Complete mitochondrial genome of Yangtze River wild common carp (Cyprinus carpio haematopterus) and Russian scattered scale mirror carp (Cyprinus carpio carpio)


Hu, G.F.; Liu, X.J.; Zou, G.W.; Li, Z.; Liang, H.W.; Hu, S.N.

Mitochondrial Dna. Part A, Dna Mapping, Sequencing, and Analysis 27(1): 263-264

2016


We sequenced the complete mitogenomes of (Cyprinus carpio haematopterus) and Russian scattered scale mirror carp (Cyprinus carpio carpio). Comparison of these two mitogenomes revealed that the mitogenomes of these two common carp strains were remarkably similar in genome length, gene order and content, and AT content. There were only 55 bp variations in 16,581 nucleotides. About 1 bp variation was located in rRNAs, 2 bp in tRNAs, 9 bp in the control region and 43 bp in protein-coding genes. Furthermore, forty-three variable nucleotides in the protein-coding genes of the two strains led to four variable amino acids, which were located in the ND2, ATPase 6, ND5 and ND6 genes, respectively.

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hftp://informahealthcare.com/mdn
ISSN:
1940-1736
(print),
1940-1744
(electronic)
Mitochondria!
DNA,
Early
Online:
1-2
©
2014
Informa
UK
Ltd.
DOI:
103109/19401736.2014.883617
Ipondto
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informs
healthcare
MITOGENOME
ANNOUNCEMENT
Complete
mitochondria!
genome
of
Yangtze
River
wild
common
carp
(Cyprinus
carpio
haematopterus)
and
Russian
scattered
scale
mirror
carp
(Cyprinus
carpio
carpio)
Guang
Fu
Hu
1
'
2
*,
Xiang
Jiang
Liu
2
*,
Gui
Wei
Zou
1
,
Zhong
Li
t
,
Hong-Wei
Liang
l
,
and
Shao-na
Hu
1
'Yangtze
River
Fisheries
Research
Institute,
The
Chinese
Academy
of
Fisheries
Sciences,
Wuhan,
China
and
2
College
of
Fisheries,
Huazhong
Agricultural
University,
Wuhan,
China
Abstract
We
sequenced
the
complete
mitogenomes
of
(Cyprinus
carpio
haematopterus)
and
Russian
scattered
scale
mirror
carp
(Cyprinus
carpio
carpio).
Comparison
of
these
two
mitogenomes
revealed
that
the
mitogenomes
of
these
two
common
carp
strains
were
remarkably
similar
in
genome
length,
gene
order
and
content,
and
AT
content.
There
were
only
55
bp
variations
in
16,581
nucleotides.
About
1
bp
variation
was
located
in
rRNAs,
2
bp
in
tRNAs,
9
bp
in
the
control
region
and
43
bp
in
protein-coding
genes.
Furthermore,
forty-three
variable
nucleotides
in
the
protein-coding
genes
of
the
two
strains
led
to
four
variable
amino
acids,
which
were
located
in
the
ND2,
ATPase
6,
ND5
and
ND6
genes,
respectively.
Keywords
Mitochondria!
genome,
Russian
scattered
scale
mirror
carp,
Yangtze
River
wild
common
carp
History
Received
12
January
2014
Accepted
12
January
2014
Published
online
12
February
2014
Common
carp
has
a
long
history
of
domestication
and
numerous
strains
have
been
developed
from
its
ancestor,
the
wild
common
carp,
Cyprinus
carpio,
both
in
Europe
and
Asia.
Population
genetics
studies
show
that
there
are
two
subspecies
of
common
carp,
C.
carpio carpio
from
Europe
and
C.
carpio
haematopterus
from
Asia
(Zhou
et
al.,
2003,
2004).
Russian
scattered
scale
mirror
carp
(C.
carpio
carpio)
is
a
traditional
and
representative
domestic
strain
in
central
and
east
Europe.
However,
Yangtze
River
wild
common
carp
(C.
carpio
haematopterus)
is
a
traditional
domestic
strain
in
China.
In
this
study,
the
complete
mitochondrial
genomes
of
the
two
carp
strains
were
amplified
by
eighteen
primers,
which
were
synthesized
according
to
the
conserved
regions
of
other
carp
strains
(Chang
et
al.,
1994;
Mabuchi
et
al.,
2006;
Wang
et
al.,
2013).
The
mitogenome
sequences
of
Yangtze
River
wild
common
carp
(JN105354)
and
Russian
scattered
scale
mirror
carp
(JN105352)
were
determined
to
all
be
16,581
bp
in
length,
including
13
protein-coding
genes,
22
tRNAs,
2
rRNAs
and
2
non-coding
regions
(Table
1).
The
overall
base
compositions
of
Yangtze
River
wild
common
carp
and
Russian
scattered
scale
mirror
carp
were,
A:
31.87%,
31.90%;
T:
24.81%,
24.84%;
*These
two
authors
contributed
equally
to
this
work.
Correspondence:
Gui
Wei
Zou,
Yangtze
River
Fisheries
Research
Institute,
The
Chinese
Academy
of
Fisheries
Science,
No.
8,
Wuhan
East-lake
Hi-tech
Development
Zone,
Wuhan
430223,
China.
E-mail:
h1092023
@hku.hk
C:
27.54%,
27.52%;
G:
15.77%,
15.74%,
respectively.
The
overall
AT
and
GC
skew
for
the
two
strains
were
all
found
to
be
0.125
and
—0.272,
respectively.
Size
variations
among
the
two
mitogenomes
presented
here
showed
55
bp
differences
in
overall
length.
About
1
bp
variation
was
located
in
rRNAs,
2
in
tRNAs,
9
in
the
control
region
and
43
in
protein-coding
genes.
All
of
the
protein-coding
genes
of
the
two
strains
were
found
to
use
the
same
pattern
start
and
stop
codons.
Forty-three
variable
nucleotides
in
the
protein-coding
genes
between
the
two
strains
led
to
four
variable
amino
acids,
which
were
located
in
ND2,
ATPase
6,
NB5
and
ND6,
respectively
(Table
1).
The
organization
of
22
tRNA
genes
in
the
two
strains
presented
here
was
similar
to
other
carp
mitogenomes.
There
were
two
nucleotide
substitutions
in
22
tRNAs
of
the
two
strains,
1
bp
was
located
in
tRNA
Gin
and
1
bp
in
tRNA
Pm
.
Both
of
the
strains
have
2
rRNA
genes,
12S
rRNA
and
16S
rRNA,
which
exhibited
the
typical
location
between
tRNA
Phe
and
tRNA
Val
,
and
separated
by
tRNA
val
in
the
two
varieties.
One
nucleotide
substitution
was
observed
in
the
12S
rRNA
genes
between
the
two
strains.
As
in
other
vertebrates,
two
non-coding
regions
were
presented
in
the
two
carp
strains
mitogenome:
an
origin
of
L-strand
replication
(O
L
)
and
D-loop.
O
L
was
located
within
a
cluster
of
five
tRNAs
(WANCY
region),
between
tRNA
mn
and
tRNA
c
Y
s
,
and
was
33
bp
in
length.
This
region
was
much
conserved
and
there
were
not
any
substitutions
between
the
two
strains.
The
main
control
regions
(D-loop)
were
located
between
tRNA
Pr°
and
tRNA
Phe
,
and
were
all
determined
to
be
927
bp
in
length
(Table
1).
Comparison
of
D-loop
sequences
revealed
a
total
of
9
nucleotide
divergences
between
the
two
strains.
2
G.
F.
Hu
et
al.
Mitochondrial
DNA,
Early
Online:
1-2
Table
1.
Comparative
analyses
of
mitochondrial
genomes,
with
identity
of
nucleotides
and
predicted
amino
acids
between
Yangtze
River
wild
common
carp
(YWC)
and
Russian
scattered
scale
mirror
carp
(RSC).
YWC
RSC
Identity
of
nuculotides
and
amino
acids
Start/Stop'
Intergenic
b
sequence
bp
(%)
as
(%)
tRNA
Phe
1-69
(69)
1-69
(69)
12S
rRNA
70-1024
(955)
70-1024
(955)
1
(99.9%)
tRNA
val
1025-1096
(72)
1025-1096
(72)
16S
RNA
1097-2775
(1679)
1097-2775
(1679)
tRNA
Lou
2776-2851
(76)
2776-2851
(76)
1
ND1
2853-3827
(975)
2853-3827
(975)
5
(99.5%)
ATG/TAA
4
tRNA
n
e
3832-3903
(72)
3832-3903
(72)
—2
tRNA
GI
'
3902-3972
(71)
3902-3972
(71)
1
(98.6%)
2
tRNA
M
e
t
3975-4043
(69)
3975-4043
(69)
ND2
4044-5090
(1047)
4044-5090
(1047)
8
(99.2%)
1
(99.7%)
ATG/TAG
—2
tRNA
Tr
P
5089-5159
(71)
5089-5159
(71)
2
tRNA
Al
a
5162-5230
(69)
5162-5230
(69)
1
tRNA
A
"
5232-5304
(73)
5232-5304
(73)
33
tRNA
c
Ys
5338-5404
(67)
5338-5404
(67)
—1
tRNA
T
Y
r
5404-5474
(71)
5404-5474
(71)
1
COI
5476-7026
(1551)
5476-7026
(1551)
4
(99.7%)
GTG/TAA
tRNA
ser
7027-7097
(71)
7027-7097
(71)
3
tRNA
As
P
7101-7172
(72)
7101-7172
(72)
13
COIF
7186-7876
(691)
7186-7876
(691)
1
(99.9%)
ATG/T
tRNA
L3
7877-7952
(76)
7877-7952
(76)
1
ATPase
8
7954-8118
(165)
7954-8118
(165)
ATG/TAG
—7
ATPase
6
8112-8795
(684)
8112-8795
(684)
3
(99.6%)
1
(99.6%)
ATG/TAA
—1
COM
8795-9580
(786)
8795-9580
(786)
4
(99.5%)
ATG/TAA
—1
tRNA
my
9580-9651
(72)
9580-9651
(72)
ND3
9652-10,000
(349)
9652-10,000
(349)
ATG/T
tRNA
A
rg
10,001-10,070
(70)
10,001-10,070
(70)
ND4L
10,071-10,367
(297)
10,071-10,367
(297)
ATG/TAA
—7
ND4
10,361-11,741
(1381)
10,361-11,741
(1381)
5
(99.6%)
ATG/T
tRNA
H
'
s
11,742-11,810
(69)
11,742-11,810
(69)
tRNA
s
er
11,811-11,879
(69)
11,811-11,879
(69)
1
tRNA
Lou
11,881-11,953
(73)
11,881-11,953
(73)
3
ND5
11,957-13,780
(1824)
11,957-13,780
(1824)
7
(99.6%)
1
(99.8%)
ATG/TAA
—4
ND6
13,777-14,298
(522)
13,777-14,298
(522)
3
(99.4%)
1
(99.4%)
ATG/TAA
tRNA
G.
14,299-14,367
(69)
14,299-14,367
(69)
5
Cyt
b
14,373-15,513
(1141)
14,373-15,513
(1141)
3
(99.7%)
ATG/T
tRNA
Thr
15,514-15,585
(72)
15,514-15,585
(72)
—1
tRNA
P
m
15,585-15,654
(70)
15,585-15,654
(70)
1
(98.6%)
D—loop
15,655-16,581
(927)
15,655-16,581
(927)
9
(99.0%)
Total
16,581 16,581
55
(99.7%)
4
(99.9%)
aTA
and
T
represent
incomplete
stop
codons.
b
Numbers
correspond
to
the
nucleotides
separating
adjacent
genes.
Negative
numbers
indicate
overlapping
nucleotides.
Acknowledgements
We
would
like
to
thank
Prof.
Pang
Guangbi
from
Yangtze
River
Fisheries
Research
Institute
for
her
help
in
the
sample
collection.
Declaration
of
interest
The
authors
report
no
conflicts
of
interest.
The
authors
alone
are
responsible
for
the
content
and
writing
of
the
paper.
The
project
was
supported
by
the
ear-maked
fund
for
China
Agriculture
Research
System
(CARS-46-01)
and
National
S
&
T
Infrastructure
Platform
of
China.
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