C in a large number of
genes [43]. Bacterial classification was carried out by

K. Sorimachi / Natural Science 2 (2010) 1104-1112
1108
another method with similar results [44].
5. GENOME EVOLUTION
All organism’s DNA consists of four nucleotides such
as G, C, T and A, and it is possible to simulate their con-
tents by a random choice of certain numbers [45]. In
addition, the relationships of the four nucleotide contents
can be mathematically expressed by linear formulae
whether or not the four values correlate to each other.
Based on the random choice of nucleotide contents, their
relationships are heteroskedastic, although nucleotide
content distributions are homogeneous [45]. On the other
hand, for example, when plotting four nucleotide con-
tents against certain nucleotide content in the complete
chloroplast genome, their relationships were expressed
by four linear regression lines with high regression coef-
ficients [28], as shown in Figure 5. The lines G and C
overlap, and the lines T and A overlap. This indicates
that G = C and T = A in chloroplast DNA. Thus, chloro-
plast genome evolution is governed by Chargaff’s sec-
ond parity rule. Plant mitochondrial evolution was also
governed by this rule, while animal mitochondrial evo-
lution deviated from the rule [28]. These organelles were
incorporated into only eukaryotes, which appeared evo-
lutionarily later than bacteria. The contents of G or C
were less than 0.25 and those of A or T were more than
0.25 [28], as shown in Figure 5. Thus, nucleotide con-
tents are biased in organelle DNA because of a shorter
evolutionary period compared with nuclear DNA.
6. CHARGAFF’S PARITY RULES
Chargaff’s first parity rule was obtained experimen-
tally in 1950 and the rule represents intraspecies: G = C,
A = T and [(G + A) = (C + T)]. Nowadays we know that
nuclear DNA structure is double-stranded [4] and the
first parity rule is easily understandable. However, the
0.00
0.10
0.20
0.30
0.40
0.50
0.00 0.05 0.100.15 0.200.25
Nucleotide Content
C Content
Figure 5. Nucleotide content relationships in chloroplasts.
Four nucleotide contents were expressed by C content. Pink
squares, C; blue diamonds, G; red triangles, T and green trian-
gles, A. This figure has been presented in Natural Science, 2(5);
519-525, 2010 and reproduced with permission.
second parity rule, which is applicable to the single DNA
strands forming the double-stranded DNA, has been an
enigma of how to make the base pairs in the single DNA
strand since being published in 1968 [3]. Recently, this
puzzle has been solved mathematically [46] based on
genome structure homogeneity [37,40] and similarity
between the forward and reverse strands [6]. To solve
this puzzle, however, the double-stranded structure was
necessary [46], as shown in Figure 6. This fact indicates
that the genome structure might be double-stranded at the
stage of primitive life. Both rules are intraspecies rules.
Mitchell and Bridge examined a large number of
complete genomes to determine whether Chargaff’s se-
cond parity rule was applicable to interspecies relation-
ships [5] and concluded that only the single DNA strand
forming the double-stranded DNA is applicable to the
second parity rule [5]. This fact indicates that Chargaff’s
second parity rule is clearly correlated to biological evo-
lution. In addition, although codon evolution with- in the
coding region is expressed by a linear formula, it devi-
ates from Chargaff’s second parity rule [6]. However,
when plotting nucleotide contents in the coding or non-
coding region agafinst nucleotide content in the com-
plete single DNA strand, genome evolution obeys Char-
gaff’s second parity rule [28], as shown in Figure 7.
Nucleotide content relationships in the coding or non-
coding regions against the nucleotide content in the com-
plete single DNA strand between chloroplast and plant
mitochondria are expressed by different regression lines
[27]. According to this plotting manner, linear regression
lines between chloroplast and plant mitochondria inter-
sect forming the “V-shape” [27], and similarly, linear
regression lines between the coding and non-coding re-
gions intersect forming the “V-shape” [27]. These two
cases clearly indicate that chloroplast and plant mito-
chondria, and the coding and non-coding regions de-
scended from similar origins.
Furthermore, when the four nucleotide contents are
3’
Gx , Cx , Tx , Ax Gy , Cy , Ty , Ay
5’ Gx’, Cx’, Tx’, Ax’ Gy’, Cy’, Ty’, Ay’
X
Com
p
lement X’Com
p
lement Y’
Y
5’
3’
Figure 6. Double-stranded DNA model. The complete genome
was divided into two fragments [46]. The contents of Gx and
Cx in the fragment X are expressed via the reverse (comple-
mentary) strand by Cy and Gy, respectively, because (Gx ≈ Gy’
= Cy) and (Cx ≈ Cy’ = Gy). Therefore, (Gx + Gy ≈ Gx + Cx)
and (Cx + Cy ≈ Cx + Gx). In both equations, as the right hand
side is equal, Gx + Gy ≈ Cx + Cy. Finally, G ≈ C. Similarly, T
≈ A.

K. Sorimachi / Natural Science 2 (2010) 1104-1112
1109
Figure 7. Nucleotide relationships in normalized chloroplast
values. Upper panel, coding region; lower panel, non-coding
region. Red squares, G; green triangles, C; blue diamonds, A;
and shallow blue crosses, T. The composition of each nucleo-
tide in the coding or non-coding region was plotted against the
G content in the complete single DNA strand. The vertical axis
represents the composition of the four nucleotides; the hori-
zontal axis represents the G content in the complete single
DNA strand. This figure has been presented in Natural Science
2; 2010 and is reproduced with permission.
plotted against the total nucleotide content among vari-
ous species, linear regression lines with high regression
coefficients are obtained: Using the normalized values,
G + C + A + T = 1, Chargaff’s parity rule is alternated as
follows: 2G + 2A = 1, A = 0.5 – G, T = 0.5 – G, C = G
and (G = G). The lines G and C overlap and the lines A
and T overlap, and the former is line symmetrical to the
latter against a line (y = 0.25), as shown in Figure 8.
Namely, four nucleotide contents expressing by two du-
plicate nucleotide contents can be expressed by only one
nucleotide content with linear formulae, as shown in
Figure 8. The two duplicate nucleotide contents (G or C
and A or T) are symmetrical. These formulae do not
possess any obvious factor that is based on “Natural Se-
lection” proposed by Charles Darwin. This fact clearly
indicates that “Natural Selection” might contribute to
biological evolution after genome alterations. According
to Chargaff’s second parity rule, the intercepts of the
0.5
0.5 0.25
0.25
0
Nucleotide Content
Nucleotide Contents
Figure 8. The “Diagonal Genome Universe”. Plotting four
nucleotide contents normalized to 1 against certain nucleotide
content (i.e., G or C content), G and G contents are expressed
by (G = G) and (G = C), respectively, and T and A contents are
expressed by (T = 0.5 – G) and (A = 0.5 – G), respectively. For
example, if G = 0.1 (white dashed line), C = 0.1, T = 0.4 and A
= 0.4. White open square, A or T; yellow closed square, C or G.
White dotted line represents the line of symmetry (y = 0.25).
Similarly, plotting nucleotide contents against T of A content,
(T = T), (T = A), (C = 0.5 – T or A) and (G = 0.5 – T or A) are
obtained.
lines G and C are close to the origin, while those of the
lines A and T are close to 0.5 at the vertical and horizon-
tal axes. The slopes of the lines G and C, and those of A
and T are 1 and –1, respectively. All organisms from
bacteria to Homo sapiens are located on the diagonal
lines of a 0.5 square—the “Diagonal Genome Universe”,
using the normalized values. These formulae are not
obtained from a simulation analysis using a random
choice of nucleotide contents assumed to be organism
nucleotide contents [45]. In this case, the nucleotide re-
lationships are completely heteroskedastic and Chargaff’s
second parity rule has not been satisfied. The line A over-
laps with the line T, and the line G overlaps with the line
C [47]. The former overlapped line intersects with the
latter overlapped line at 0.25 [47]. Thus, the exchanges
of G and C or A and T never take place, while the ex-
changes of G or C with T or A must take place synchro-
nously, not only within the putative small unit, but also
over the entire genome according to Chargaff’s second
parity rule. The pair of two duplicate points, G = C and
A = T, are symmetrical around y = 0.25, as shown in
Figure 8. As a result of the synchronous nucleotide al-
terations over the genome, the structure of the genome
has become homogeneous. Samples that are applicable
to Chargaff’s parity rules must satisfy these conditions.
Thus, all nucleotide alterations are strictly controlled,
not only by the total homo-nucleotide contents and their

K. Sorimachi / Natural Science 2 (2010) 1104-1112
1110
analog contents, but also by the total hetero-nucleotide
and their analog contents, in the complete single DNA
strand under Chargaff’s second parity rule [28]. In ani-
mal mitochondrial evolution, which deviates from the
rule, nucleotide alterations are strictly controlled by just
homo-nucleotides and their analog total contents [28].
7. ORIGIN OF LIFE
Four nucleotide relationships within the coding or
non-coding regions are linear; however, Chargaff’s sec-
ond parity rule is not satisfied [6]. On the other hand,
when plotting nucleotide contents in the coding or non-
coding regions against the nucleotide content in a com-
plete single DNA strand, their relationships are expre-
ssed by linear regression lines with high regression coef-
ficients in nuclear, chloroplast and plant mitochondrial
DNA [27]. Furthermore, Chargaff’s second parity rule is
satisfied in both coding and non-coding regions of these
DNA strands [28]. In animal mitochondrial DNA, strong
regulation is observed in homo- and their analog nucleo-
tide relationships in both coding and non-coding regions
[27,28]. Mitchell and Bridge reported that the four nu-
cleotide relationships in organelle DNA were heteroske-
dastic [5], while Nikolaou and Almirantis reported that
mitochondria should be classified into three groups, and
that chloroplast genome evolution resembled bacterial
genome evolution [48]. It has been shown that classifi-
cation of organelles into chloroplast, plant mitochondria,
vertebrate mitochondria, invertebrate I mitochondria and
invertebrate II mitochondria, makes it possible to ex-
press their genome evolution by linear formulae [47].
Thus, in respect to complete genome evolution, it is
clear that all nucleotide alterations are expressed by lin-
ear formulae: y = ax + b, where “y” and “x” represent
nucleotide contents, and “a” and “b” are constant values
representing alteration rates and initial nucleotide con-
tents, respectively.
When evolutionary processes are expressed by the
same regression line, these evolutionary processes must
be controlled by the same rule. Therefore, the fact that
two linear regression lines intersect at the top of the
“V-shape” indicates that the two groups diverged from
the same single origin (Figure 9(a)). Classifying inver-
tebrate mitochondria into two groups, I and II, two linear
regression lines based on nucleotide relationships inter-
sect forming the “V-shape” [47]. Furthermore, as mito-
chondria and chloroplast are derived from proteobacteria
[49] and cyanobacteria [50], respectively, their regres-
sion lines intersected at a point [47]. As the origin of
these organelles appears to be from bacteria, their re-
gression lines must intersect at a point [47]. The fact that
many lines intersect at the same point indicate that many
groups diverged from a single origin (Figure 9(b)). On
●
●●
●
●
●
●
● ●
●
a
c
b
d
e
●● ●● ● ●
Figure 9. Assumed numbers(s) of origin of life based on nu-
cleotide regression lines. (a) and (b), single origin of life; (c),
(d) and (e), multiple origins of life. Closed circles represent the
origin of life.
0.35
0.30
0.25
0.20
0.15
0.10
0.05
0.00
G Conten
t
C Content
0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35
Figure 10. C content (horizontal axis) and G content (vertical
axis) in nuclei and various organelles. Blue diamonds, inverte-
brate I and vertebrate mitochondria; pink diamonds, inverte-
brate II mitochondria; red squares, plant mitochondria; green
triangles, chloroplasts; and black squares, nuclei. This figure
has been presented in Natural Science, 2(5); 519-525, 2010
and reproduced with permission.
the other hand, many parallel regression lines indicate
that there are many origins (Figure 9(c)), and the exis-
tence of many crossing points (Figure 9(d)) also indi-
cates the existence of many origins. However, when all
evolutionary processes obey the same rule, the number
of origins cannot be determined (Figure 9(e)). When
plotting nucleotide contents against each individual nu-
cleotide content, linear regression lines intersect at a
single point among nuclear, chloroplast and mitochon-
drial DNA [47], as shown in Figure 10. This fact clearly
indicates that the origin of all species is a single life
form [47]. This is the first demonstration that all species

K. Sorimachi / Natural Science 2 (2010) 1104-1112
1111
have a common ancestor and a single origin based on
scientific data. Charles Darwin discussed on the evolu-
tion over the course of generation through a presence of
natural selection in “On the Origin of Species by Means
of Natural Selection or the Preservation of Favoured
Races”, while he discussed on neither “a single origin”
nor “a common ancestor” of species. This concept has
been presumed from Darwin’s theory since being pub-
lished in 1859, and eventually phylogenetic trees, which
have been drawn, represent apparently a single origin of
species.
8. CONCLUSIONS
Evolution of all species, from bacteria to Homo sapiens,
is governed by genome alterations based on simple lin-
ear formulae, including Chargaff’s second parity rule,
although their phenotypic expressions show immeasur-
able spectra over the past 3.5 billion years. Evolution
based on genome alterations can be represented by two
lines (G or C and A or T) that are symmetrical about y =
0.25 – the “Diagonal Genome Universe”.
9. ACKNOWLEDGEMENT
The author expresses his great thanks to Prof. Kuo-Chen Chou, Edi-
tor-in-Chief of Natural Science, for the opportunity to present this
mini-review.
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