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The complete mitochondrial DNA of white shark

(Carcharodon carcharias) from Isla Guadalupe,
Mexico
ARTICLE in MITOCHONDRIAL DNA AUGUST 2014
Impact Factor: 1.7 DOI: 10.3109/19401736.2014.945556

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Pndaro Daz-Jaimes

Silvia Hinojosa-Alvarez

Universidad Nacional Autnoma de Mxico

Universidad Nacional Autnoma de Mxico

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ISSN: 1940-1736 (print), 1940-1744 (electronic)
Mitochondrial DNA, Early Online: 12
! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.945556

MITOGENOME ANNOUNCEMENT

The complete mitochondrial DNA of white shark (Carcharodon

carcharias) from Isla Guadalupe, Mexico
Pindaro Diaz-Jaimes1, Silvia Hinojosa-Alvarez1, Xochitl Sanchez-Hernandez1, Mauricio Hoyos-Padilla2, and
Francisco J. Garca-De-Leon3

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Laboratorio de Genetica de Organismos Acuaticos, Instituto de Ciencias del Mar y Limnologa, Circuito Interior s/n, Ciudad Universitaria, Mexico
DF, Mexico, 2Pelagios-Kakunja A.C., Sinaloa 1540, La Paz, Mexico, and 3Laboratorio de Genetica para la Conservacion, Centro de Investigaciones
Biologicas del Noroeste, Instituto Politecnico Nacional 195, La Paz, Mexico

Abstract

Keywords

The Isla Guadalupe white shark mitochondrial structure is similar to the one previously reported
for a white shark individual from Taiwan with a total length of 16,745 and 16,742 bp
respectively; the base composition of the genomes was as follow A (30.60%), T (28.67%), C
(26.86%) and G (13.87%), contains 13 protein-coding genes and 24 tRNA genes and the noncoding control region. The tRNA genes range from 7072 bp. Gene order is the same as in other
vertebrates and teleosts.

Elasmobranches, mitochondrial genome,

white shark

The white shark Carcharodon carcharias is one of the larger

pelagic predatory fish distributed in temperate and sub-tropical
waters of both north and south hemispheres although main
abundance areas are reported from South Africa, Australia,
California (USA), and Baja California (Mexico). The great white
shark is the most widely protected elasmobranch; the capture
and trade of this species is prohibited in South Africa, Namibia,
Malta, U.S., Australia and Mexico (Compagno, 2002). It has
been catalogued as Vulnerable by the International Union for
the Conservation of Nature (IUCN) Red List of Threatened
Species (IUCN, 2004) and since 2002 included in Appendix II
(and III by the Convention on International Trade of Endangered
Species (CITES)). Despite of its long-distance movement
capacity and wide dispersal, white sharks shows propensity to
exhibit a philopatric behavior. Because of this, there have been
identified at least 4 known mtDNA lineages across its
distributional range (Jorgensen et al., 2010; Pardini et al.,
2001; Tanaka et al., 2010). A genetic divergent population in the
Northeastern Pacific (NEP) has been characterized based on
sequences of the mtDNA control region off Central California
U.S. In Mexico the main abundance area for adults is reported in
waters surrounding Isla Guadalupe whereas juveniles and young
of the year (YOY) individuals have been widely encountered at
Sebastian Vizcaino Bay which is suspected to represent a
nursery ground (Santana-Morales et al., 2012).
We sequenced the complete mitochondrial genome of the
white shark (GeneBank accession number KJ934896) of a
specimen collected at Isla Guadalupe Mexico from which was
obtained a biopsy that has been deposited in the Laboratorio de

Correspondence: Francisco J. Garca-De-Leon, Laboratorio de Genetica

para la Conservacion, Centro de Investigaciones Biologicas del Noroeste,
Instituto Politecnico Nacional 195, Playa Palo de Santa Rita Sur; La Paz,
B.C.S. CP 23096, Mexico. E-mail: fgarciadl@cibnor.mx

History
Received 26 June 2014
Accepted 27 June 2014
Published online 13 August 2014

Genetica de Organismos Acuaticos at the Instituto de Ciencias del

Mar y Limnologa (ICMyL), Universidad Nacional Autonoma de
Mexico (UNAM). DNA was sheared on a Bioruptor to an average
size of 500 bp and libraries were prepared using enzymes and
protocols from Kapa Bioscience with slight modifications.
Adapters consisted of Illumina TruSeq read1 and read2
oligonucleotides, dual size selection was used prior to cycling
and primers included custom 8 nucleotide (nt) indices (Faircloth
& Glenn, 2012) to produce a library equivalent to Illumina
TruSeqHT with the exception of custom indices. Following
purification and normalization, we sequenced the library using an
Illumina MiSeq v2 500 cycle kit to produce paired-end 250 nt
reads. Sequences were assembled using SOAP de novo (Li et al.,
2010), and contigs belonging to the mtDNA were selected.
Annotation of the assembled mitogenome was performed using
DOGMA (Wyman et al., 2004).
The white shark mitochondrial structure is similar to most
other elasmobranchs such as the thresher shark, Alopias pelagicus
(Chen et al., 2013). The base composition of the genomes was as
follow A (30.60%), T (28.67%), C (26.86%) and G (13.87%),
which demonstrated an A + T (62.7%) rich feature, similar to
other elasmobranch mitogenomes. The mitochondrial genome
contains 13 protein-coding genes and 23 tRNA genes which range
from 7072 bp. Gene order is the same as in other vertebrates and
teleosts and has a length of 16,745 bp similar to that of a white
shark individual from Taiwan (Table 1; Chang et al., 2013). The
mean nucleotide divergence between both individual white shark
mitochondrial genomes was of 0.24% corresponding to an average
number of nucleotide differences of 42 bp, a lower value as
compared to the divergence of 4% estimated for the hypervariable
mtDNA control region between white shark populations from
South Africa and Australia/New Zeland (Pardini et al., 2001).
This new mitochondrial genome will provide insights in assessing
population divergence for identification of key areas for species
conservation.

P. Diaz-Jaimes et al.

Mitochondrial DNA, Early Online: 12

Table 1. Comparison between the reported mitogenome of a white shark specimen from the western Pacific (Genbank accession
number KC914387.1) and the white shark mitogenome from Isla Guadalupe Mexico (KJ934896).
C. carcharias Mexico

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Start
241
1113
1186
2137
2275
3880
3955
4932
4999
5072
5141
6182
6256
6325
6431
6497
6568
8124
8199
8272
8963
9038
9196
9879
10,667
10,737
11,086
11,157
11,447
13,210
13,279
13,346
13,418
15,246
15,765
15,837
16,982

End
296
1183
2132
2208
3873
3954
4926
5000
5070
5140
6181
6254
6324
6397
6497
6566
8112
8194
8267
8961
9036
9199
9876
10,661
10,736
11,084
11,156
11,450
13,205
13,278
13,345
13,417
15,244
15,764
15,834
16,979
17,928

Gene
tRNA-Asn
tRNA-Phe
12sRNA
tRNA-Val
16sRNA
tRNA-Leu
nad1
tRNA-Ile
tRNA-Gln
tRNA-Met
nad2
tRNA-Trp
tRNA-Ala
tRNA-Asn
tRNA-Cys
tRNA-Tyr
cox1
tRNA-Ser
tRNA-Asp
cox2
tRNA-Pro
atp8
atp6
cox3
tRNA-Gly
nad3
tRNA-Arg
nad4l
nad4
tRNA-His
tRNA-Second Ser
tRNA-Second Leu
nad5
nad6
tRNA-Glu
cob
control region

C. carcharias (Chang et al., 2013)

Length

Start

End

55
70
946
71
1598
74
971
68
71
68
1040
72
68
72
66
69
1544
70
68
689
73
161
680
782
69
347
70
293
1758
68
66
71
1826
518
69
1142
946

1
74
1025
1163
2767
2842
3819
3886
3959
4028
5071
5143
5143
5212
5318
5455
7011
7086
7159
7850
7925
8083
8766
9554
9624
9973
10,044
10,334
11,715
11,784
11,851
11,923
13,751
14,270
14,342
15,487
15,561
15,630

71
1020
1096
2760
2841
3813
3887
3957
4027
5071
5141
5222
5211
5284
5384
6999
7081
7154
7848
7923
8086
8763
9548
9623
9971
10,043
10,337
11,710
11,783
11,850
11,922
13,749
14,269
14,339
15,484
15,558
15,629
16,744

Declaration of interest
The authors report no conflicts of interest. The authors alone are
responsible for the content and writing of the paper. Support was
provided by CIBNOR and ICMyL through the Subsistema Nacional de
Recursos Geneticos Acuaticos, SUBNARGENA, of the Secretara de
Ganadera, Agricultura, Desarrollo Rural, Pesca y Alimentacion,
SAGARPA. Field work support was provided by WWF/Telcel
Alliance.

References
Chang CH, Shao KT, Lin YS, Fang YC, Ho HC. (2013). The complete
mitochondrial genome of the great white shark, Carcharodon
carcharias (Chondrichthyes, Lamnidae). Mitochondrial DNA. [Epub
ahead of print]. doi:10.3109/19401736.2013.803092.
Chen X, Xiang D, Ai W, Shi X. (2013). Complete mitochondrial genome
of the pelagic thresher Alopias pelagicus (Lamniformes: Alopiidae).
Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/
19401736.2013.830294.
Compagno L. (2002). Sharks of the world: An annotated and illustrated
catalogue of shark species known to date. Volume 2: Bullhead,
mackerel and carpet sharks (Heterodontiformes, Lamniformes,
Orectolobiformes). Rome, Italy: Food and Agriculture Organization
of the United Nations.

Gene
tRNA-Phe
12sRNA
tRNA-Val
16sRNA
tRNA-Leu
nad1
tRNA-Ile
tRNA-Gln
tRNA-Met
nad2
tRNA-Trp
tRNA-Ala
tRNA-Asn
tRNA-Cys
tRNA-Tyr
cox1
tRNA-Ser
tRNA-Asp
cox2
tRNA-Pro
atp8
atp6
cox3
tRNA-Gly
nad3
tRNA-Arg
nad4l
nad4
tRNA-His
tRNA-Second Ser
tRNA-Second Leu
nad5
nad6
tRNA-Gly
cob
tRNA-Thr
tRNA-Pro
control region

Length
70
946
71
1597
74
971
68
71
68
1043
70
79
68
72
66
1544
70
68
689
73
161
680
782
69
347
70
293
1376
68
66
71
1826
518
69
1142
71
68
1114

Faircloth BC, Glenn TC. (2012). Not all sequence tags are created equal:
Designing and validating sequence identification tags robust to indels.
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IUCN. (2004). IUCN Red List of Threatened Species. Version 2014.2.
Available at: http://www.redlist.org/ (Accessed 24 July 2014)
Jorgensen SJ, Reeb CA, Chapple TK, Anderson S, Perle C, Van
Sommeran SR, Fritz-Cope C, et al. (2010). Philopatry and migration of
Pacific white sharks. Proc R Soc B 277:67968.
Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, et al. (2010). The
sequence and de novo assembly of the giant panda genome. Nature
463:31117.
Pardini AT, Jones CS, Noble LR, Kreiser B, Malcolm H, Bruce BD,
Stevens JD, et al. (2001). Sex-biased dispersal of great white sharks.
Nature 412:13940.
Santana-Morales O, Sosa-Nishizaki O, Escobedo-Olvera MA, OnateGonzalez EC, OSullivan JB, Cartamil D. (2012). Incidental catch and
ecological observations of juvenile white sharks, Carcharodon
carcharias, in Western Baja California, Mexico. In: Domeier ML,
editor. Conservation implications global perspectives on the biology
and life history of the white shark. Boca Raton, FL: CRC Press;
2012:18798.
Tanaka S, Kitamura T, Mochizuki T, Kofuji K. (2010). Age, growth and
genetic status of the white shark (Carcharodon carcharias) from
Kashima-nada. Japan Mar Fresh Res 62:54856.
Wyman SK, Jansen RK, Boore JL. (2004). Automatic annotation of
organellar genomes with DOGMA. Bioinformatics 20:32525.