http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 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, Xo´chitl Sa´nchez-Herna´ndez1, Mauricio Hoyos-Padilla2, and Francisco J. Garcı´a-De-Leo´n3
Mitochondrial DNA Downloaded from informahealthcare.com by University of Queensland on 10/11/14 For personal use only.
1
Laboratorio de Gene´tica de Organismos Acua´ticos, Instituto de Ciencias del Mar y Limnologı´a, Circuito Interior s/n, Ciudad Universitaria, Me´xico DF, Me´xico, 2Pelagios-Kakunja´ A.C., Sinaloa 1540, La Paz, Me´xico, and 3Laboratorio de Gene´tica para la Conservacio´n, Centro de Investigaciones Biolo´gicas del Noroeste, Instituto Polite´cnico Nacional 195, La Paz, Me´xico
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 70–72 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 (Me´xico). 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 Me´xico (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. Garcı´a-De-Leo´n, Laboratorio de Gene´tica para la Conservacio´n, Centro de Investigaciones Biolo´gicas del Noroeste, Instituto Polite´cnico Nacional 195, Playa Palo de Santa Rita Sur; La Paz, B.C.S. CP 23096, Me´xico. E-mail: [email protected]
History Received 26 June 2014 Accepted 27 June 2014 Published online 13 August 2014
Genetica de Organismos Acua´ticos at the Instituto de Ciencias del Mar y Limnologı´a (ICMyL), Universidad Nacional Auto´noma de Me´xico (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 70–72 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.
2
P. Diaz-Jaimes et al.
Mitochondrial DNA, Early Online: 1–2
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
Mitochondrial DNA Downloaded from informahealthcare.com by University of Queensland on 10/11/14 For personal use only.
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 Gene´ticos Acua´ticos, SUBNARGENA, of the Secretarı´a de Ganaderı´a, Agricultura, Desarrollo Rural, Pesca y Alimentacio´n, 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. PLoS One 7:e42543. 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 277:679–68. 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 463:311–17. 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 412:139–40. Santana-Morales O, Sosa-Nishizaki O, Escobedo-Olvera MA, OnateGonzalez EC, O’Sullivan 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; 2012:187–98. 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 62:548–56. Wyman SK, Jansen RK, Boore JL. (2004). Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252–5.
MITOGENOME ANNOUNCEMENT
The complete mitochondrial DNA of white shark (Carcharodon carcharias) from Isla Guadalupe, Mexico Pindaro Diaz-Jaimes1, Silvia Hinojosa-Alvarez1, Xo´chitl Sa´nchez-Herna´ndez1, Mauricio Hoyos-Padilla2, and Francisco J. Garcı´a-De-Leo´n3
Mitochondrial DNA Downloaded from informahealthcare.com by University of Queensland on 10/11/14 For personal use only.
1
Laboratorio de Gene´tica de Organismos Acua´ticos, Instituto de Ciencias del Mar y Limnologı´a, Circuito Interior s/n, Ciudad Universitaria, Me´xico DF, Me´xico, 2Pelagios-Kakunja´ A.C., Sinaloa 1540, La Paz, Me´xico, and 3Laboratorio de Gene´tica para la Conservacio´n, Centro de Investigaciones Biolo´gicas del Noroeste, Instituto Polite´cnico Nacional 195, La Paz, Me´xico
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 70–72 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 (Me´xico). 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 Me´xico (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. Garcı´a-De-Leo´n, Laboratorio de Gene´tica para la Conservacio´n, Centro de Investigaciones Biolo´gicas del Noroeste, Instituto Polite´cnico Nacional 195, Playa Palo de Santa Rita Sur; La Paz, B.C.S. CP 23096, Me´xico. E-mail: [email protected]
History Received 26 June 2014 Accepted 27 June 2014 Published online 13 August 2014
Genetica de Organismos Acua´ticos at the Instituto de Ciencias del Mar y Limnologı´a (ICMyL), Universidad Nacional Auto´noma de Me´xico (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 70–72 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.
2
P. Diaz-Jaimes et al.
Mitochondrial DNA, Early Online: 1–2
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
Mitochondrial DNA Downloaded from informahealthcare.com by University of Queensland on 10/11/14 For personal use only.
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 Gene´ticos Acua´ticos, SUBNARGENA, of the Secretarı´a de Ganaderı´a, Agricultura, Desarrollo Rural, Pesca y Alimentacio´n, 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. PLoS One 7:e42543. 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 277:679–68. 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 463:311–17. 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 412:139–40. Santana-Morales O, Sosa-Nishizaki O, Escobedo-Olvera MA, OnateGonzalez EC, O’Sullivan 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; 2012:187–98. 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 62:548–56. Wyman SK, Jansen RK, Boore JL. (2004). Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252–5.
